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https://openalex.org/W2274817238 | https://equityhealthj.biomedcentral.com/counter/pdf/10.1186/s12939-016-0304-1 | English | null | Evidence and knowledge gaps on the disease burden in sexual and gender minorities: a review of systematic reviews | International journal for equity in health | 2,016 | cc-by | 8,496 | REVIEW Open Access Open Access © 2016 Blondeel et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Evidence and knowledge gaps on the
disease burden in sexual and gender
minorities: a review of systematic reviews Karel Blondeel1*, Lale Say2, Doris Chou2, Igor Toskin2,3, Rajat Khosla2, Elisa Scolaro2 and Marleen Temmerman1,2 Blondeel et al. International Journal for Equity in Health (2016) 15:16
DOI 10.1186/s12939-016-0304-1 Blondeel et al. International Journal for Equity in Health (2016) 15:16
DOI 10.1186/s12939-016-0304-1 Blondeel et al. International Journal for Equity in Health (2016) 15:16
DOI 10.1186/s12939-016-0304-1 Abstract Sexual and gender minorities (SGM) include individuals with a wide range of sexual orientations, physical
characteristics, and gender identities and expressions. Data suggest that people in this group face a significant and
poorly understood set of additional health risks and bear a higher burden of some diseases compared to the
general population. A large amount of data is available on HIV/AIDS, but far less on other health problems. In this
review we aimed to synthesize the knowledge on the burden of communicable and non-communicable diseases,
mental health conditions and violence experienced by SGM, based on available systematic reviews. We conducted
a global review of systematic reviews, including searching the Cochrane and the Campbell Collaboration libraries, as
well as PubMed, using a range of search terms describing the populations of interest, without time or language
restrictions. Google Scholar was also scanned for unpublished literature, and references of all selected reviews were
checked to identify further relevant articles. We found 30 systematic reviews, all originally written in English. Nine
reviews provided data on HIV, 12 on other sexually transmitted infections (STIs), 4 on cancer, 4 on violence and 3
on mental health and substance use. A quantitative meta-analysis was not possible. The findings are presented in a
narrative format. Our review primarily showed that there is a high burden of disease for certain subpopulations of
SGM in HIV, STIs, STI-related cancers and mental health conditions, and that they also face high rates of violence. Secondly, our review revealed many knowledge gaps. Those gaps partly stem from a lack of original research, but
there is an equally urgent need to conduct systematic and literature reviews to assess what we already know
on the disease burden in SGM. Additional reviews are needed on the non-biological factors that could
contribute to the higher disease burden. In addition, to provide universal access to health-care for all, more
information is needed on the barriers that SGM face in accessing health services, including the attitudes of
health-care providers. Understanding these barriers and the additional health risks they impose is crucial to
improving the health status of SGM. Keywords: Sexual and gender minorities, Disease burden, LGBT, Health difficulties than others in reaching this standard of
health [2]. Those populations can be defined by age,
gender, race or ethnicity, geography, wealth, disability,
and also by sexual orientation and gender identity. * Correspondence: karel.blondeel@ugent.be
1Ghent University, Ghent, Belgium
Full list of author information is available at the end of the article g
p
p
of this article we have grouped men who have sex w
men (MSM), women who have sex with women (WSW
* Correspondence: karel.blondeel@ugent.be
Ghent University, Ghent, Belgium
Full list of author information is available at the end of the article
© 2016 Blondeel et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Review
Background The Constitution of the World Health Organization
(WHO) states that the “enjoyment of the highest attain-
able standard of health is one of the fundamental rights
of every human being without distinction of race, reli-
gion, political belief, economic or social condition” [1]. Although medical ethics require health services to be in-
clusive of all people, some populations have more Populations defined by sexual orientation and gender
identity include individuals with a wide range of sexual
orientations, physical characteristics (as in intersex per-
sons), gender identities and expressions, all of which
they may experience differently depending on societal
gender norms and cultural traditions. For the purposes
of this article we have grouped men who have sex with
men (MSM), women who have sex with women (WSW), * Correspondence: karel.blondeel@ugent.be
1Ghent University, Ghent, Belgium
Full list of author information is available at the end of the article Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 2 of 9 Page 2 of 9 ‘homosexuality’. We searched PubMed for the terms ‘sys-
tematic’ AND ‘review’ combined with a search strategy
(see Additional file 1) for sexual and gender minorities
(SGM). No language, time or geographical restrictions
were applied. The concept of ‘burden of disease’ was not
specified in search strategies. Google Scholar was searched
in English and references of the included reviews were
checked to identify further relevant articles. transgender and intersex persons, all defined by the Joint
United
Nations
Programme
on
HIV
and
AIDS
(UNAIDS), together under the name of ‘sexual and gen-
der minorities’ or SGM [3]. For research, health policy
and advocacy reasons, estimating the size of populations
of interest is important [4]. Due to stigma associated
with homosexuality and non-gender-normative behav-
iours, estimates of SGM populations are scarce, but
studies show that SGM comprise substantial proportions
of the population in countries worldwide [5–7]. transgender and intersex persons, all defined by the Joint
United
Nations
Programme
on
HIV
and
AIDS
(UNAIDS), together under the name of ‘sexual and gen-
der minorities’ or SGM [3]. For research, health policy
and advocacy reasons, estimating the size of populations
of interest is important [4]. Due to stigma associated
with homosexuality and non-gender-normative behav-
iours, estimates of SGM populations are scarce, but
studies show that SGM comprise substantial proportions
of the population in countries worldwide [5–7]. Inclusion and exclusion criteria Data suggest that SGM face a significant and poorly
understood set of additional health risks and bear a
higher burden of some diseases compared to the general
population [8, 9]. There have been international calls to
answer the unique health-care needs of SGM [10, 11]. It
is therefore indispensable to understand where we are
with the knowledge on the health burden of SGM. In
2002 Boehmer showed that research was limited in
scope, concentrating mostly on HIV and STIs and MSM
[12]. In high-income countries the research scope has
been broadening since, but the situation in middle- and
low-income countries is less clear [13]. In this review we
aimed to collate the knowledge and identify the know-
ledge gaps on the burden of communicable and non-
communicable diseases, mental health conditions and
violence experienced by SGM globally, based on avail-
able systematic reviews. Figure 1 shows how publications were selected for re-
view. Our initial search generated 399 publications. Based on a review of the abstracts, the following exclu-
sions were made: duplicates, one publication lacking an
abstract, one protocol of a systematic review, publica-
tions that were not systematic reviews, publications
without data on disease burden, and publications with-
out data on SGM or with data on only a very specific
subset of SGM. We then retrieved and read the full text
of 50 retained publications. Those were all publications
we found on PubMed, the search on the Cochrane Data-
base of Systematic Reviews and the Campbell Collabor-
ation Library of Systematic Reviews did not generate
reviews of interest. Next, we further excluded national
reviews if they were included in larger reviews, and re-
views that were redundant due to newer published re-
views on the same subject and population. Twenty-five
articles were retained. An additional five eligible reviews
were identified from references and Google Scholar,
bringing the total to 30. Search strategy
d
d y
We conducted a review of systematic reviews in con-
cordance
with
the
PRISMA
statement
[16]. The
Cochrane Database of Systematic Reviews and the
Campbell Collaboration Library of Systematic Reviews
were searched using the following terms to identify re-
views on the populations of interest: ‘gay’, ‘lesbian’, ‘trans-
gender’, ‘WSW’, ‘women who have sex with women’,
‘MSM’, ‘men who have sex with men’, ‘same sex’, ‘sexual
orientation’, ‘gender identity’, ‘sexual minority’, ‘intersex’ and Methods A review of systematic reviews can aim to bring together a
series of reviews on an important topic or summarize re-
views on a variety of topics with a common main theme
[14]. This review is of the latter type and while it is un-
likely to be of interest to clinicians and patients deciding
how best to address a specific problem, it may be relevant
to policy makers or to addressing questions that cut across
the different reviews [15]. The outcome of a review of re-
views is typically a summary of review results. Conducting
additional meta-analysis in a review of systematic reviews
is a major challenge due to the heterogeneity of the
methods, analyses and results of the original reviews. Therefore meta-analysis is not a relevant method to this
review of systematic reviews and is descriptive in nature. Quality assessment y
The quality of the systematic reviews was assessed with
the AMSTAR scale (see Additional file 2) (http://
amstar.ca/). AMSTAR stands for A Measurement Tool
to Assess Systematic Reviews and was initially developed
to assess systematic reviews of randomised controlled
trials [17]. However, it is increasingly being used to as-
sess those that include observational studies as well. The
scale consists of 11 items. We considered systematic re-
views with a score from 0 to 3 as low quality, from 4 to
6 as medium quality, and from 7 up as high quality. The
AMSTAR score was not used as an exclusion criterium,
but used as an analytic tool. Regardless of the quality,
we did not find inconsistencies in the conclusions of the
included individual reviews. Data extraction We created a master table in Microsoft Excel containing
key information from each of the included reviews (see
Additional file 2): health topic, time range of the search,
year published, geographical scope, databases searched,
the SGM subpopulation, number of studies included,
measures,
comparison
groups,
a
summary
of
the Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 3 of 9 Potentially relevant publications
identified through search in
PubMed (n=361)
Potentially relevant publications
identified through search in the
Cochrane Database of Systematic
Reviews (n=13)
Potentially relevant publications
identified through search in the
Campbell Collaboration Library
of Systematic Reviews (n=25)
Publications retained for further
analysis, full text retrieved
(n=50)
Publications excluded by title or abstract:
– duplicates (n=6)
– not a systematic review (n=94)
– no SGM population (n=77)
– very specific SGM population (n=7)
– no data on disease burden (n=163)
– protocol of systematic review (n=1)
– no abstract available (n=1)
Publications excluded because of geographical
scale, no new data or insufficient data (n=25)
Publications identified and included from lists
of references and Google Scholar (n=5)
Publications included in the
review (n=30)
Fig. 1 Flowchart of inclusion criteria for reviews Potentially relevant publications
identified through search in the
Cochrane Database of Systematic
Reviews (n=13) Potentially relevant publications
identified through search in the
Cochrane Database of Systematic
Reviews (n=13) Potentially relevant publications
identified through search in
PubMed (n=361) Potentially relevant publications
identified through search in the
Campbell Collaboration Library
of Systematic Reviews (n=25) Potentially relevant publications
identified through search in the
Campbell Collaboration Library
of Systematic Reviews (n=25) Publications excluded by title or abstract:
– duplicates (n=6)
– not a systematic review (n=94)
– no SGM population (n=77)
– very specific SGM population (n=7)
– no data on disease burden (n=163)
– protocol of systematic review (n=1)
– no abstract available (n=1) Publications retained for further
analysis, full text retrieved
(n=50) Publications excluded because of geographical
scale, no new data or insufficient data (n=25) Publications identified and included from lists
of references and Google Scholar (n=5) Publications included in the
review (n=30) quantitative and/or qualitative data on disease burden
and quality assessment score. on violence [37–40], 4 on cancer [32, 41–43] and 3 on
mental health and substance use [44–46]. One review pro-
vided data on both HIV and STIs [21]; another yielded
data on STIs as well as cancer [32]. Data extraction Twenty-five reviews
provided data on MSM, 8 on WSW and 5 on transgender
persons (some reviews included more than one subpopu-
lation). Twenty-four studies compared data to the general
population or other groups, of which one half on the basis
of meta-analysis and the other half based on qualitative
observations. Fourteen reviews were considered high Sexually transmitted infections y
Twelve systematic reviews included data on STIs other
than HIV in SGM, including 6 global, 4 regional and 2
national-level reviews [21, 26–36]. Nine of these reviews
were on MSM, 2 on WSW and 1 on MSM and trans-
gender persons. Men who have sex with men (MSM) Among the 6 re-
views that provided data on MSM, 3 were exclusively on
MSM. One review was global [24] and 5 were regional
[6, 18, 19, 23, 25], of which 4 were mainly on low- and
middle-income countries (LMICs). Except for one re-
view from 2007, all were published in 2010 or later. All
reviews showed a high burden of HIV in MSM. The re-
gion with the highest HIV prevalence in MSM was the
Caribbean with 25.4 %, followed by sub-Saharan Africa
with 17.9 % [24]. In contrast, some countries in the Mid-
dle East and North Africa show very low HIV prevalence
in MSM [6]. In Asia, high rates of incident HIV-
infections in MSM were observed wherever studied [18],
and across the region of Latin America and the Carib-
bean MSM was the population most affected by HIV
[19]. MSM in LMICs have on average a 19.3 times
higher chance of being infected with HIV compared with
the general population [23]. In high-income countries,
Sullivan et al. showed that among new HIV cases, the
proportion attributed to male–male sex increased in all
the included countries between 2006 and 2011 [25]. MSM Three reviews reported on syphilis in MSM. Zoni
et al. showed high rates of active syphilis prevalence in
MSM in Latin America, with rates of 7.5 % or more in
half of the included studies [27]. In China, the median
syphilis prevalence, based on a review of four studies in
MSM, was 14.5 %, making MSM the group at highest
risk for syphilis in China [28]. Caceres et al. found that
syphilis prevalence among MSM in 16 LMICs ranged
from 1.5 % in Bangladesh to 29 % in Peru [35]. Hepatitis prevalence was reported in four reviews. A
2003 low quality global systematic review on hepatitis A
virus (HAV) did not find an important difference in
anti-HAV positivity between MSM and control groups
[29]. Two reviews on hepatitis B and C viruses (HBV
and HCV) in Europe presented disaggregated data for
MSM [30, 31]. Results All 30 reviews were originally written in English. Fifteen
reviews were global in scope, while 11 were regional and 5
were national. Nineteen reviews were exclusively or pre-
dominantly based on data from high-income countries. Nine reviews provided data on HIV [6, 18–25], 12 on
other sexually transmitted infections (STIs) [21, 26–36], 4 Page 4 of 9 Blondeel et al. International Journal for Equity in Health (2016) 15:16 quality [6, 19, 20, 22, 23, 26, 27, 32, 36, 38, 42, 44–47], 9
medium quality [18, 24, 30, 31, 34, 35, 37, 39, 40] and 7
low quality [21, 25, 28, 29, 33, 41, 43]. We found no re-
views on intersex people. Detailed results are presented in
narrative form under five health topic sub-sections, by
SGM subpopulation, as shown in Table 1. estimated a prevalence of 19.1 % and reported that this
population has a 48.8 times higher chance of being in-
fected with HIV than the general population of adults
aged between 15 and 49 [22]. We found no reviews on
HIV infection in female-to-male transgender persons. Women who have sex with women (WSW) A low
quality systematic review on STIs in WSW globally did not
generate any HIV prevalence data in this population [21]. HIV/AIDS Nine systematic reviews assessed the burden of HIV in
SGM, including 5 global and 4 regional reviews [6, 18–25]. Six of these reviews were on MSM, 2 were on male-to-
female transgender persons and 1 was on WSW. Sexually transmitted infections One showed higher hepatitis C virus anti-
bodies and hepatitis B surface antigen prevalence than in
the general population, based on three country estimates
[30]. In LMICs, data on HBV prevalence was even
sparser. With rates of HBV up to 38 % in Argentina and
31 % in Vietnam, MSM seem to be a high-risk group
[35]. A global review comparing incidence of acute HCV
in HIV-negative versus HIV-positive MSM found that
the incidence in the latter group was four times higher;
the incidence rates in HIV-negative MSM were similar Transgender persons Two systematic reviews, both of
high quality, provided data on HIV infection in male-to-
female transgender persons [20, 22]. The reviews were
global, collectively including studies from 20 countries. One publication calculated an HIV prevalence of 14.7 %
in transgender persons who did not engage in sex work
and 27.3 % in those who did [20]. The second review Table 1 Number of reviews selected, by health topic and subpopulation
Health topic
Men who have sex with
men (MSM)
Women who have sex with
women (WSW)
Transgender
persons
Total number
of reviews
HIV/AIDS
6
1
2
9
STI
10
2
1
12
Cancer
3
1
0
4
Mental health and substance use
2
2
1
3
Violence
4
2
0
4
Total
25
8
5
30 Table 1 Number of reviews selected, by health topic and subpopulation Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 5 of 9 Page 5 of 9 to heterosexual populations [36]. The Pan American
Health Organization (PAHO) is currently conducting a
review of hepatitis B and C in the countries of the
Americas; so far the findings point to a higher burden
for MSM (personal communication, Rafael Mazin, focal
point for HIV/STIs and hepatitis in key populations,
PAHO, 30 May 2014). MSM Anal HPV is common in MSM, as are HBV and
human herpesvirus 8 (HHV-8) infections. These viruses
can lead to anal cancer, liver cancer and Kaposi sarcoma,
respectively. One review considered MSM at high risk
for anal cancer, and found that HIV-positive MSM were
at highest risk [43]. Systematic reviews on HPV and on
cancer in general in MSM found that HIV-positive
MSM had a high incidence of anal cancer, similar to the
incidence of cervical cancer in the general female popu-
lation
before
the
introduction
of
national
cervical
screening programmes [32, 41]. Boehmer et al. Sexually transmitted infections found
that only 1 of the 47 studies included in their review on
cancer in MSM was not linked to STIs [41]. In one low quality global review, prevalence of herpes
simplex virus 2 (HSV-2) was demonstrated to be higher
among male homosexual than among male heterosexual
populations [33]. Chlamydia trachomatis and Neisseria gonorrhoeae
have not been the subject of global systematic reviews in
SGM. One review reported data from nine LMICs with
prevalence rates ranging from 0 % (Peru) and 2.1 %
(Nepal) up to 14.9 % and 16.1 % (both in Timor-Leste)
[35]. A national review on C. trachomatis in Australia
designated MSM amongst the populations with the
greatest burden, calculating a pooled prevalence for rec-
tal C. trachomatis of 5.6 % [34]. WSW Meads & Moore systematically reviewed studies
on breast cancer in lesbian and bisexual women. This re-
view included nine studies with prevalence estimates, of
which two showed higher prevalence of breast cancer in
lesbian
and
bisexual
women
then
in
heterosexual
women, four showed no difference, one showed mixed
results and two could not be compared. Though the re-
view was of high quality, all the included studies were
small and of poor quality. The reviewers concluded that
there was no convincing evidence of a higher disease
burden of breast cancer in WSW [42]. In a high quality global systematic review, Machalek
et al. showed a pooled prevalence of any type of anal hu-
man papillomavirus (HPV) of 53.6 % in HIV-negative
MSM and 89.0 % in HIV-positive MSM [32]. High-grade
anal intraepithelial neoplasia was present in 20–30 % of
all MSM [32]. Mental health and substance use Three high quality reviews – 2 global and 1 national –
provided data on mental health and substance use in
SGM [44–46]. Two of these were in MSM and WSW
while 1 was in transgender persons. WSW Two global systematic reviews on bacterial vagin-
osis and on STIs in WSW showed a positive association
between a history of female sexual partners and risk of
bacterial vaginosis [21, 26]. There was no evidence of a
higher burden of STIs in WSW compared with the gen-
eral population of adult women [21]. MSM and WSW In their global review, King et al. cal-
culated an overall 2.47 times increased risk of lifetime
suicide attempts in lesbian, gay and bisexual (LGB)
people compared to heterosexuals; the risk ratio for life-
time suicidal ideation was 2.04, and it was 2.05 for
12 months prevalence of depression, one of the most
common mental illnesses [45]. The reviewers also calcu-
lated a pooled risk ratio of 1.88 in gay and bisexual
males for 12 months prevalence of anxiety disorders
(specific disorders were not specified), but the results for
lesbian and bisexual females were less convincing due to
heterogeneity in the study methods (I2 = 49.2 %). The re-
view also found that alcohol and substance dependence
were at least 1.5 times more common in these popula-
tions than in the heterosexual population. Marshal et al. calculated that the odds for substance use among LGB
youth globally were 190 % higher than for heterosexual
youth [46]. Transgender persons Zoni et al. found syphilis preva-
lence rates ranging from 6.5 % in El Salvador to 43.3 %
in Brazil, the latter being the highest rate among high-
risk populations (MSM, sex workers and transgender
persons) in Latin America and the Caribbean [27]. Pre-
liminary results of an ongoing review on hepatitis B and
C by PAHO in the region of the Americas show a higher
burden for male-to-female transgender persons (per-
sonal communication, Rafael Mazin, focal point for
HIV/STIs and hepatitis in key populations, PAHO, 30
May 2014). Cancer Four reviews, two high and two low quality, included
data on cancer in SGM; all were global in scope [32, 41–
43]. Three of these reviews were in MSM and 1 in
WSW; no reviews were found on cancer burden in
transgender persons. Transgender persons We found data on mental health
in transgender persons in a systematic review on the
prevalence of HIV and contextual factors potentially Page 6 of 9 Page 6 of 9 Blondeel et al. International Journal for Equity in Health (2016) 15:16 associated with HIV risk in the United States of America
(USA). High rates of suicidal thoughts (weighted mean,
53.8 %) and lifetime suicide attempts (weighted mean,
31.4 %) were reported in male-to-female transgender
persons [44]. Limited research on HIV in male-to-female trans-
gender persons suggests a high burden. For WSW, a re-
view generated no results but was low in quality [21]. For female-to-male transgender persons and intersex
people we found no reviews. The feasibility of conduct-
ing a systematic review on disease burden of HIV in
these populations should be investigated. Violence Violence is one of the more visible health issues in
SGM, and the subject of many advocacy efforts. We
found four systematic reviews on the prevalence of vio-
lence in SGM, including 1 global, 1 regional (North
America and Europe) and 2 national-level reviews (USA)
[37–40]. All four were on LGB people; there were no re-
views on violence in transgender persons. Reviews on STIs reported a high burden of syphilis in
MSM in Latin America, China and LMICs where preva-
lence was measured. A report by the European Surveil-
lance
of
Sexually
Transmitted
Infections
(ESSTI)
network confirms that MSM also bear a disproportion-
ate burden of syphilis across Western Europe and that
there is clear evidence that it has increased considerably
[50]. Syphilis has been identified as a growing problem
among MSM in a number of countries, based on the
Global AIDS Response Progress Reports [51]. MSM and WSW A global review found high rates of
physical assault (28 %) and sexual assault (27 %) in LGB
individuals, and suggested that they experience more
victimization than heterosexuals [37]. Peterson et al. concluded that rates of adult sexual assault among gay
and bisexual males in North America and Europe far ex-
ceed the rates in community samples of men [40]. LGB
people in the USA seem to be at increased risk for sex-
ual violence victimization compared with their hetero-
sexual counterparts [38]. Focusing on the subset of
intimate partner violence, Finnerman & Stephenson
concluded that emergent evidence in the USA demon-
strates that prevalence of intimate partner violence is
high in male–male partnerships [39]. g
HAV burden was not found to be higher in MSM
compared to heterosexual men in high income countries
[29], but a more recent report on viral hepatitis in Euro-
pean MSM did show an elevated prevalence [52]. In-
creasing attention is being paid to HBV as an STI in
MSM. While a 2004, non-sysytematic, review on disease
burden of HBV only mentioned homosexual activity as
one of the risk factors, alongside heterosexual activity
[53], a more recent epidemiological report estimated
that HBV incidence among MSM is 20 times higher
than in the general population [52]. The same report
also looked at HCV, but did not clarify whether its high
burden was only in HIV-positive MSM or in MSM in
general [52]. Conclusions Our review primarily shows that there is a high burden
of disease for certain subpopulations of SGM in HIV,
STIs, STI-related cancers and mental health conditions,
and that they also face high rates of violence. Secondly,
our review revealed many knowledge gaps. Those gaps
partly stem from a lack of original research, which needs
to be addressed, but there is an equally urgent need to
conduct high quality systematic and literature reviews to
assess what we already know on the disease burden in
SGM. Mental health is a poorly reviewed health issue in
SGM. The most recent global systematic review on men-
tal health in SGM, although high quality, dated from
2008 and suggested an elevated burden in a variety of
mental health issues, but it did not include transgender
persons [45]. Eating disorders and obesity were not dis-
cussed, although they are mentioned in a review on the
health of SGM by the United States Institute of Medi-
cine [9]. Regarding substance use, we found that sexual
orientation is an important mediating factor of adoles-
cent substance use [46]. Adding to this, Bourne et al. conducted a global literature review on drug use in
MSM and concluded that the prevalence of drug use is
high [59]. Some party drugs used by MSM, such as crys-
tal
methamphetamine
or
gamma-butyrolactone,
can
have detrimental effects on mental and sexual health (an
internet survey in Asia reported 4 % and 2.3 % use in
MSM, respectively, in the last six months) [59]. We recommend that systematic reviews on HIV and
HPV in MSM be regularly updated. Reviews on herpes
in MSM, STIs in WSW, and on mental health, violence
and substance use in MSM and WSW, urgently need to
be updated. Special attention should be given to violence
based on sexual orientation and gender identity. Global
reviews on syphilis, hepatitis, C. trachomatis and N. gonorrhoeae in MSM, and on all of the most common
STIs, mental health and violence in the transgender
population need to be conducted. In particular, research
on female-to-male transgender persons should be con-
sidered, as there are virtually no epidemiologic data on
the burden of disease in this population. Literature re-
views should include publications on the burden of can-
cers that are not related to infectious causes and other
non-communicable diseases in all SGM. Discussion International Journal for Equity in Health (2016) 15:16 Page 7 of 9 Page 7 of 9 indicated that among all N. gonorrhoeae cases diagnosed
in men in Europe in 2011, 53 % were in MSM [55]. Moreover, there are indications that MSM are one of the
core groups that are key to the emergence, onward
transmission and outbreaks of antimicrobial-resistant N. gonorrhoeae [56]. hotline calls, social service records and police reports
[60]. All these sources indicated that violence against
transgender persons starts early in life, that they are at
risk for multiple types and repeated incidents of vio-
lence, particularly sexual violence, and that this threat
lasts throughout their lives. Except for the reviews that reported on cancer and
mental health, there are no systematic reviews on non-
communicable diseases in SGM. Nevertheless, there is a
growing body of research on the health of SGM. We
analysed data from systematic reviews only; therefore
the results of research that have not yet been included in
a systematic review are not reflected in this article. More
extensive reporting, which includes the results of these
studies and of studies on risk, contextual and contribut-
ing factors of health disparities and specific health issues
in SGM, is beyond the scope of this review. Methodo-
logically, this review is limited by the databases we
searched and the use of exclusively English search terms
on Google Scholar. The burden of anal HPV is well documented in MSM;
the review by Machalek at al. showed high prevalence in
MSM in general and very high prevalence in HIV-positive
MSM in particular [32]. We found no review on the
prevalence of oral HPV, though studies show it is high in
MSM, and is a risk factor for oropharyngeal cancer [57]. The systematic review on STI/HIV in WSW did not
show a higher burden in this population [21]. Nonethe-
less, the authors concluded that WSW should not be
presumed to be at lower risk based on their sexual
orientation, since they can acquire HIV and other STIs
through other modes, including injection drug use and
sexual contact with high-risk male partners. Available research on cancer burden in MSM focuses
mainly on cancers that are causally linked to STIs; most
other cancers have yet to be studied in this subpopula-
tion [41]. Lee et al. Discussion Our review found that HIV and STIs are the most
researched topics for those studying the disease burden
in SGM, and that the subpopulation of MSM is the most
intensively studied. A 2014 protocol for a global systematic review on the
prevalence
of
HHV-8
described
the
investigators’
intention to examine the hypothesis that MSM have a
high prevalence of the HHV-8 antibody – the infectious
disease underlying Kaposi sarcoma – and to determine if
the prevalence is increasing [54]. The results have not
been published yet. The six included reviews on HIV in MSM (all pub-
lished in 2007 or later) show a high burden in this popu-
lation. UNAIDS reports that the median HIV prevalence
among MSM exceeds 1 % in all regions of the world and
is substantially higher than prevalence among men over-
all, in every context studied [47]. Furthermore, there is
no evidence of a decline in the HIV epidemic in MSM
[18, 24, 47]. HIV prevalence among MSM in some low-
income countries could be underreported because the
data are too limited; male same-sex sexual behaviour
takes multiple forms and HIV has huge potential to in-
crease further in MSM in the next decade [48, 49]. Abu-
raddad et al. indicated growing – in some cases rapidly
growing – HIV epidemics in MSM in several countries,
including Egypt, Morocco, Pakistan, Sudan, Tunisia and
Yemen [49]. Systematic reviews of the existing research
of HIV burden in MSM seem to be up to date and of
reasonable quality, though original research and data are
still lacking in many countries. Our results suggested a high burden of C. trachomatis
in MSM, based on sparse data from medium quality re-
views [34, 35]. Moreover, the most recent annual epi-
demiological report of the European Centre for Disease
Prevention and Control (ECDC), published in 2013, in-
dicated that 99 % of cases of the L2b variant of C. trachomatis, which causes the majority of lymphogranu-
loma venerum infections, are in MSM [55]. Among
those cases with known HIV status, 88 % were HIV-
positive. Data from systematic reviews on the burden of N. gonorrhoeae in SGM were too scarce to support any
conclusions, but an ESTTI report suggested that MSM
bear a disproportionate burden of gonococcal infection
in many Western European and some Central and East-
ern European countries [50]. The ECDC report also Blondeel et al. Discussion showed that there might be reason
to believe there are also disparities in other cancers, as
sexual minorities in the USA are 1.5 to 2.5 times more
likely to be smokers than the heterosexual population
[58]. Smoking is a major risk factor for lung cancer and
a risk factor for a myriad of other cancers. Competing interests 15. Becker LA, Oxman AD. Chapter 22: Overviews of reviews. In: Higgins JPT,
Green S (editors), Cochrane Handbook for Systematic Reviews of
Interventions Version 5.1.0 (updated March 2011). The Cochrane
Collaboration, 2011. Available from www.cochrane-handbook.org 15. Becker LA, Oxman AD. Chapter 22: Overviews of reviews. In: Higgins JPT,
Green S (editors), Cochrane Handbook for Systematic Reviews of
Interventions Version 5.1.0 (updated March 2011). The Cochrane
Collaboration, 2011. Available from www.cochrane-handbook.org Authors’ contributions KB and ES performed the literature review. KB, DC, ES, MT, RK and LS
conceived of the study, and participated in its design and coordination. KB
wrote the manuscript, with the help of DC, LS, RK, IT, MT and ES. All authors
read and approved the final manuscript. 16. Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group. Preferred
reporting items for systematic reviews and meta-analyses: The PRISMA
Statement. PLoS Med. 2009;6(6):e1000097. 17. Shea BJ, Hamel C, Wells GA, Bouter LM, Kristjansson E, et al. AMSTAR is a
reliable and valid measurement tool to assess the methodological quality of
systematic reviews. J Clin Epidemiol. 2009;62(10):1013–20. Author details
1 1Ghent University, Ghent, Belgium. 2Department of Reproductive Health and
Research, World Health Organization, Geneva, Switzerland. 3I.M. Sechenov
First Moscow State Medical University, Moscow, Russian Federation. The majority of the currently available systematic reviews
are on MSM and the burden of HIV and STIs. This sug-
gests that a substantial portion of the burden of disease in
SGM is related to their sexual behaviours, which means it
is preventable. WHO and UNAIDS have been building on
that knowledge, issuing guidelines, recommendations and
tools, including tools for estimating the numbers of specific
populations, and for monitoring and evaluating policies and
interventions to remediate the burden of HIV and STI in
these populations [2, 61–63]. Additional reviews should be
conducted on the non-biological factors that contribute to
higher disease burden. In order to provide universal access
to health-care, more knowledge is needed on the barriers
that SGM face in accessing health services, including the at-
titudes of health-care providers, who are ethically bound to
provide good quality services, regardless of the personal
history or characteristics of the patient. Understanding
these barriers and the additional health risks they impose is
crucial to improving the health status of SGM. Received: 5 June 2015 Accepted: 13 January 2016 References 1. Preamble to the Constitution of the World Health Organization as adopted
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https://openalex.org/W2538234963 | https://zenodo.org/record/2290094/files/article.pdf | English | null | On the Embryo of Welwitschia1 | Annals of botany | 1,910 | public-domain | 4,093 | 2 Pearson, 1909 A, pp. 364-368. [Annals of Botany, Vol. XXIV. No. XCVI. October, igio.] 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3.
2 P
1909 A
364 368 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3.
2 Pearson, 1909 A, pp. 364-368. 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3.
2 Pearson, 1909 A, pp. 364-368.
[Annals of Botany, Vol. XXIV. No. XCVI. October, igio.]
3 F 2
. [Annals of Botany, Vol. XXIV. No. XCVI. October, igio.]
3 F 2 Percy Sladen Memorial Expedition in South west Africa, 1908 1909, Report No. 3.
2 Pearson, 1909 A, pp. 364-368. On the Embryo of Welwitschia.1 BY
H. H. W. PEARSON, Sc.D., F.L.S. With Plate LXIV and two Figures in the Text. In the
absence of any indications as to the later history of the terminal group of
thirty-two cells it was provisionally compared with the corresponding region
of the proembryo of Araucaria brasiliana, to which it bears a curious
resemblance.1 And although it was known that the ' cap' cells of Wel-
witschia are not thrown off in the stages immediately following,2 as is the
case in Araucaria, it nevertheless seemed probable that the embryo was
formed from similarly situated regions in the two cases, viz. from the
so-called 'embryonic plate' (Text-fig. i,e.). It was further assumed that
the cells of the lower ring in due course contributed additions to the
suspensor.3 It was arranged that the Percy Sladen Memorial Expedition in South-
west Africa should visit Welwitsch in Damaraland after the end of February
in order to collect material of the later stages. The results now recorded
have been obtained from ovules gathered there between March 2 and 9,
1909. An expedition to Welwitsch's own locality near Mossamedes in
South Angola, in the following month, has yielded no additional information,
as the older cones obtained there were diseased.4 This investigation has settled all the doubtful points referred to above. The development of the embryo, as far as the stage of Fig. 4, proceeds,
apparently without any interruption, while the cone is still in position and
intact; and since cones collected by Baines at Haikamchab on May 10,
1861, contained ripe seeds,5 it is probable that embryo-development is con-
tinuous until the seed is mature. The period intervening between the
occurrence of fertilization and the completion of the intraseminal growth of
the embryo is thus less than four months. In this respect Welwitschia
shows an agreement with Ephedra 6 rather than with Gnetunt; but in view
of the extreme xerophytic conditions to which Welwitschia has become
adapted this cannot be regarded as of phylogenetic significance. Stras-
burger's statement that the ' cap ' cells are not thrown off is confirmed ;
in the stage shown in Text-fig. 1 they are still the initial cells of the pro-
embryo ; their descendants occupying a similar position retain this character
until the superficial layer becomes dermatogen and a cell-mass underlying
it at the apex is organized as a meristematic group ; the identification of the
internal cell-plate (e.) as the 'embryonic plate' was therefore erroneous. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. AN
l \ . f AN account of the development of the proembryo of Welwitschia up to
l \ . the stage represented in the diagram (Text-fig, i) has been given in
a former paper.2
In this condition the proembryo consists of a suspensor
and a terminal cell-group. From the latter have been formed twenty-four
of the twenty-five cells of which the suspensor consists ; it also gives rise to TEXT-FIG, I. Diagram of an almost median longitudinal section through the distal end of
the pro-embryo of Welwitschia at ihe stage figured in Pearson, 1909 A, PI. 30, Fig. 85. p. s.\
( primary
)
«'. c. r.\
= I inner cortical ring > cells of the suspensor (cf. Pearson, 1. c , Fig. 87). 0. c. r. )
/ outer cortical ring )
e. = 3 of the 8 cells of the ' presumed embryonic plate' (cf. Pearson, 1. c., Fig. 86 B). x. - 2 of the 16 cells of the ' lower ring' (cf. Pearson, 1. c, Fig. 86 B). c. = 4 of the ' cap' cells (cf. Pearson, 1. c, Fig. 86 A). the embryo itself. The terminal group at this stage contains (1) eight
or more ' cap' cells (Text-fig. i,c); (2) a ring of sixteen peripheral cells just
below the suspensor—the ' lower ring' [x.); this surrounds (3) an internal
plate of eight cells, the ' presumed embryonic plate ' (e.). This was the latest stage found in material collected in Damaraland
between January 21 and February 1, 1907. As it was seen many times it
seemed possible that further development was preceded by a resting period. ,
3 F 2 Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
by Insead user Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
by Insead user
on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 760 This suggested the further possibility that the completion of intraseminal
growth might be deferred until after the fall of the seed ; in certain species
of Gnetunt, as is well known, the embryo does not appear while the ovule is
still in position, and this is probably characteristic for the genus. 1 Strasburger, 1879, Taf. sex.
' Cf. Hooker, 1863, PI. 10, Fig. 25.
5 Hooker, 1863, p. 3. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
by Insead user
on 08 March 2018 Pearson.— On the Embryo of Welwitschia. 761 After the condition indicated in Text-fig. 1, the terminal initial
(' cap' cells) undergo both periclinal and anticlinal divisions with the re
that new cells are added beneath those of the plate e., and similar to
and the number of cells in the superficial layer increases (PI. LXIV, Fig
6, 7). The cells of the' embryonic plate' (e.) may divide further ; they or
descendants lie at the extreme tip of the primary root-cap of which
form a part. Even as late as the stage of Fig. 3, all the superficial cells
not ceased to divide by periclinal walls, though many of them have no d
become constituents of a dermatogen, and in somewhat more adva
stages they have all acquired this character. After the stage of F
cell-division becomes localized in a more or less definite suba
growing region. The activity of this meristematic group results in
formation, on the side towards the suspensor,
of a massive tissue whose cells are for the
most part arranged in longitudinal rows. This is already indicated in Fig. 3, and
becomes much more strongly marked in
the axial core of later stages (' Periblem-
saule')—see Figs. 4 and 5. For some time,
therefore, the root-cap constitutes the greater
part of the bulk of the embryo, in which
character, as well as in the details of its
formation, Welwitschia remains true to the
Gymnosperm type. In the embryo shown
in Fig. 4 the original meristematic group
has become divided into two by permanent
tissue; separate growing points for stem
(St.) and root (R) are thus established. The
stem apex quickly becomes externally dis-
tinguishable from the rest of the embryo by
reason of its smaller diameter and dome-like
surface (Fig. 4). Its elongation is very slow compared with that of the r
in the embryo of the mature seed (Fig. 5), in which the two regions are
easily distinguished by the difference of breadth, the stem is hardly m
than one-fifth of the length of the root. Strasburger showed that
cotyledons arise early from the stem-dome (Text-fig. 2) ; they grow f
rapidly and usually somewhat unequally (Fig. 5). In the embryo of
mature seed, thin median sections disclose two small exogenous outgro
from the stem apex, occupying axillary positions with respect to
cotyledons. With Plate LXIV and two Figures in the Text. The suggestion that the cells of the lower ring (x.) produce further additions
to the suspensor is confirmed. * 1. c , p. 155. * Pearson, 1909 B. « Land, 1907, p. 381. 1 Strasburger, 1879, Taf. sex. ' Cf. Hooker, 1863, PI. 10, Fig. 25. 5 Hooker, 1863, p. 3. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.— On the Embryo of Welwitschia. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 TEXT-FIG. 2.
Outline of longi-
tudinal section through distal end of the
embryo of Welwitschia (after Stras-
burger, 1879, Taf. xxii, Fig. 91).
s. = stem-apex ; c. = cotyledons ;
r. = growing-point of root. Pearson.— On the Embryo of Welwitschia. Stages immediately following this are not available for c
parison, but there can be no doubt that these are the ' lateral con
Their appearance thus early in acropetal succession to the cotyledons
1 Cf. Bower, 1881, pp. 579, 580, Fig. vii. '•3. TEXT-FIG. 2. Outline of
tudinal section through distal end
embryo of Welwitschia (after
burger, 1879, Taf. xxii, Fig. 91)
s. = stem-apex ; c. = cotyle
r. = growing-point of root. '•3. TEXT-FIG. 2. Outline of longi-
tudinal section through distal end of the
embryo of Welwitschia (after Stras-
burger, 1879, Taf. xxii, Fig. 91). s. = stem-apex ; c. = cotyledons ;
r. = growing-point of root. '•3. TEXT-FIG. 2. Outline of longi-
tudinal section through distal end of the
embryo of Welwitschia (after Stras-
burger, 1879, Taf. xxii, Fig. 91). s. = stem-apex ; c. = cotyledons ;
r. = growing-point of root. 1 Cf. Bower, 1881, pp. 579, 580, Fig. vii. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 762 in their axils tends to confirm the view advanced by Bower x and more
recently supported by Henriques, that they are axillary buds. Meantime the mass of the suspensor has greatly increased. The
growth of the cells of the ' lower ring' (x) is seen in Fig. 1, while in Fig. 2
they already form part of the suspensor. The peripheral cells immediately
beneath these (Fig. %,y) in their turn behave in the same way, and, as the
embryonic mass elongates, acropetally developed additions to the suspensor
are produced until this structure has attained its final form. These later
formed suspensor cells frequently show a considerable degree of independ-
ence of growth, as was observed by Hooker.2 Cases are seen in Fig. 1 and
more markedly in Fig. 3. In both, suspensor-cells with free ends occur ; in
the latter some are growing parallel with the main body of the suspensor (a),
others appear to be spreading laterally (d), while two (b) have turned down-
wards and are advancing into the endosperm in the same direction as the
embryo. This may perhaps be of the nature of a structural adaptation to
the growing demands of the embryo for food-supplies. 1 Bower, I.e.; Henriques, 1910.
3 Cf. Land, 1907, p. 280.
5 I.e..A,A-
' 2 Hooker, 1863, PI. x, Fig. 25.
l Pearson, 1909, Text-figure,pltpa.
6 l-c,rf. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 763 mass. While the mechanical force developed by the whole system is
without doubt of second-rate importance compared with the results of
enzyme-action in front of the flattened, bluntly-pointed tip of the embryo,
the crushed cells which commonly lie in contact with it bear witness to the
exertion of a definite pushing force. No ovule in which the endosperm was not obviously withered has been
found to be without an embryo. This tends to confirm the observation
previously recorded x that the second phase of the growth of the trophophyte
is dependent upon the occurrence of fertilization—either directly or through
the embryonic activity which follows it. One case only has been seen
in which the one remaining embryo in an ovule was clearly breaking down. The proportion of fertile seeds in normal cones appears to be fairly high,2
and the efficiency of seed-production in Damaraland is in striking contrast
to the rarity of the occurrence of successful germination in that region.3 y
g
g
In early stages, as has been already recorded,4 the ovule usually con-
tains a number of proembryos ; but sooner or later all but one disintegrate. It very rarely happens that an advanced ovule is polyembryonic owing to
the persistent development of more than one proembryo. In one such case
the larger of two embryos (about the stage of Fig. 3) lies deep in the
axis of the endosperm, while a second (younger than Fig. 1), having pene-
trated almost to the depth of the former, has turned abruptly through
an angle of 1800 and now lies near the boundary of the disorganized region
of the endosperm5 with its apex directed towards the nucellus. This
appears to be another instance of the readiness with which the Welwitschia
embryo changes its direction of growth in response to a nutritive stimulus.0
While no case of the branching of the suspensor has been observed, poly-
embryony due to the branching of the embryo itself is fairly common. This frequently occurs in the manner indicated in Fig. 6, in which an
approximate bifurcation has taken place. Examples of lateral branching, in
which an embryo produces a second one smaller than itself, are by no means
rare (Fig. 7). While the former may be compared with the fission of the
embryonic group in Pinus and other Conifers, the latter recalls the remarkable
proliferation of the suspensor in Gnetum Gnemon? 1 Pearson, 1909, pp. 352, 370.
2 Mr. Lynch informs me that of a considerable number of selected seeds sent to Cambridge from
Damaraland in 1907, about 80 per cent, germinated.
3 Pearson, 1907, p. 536.
4 Pearson, 1909 A, p. 368.
5 Pearson, 1909 A, Text-fig, c.
* 1. c, p. 364.
7 Bower, 1882, p. 284. A similar proliferation occurs in C. scandcm. Pearson.— On the Embryo of Welwitschia. In earlier stages,
while the suspensor is still slender and compact and the embryonic cell-mass
small, absorption by the cells of the peripheral layers of both regions
is sufficient. But as they become more massive and the depletion of the
endosperm advances, the difficulty of maintaining an increasing rate of
absorption must become greater. The common behaviour of the younger
suspensor-cells suggests that they have to some extent taken over the
functions of rqot-hairs; morphologically, of course, they are outgrowths
from the root-cap.3 At length the suspensor has assumed its maximum
thickness, and henceforward the surface of the root-cap remains smooth
(Fig. 4). An interesting and suggestive relation appears to exist between
the life-conditions of the embryo in certain parts of its course and the
structure of its suspensor. In early stages,4 when the young embryonic
group is growing towards the endosperm, frequently by a route to some
extent predetermined by the embryo-sac tube, the suspensor is simply the
elongated hypobasal cell. As soon as it enters the endosperm where
it meets competing embryos in a narrow area which quickly becomes
depleted of food supplies, the suspensor thickens.6 There is very little
doubt that the embryo which first reaches the starch-bearing region of the
endosperm6 normally becomes the embryo of the seed, and, broadly speak-
ing, the more quickly this occurs the greater is the chance that a fertile
seed will result. A suspensor which has acquired some degree of rigidity
by reason of the addition to its bulk of several series of peripheral cells, and
whose more OF less spiral form gives to it a certain elasticity, will play an
important part in assisting the embryo to penetrate the underlying cell-. 5 I.e..A,A- Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 4 Pearson, 1909 A, p. 368. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.—On the Embryo of Welwitschia. in which there is little
doubt that the outer cells of the massive suspensor are epibasal in origin
as they are in Welwitschia. More than two embryos in one ovule have
not been certainly seen; in one doubtful case there are perhaps three. That the polyembryony of Welwitschia is very much more limited than in
Gnetum is in keeping with the higher degree of specialization to which Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
by Insead user Pearson.—On the Embryo of Welwitschia. 764 the former has attained. There appears to be no record of the presence
of more than one embryo in the mature seed of Welwitschia, and no
doubt here, as in Gnetum Gnemon, all but one sooner or later are crowded
out of existence. The endosperm from which the stage shown in Fig. 3 was taken has
almost exhausted the tissue in the remains of which it is enclosed. As
Hooker1 observed, most of this tissue is not part of the original nucellus,
but is mainly formed by intercalary growth below the insertion of the
integument. The endosperm is quite free from the surrounding tissue, and
has a smooth firm surface composed of a well-defined and regular cell-layer. Its shape is little changed from that outlined in Fig. 89 k of my former paper.2
The upper third is, however, broader in proportion, and the lower region
slopes more gently to the broad tip. The cavity marked c in the figure last
cited has extended with the further penetration of the embryo. Between
the embryo and the lower end of the endosperm the cells of an axial
cylinder are looser than those nearer the periphery; they contain for the
most part very little visible starch and they are usually binucleate;
occasionally they contain three or more nuclei. This condition is of
common occurrence in the endosperm-cells of Gymnosperms in the neighs
bourhood of growing embryos and archegonia.3
In Welwitschia the
multinucleate state is the result of direct nuclear division. It is generally assumed that the seeds of Welwitschia retain their
power of germinating for a long period. Some evidence bearing on this
question is now forthcoming. A number of seeds collected in Damaraland
in January, 1907, were stored in this laboratory. They were exposed to the
atmosphere, but otherwise were kept as dry as possible. Four were sown
in the last week of February, 1910. 1 Hooker, 1863, p. 33. See also Pearson, 1906, p. 287.
3 Pearson, 1. c, p. 356. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 SUMMARY. 1. The intraseminal development of the embryo is continuous, and
is apparently completed before the seed falls. It occupies not more than
four months from the time of fertilization. 1. The intraseminal development of the embryo is continuous, and
is apparently completed before the seed falls. It occupies not more than
four months from the time of fertilization. 2. A few terminal initial cells (Figs, i, 2, 6, 7) are replaced by a single
massive meristematic group (Fig. 3) which in due course gives rise to
distinct root and stem growing points (Fig. 4). g
g p
g
3. The ' lateral cones' are visible as small protuberances in the axils of
the cotyledons in the embryo of the seed. 3. The ' lateral cones' are visible as small protuberances in the axils of
the cotyledons in the embryo of the seed. y
y
4. The suspensor becomes greatly increased in thickness by centrifugal
additions formed, as in Ephedra, in acropetal succession from superficial
cells of the root-cap. The later formed of these usually show a degree
of independence of the rest of the suspensor in the direction of their growth,
and it may be that they are specially adapted to the function of absorption. 5. In intermediate stages the ovules are frequently polyembryonic,
owing to the branching of the embryonic mass. g
g
y
6. So far as is known the mature seed never contains more than one
embryo. 7. Two seeds collected in Damaraland in January, 1907, germinated
readily in April, 1910. BOTANICAL LABORATORY,
SOUTH AFRICAN COLLEGE,
CAPE TOWN. Pearson.—On the Embryo of Welwitschia. Of these, two have not germinated ;
the cotyledons of one seedling, appeared above the ground on April 4
and those of a second followed after an interval of about fourteen days. The
latter is living (May 21), but shows signs of damping off; the older of the
two appears to be still thoroughly healthy and vigorous. These seeds were
shed certainly not later than June or July, 1906. They have therefore
retained their vitality for forty-three months, during which they have
survived the almost continuously damp atmosphere of Cape Town and the
low temperatures of three Cape winters—conditions which it might be
expected would be particularly trying to the seeds of tropical desert plants. It is therefore probable that the most resistant seeds are capable of lying
dormant for a much longer period under natural conditions. ' Pearson, 1909 A. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 Pearson.—On tJie Embryo of Welwitschia. Pearson.—On tJie Embryo of Welwitschia. 765 BOTANICAL LABORATORY,
SOUTH AFRICAN COLLEGE,
CAPE TOWN. Pearson.—On the Embryo of Welwitschia. 766 Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 LITERATURE CITED. BOWER, F. O., 1881: On the further development of Welwitschia mirabilis. QJ.M.S. xxl (N.S.),
P- 571- P 571
, 1882: The Germination and Embryology of Gnetum. Gnemon. I.e. xxii (N.S.)(
p. 278. p
HENRIQUES, J., 1910 : Welwitschia mirabilis. Gardeners' Chronicle, April 2, 1910. HOOKER, J. D., 1863: On Welwitschia, a new genus of Gnetacese. Linn. Soc. Lond. Trans.,
xxiv, p. 1. p
LAND, W. J. G., 1907 : Fertilization and Etnbryogeny in Ephedra trifurca. Botanical Gazette,
xliv. 273. PEARSON, H. H. W., 1906 : Some Observations on Welwitschia mirabilis, Hook. fil. Phil. Tran3. Roy. Soc. B. 198, p. 265. y
p
1907 : The Living Welwitschia. Nature, April 4, 1907. 1909 (A) : Further Observations on Welwitschia. Phil. Trans. Roy. Soc. B. 200, P- 331- ,
1909 (B) : Percy Sladen Memorial Expedition in South-West Africa, 1908-9, ii. Nature, October 21, 1909. STRASBURGER, E., 1870 : Die Angiospermen und die Gymnospermen. Jena. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 EXPLANATION OF PLATE LXIV. Illustrating Prof. Pearson's paper on the Embryo of Welwitschia. All the figures are prepared from longitudinal and approximately median sections. Figs. 4 and 5 are microphotographs. g
p
g
p
Figs. 1-3, 6 and 7 are drawn under Zeiss D, ocular 2, with the aid of the camera lucida. x 305. Fig. 1. A stage somewhat more advanced than that of Text-fig. 1. x = cells of' lower ring';
c = apical initial cells. p
Fig. 2. A slightly more advanced stage, x = additions to the suspensor derived from the cells
of the ' lower ring ' ; y = the cells which will form the next additions to the Euspensor; c — apical
initial cells. Fig. 2. A slightly more advanced stage, x = additions to the suspensor derived from the cells
of the ' lower ring ' ; y = the cells which will form the next additions to the Euspensor; c — apical
initial cells. Fig. 3. A more advanced stage, a, b, d = suspensor cells; end. = endosperm cells. Fig. 4. A more advanced stage in which the suspensor (S) has completed its growth in thi
ness. St. = stem dome ; R = root meristem. This precedes the stage shown in Text-fig. 2. ness. St. = stem dome ; R = root meristem. This precedes the stage shown in Text-fig. 2. Fig. 5. Embryo of mature seed, c = cotyledons; I.e. = lateral cones; other lettering as in
Fig 4 Fig. 5. Embryo of mature seed, c = cotyledons; I.e. = lateral cones; other lettering as
Fig. 4. Fig. 6. Twin-embryos resulting from bifurcation. g
Fig. 6. Twin-embryos resulting from bifurcation. g
y
g
Fig. 1. A young embryo formed as a lateral branch from an older one. One of the initial cells
of the latter is in course of division. Fig. 1. A young embryo formed as a lateral branch from an older one. One of the initial cells
of the latter is in course of division. '•Aiuwdbs of
Botany'. 0,-MS.J j I
1. c. b. PEARSON. WELWITSCHI A. from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
user
h 2018 '•Aiuwdbs of
Botany'. Vol. xxiv
puxn '•Aiuwdbs of
Botany'. St. b. PEARSON. WELWITSCHI A. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
by Insead user
on 08 March 2018 b. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042
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on 08 March 2018 |
https://openalex.org/W2995958582 | https://openpub.fmach.it/bitstream/10449/58855/2/molecules-25-00004.pdf | English | null | Lipid Profiling and Stable Isotopic Data Analysis for Differentiation of Extra Virgin Olive Oils Based on Their Origin | Molecules/Molecules online/Molecules annual | 2,019 | cc-by | 13,963 | Lipid Profiling and Stable Isotopic Data Analysis for
Differentiation of Extra Virgin Olive Oils Based on
Their Origin Igor Luki´c 1,†
, Alessio Da Ros 2,†
, Graziano Guella 3
, Federica Camin 2,
Domenico Masuero 2
, Nadia Mulinacci 4, Urska Vrhovsek 2,* and Fulvio Mattivi 2,3,* Igor Luki´c 1,†
, Alessio Da Ros 2,†
, Graziano Guella 3
, Federica Camin 2,
Domenico Masuero 2
, Nadia Mulinacci 4, Urska Vrhovsek 2,* and Fulvio Mattivi 2,3,* 2
Fondazione Edmund Mach, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all’Adige,
Italy; darosalessio92@gmail.com (A.D.R.); federica.camin@unitn.it (F.C.);
domenico.masuero@fmach.it (D.M.) 3
Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo Trento, Italy;
graziano.guella@unitn.it 4
NEUROFARBA, Pharmaceutical and Nutraceutical Division, University of Florence, Via Ugo Schiff6,
50019 Sesto Fiorentino, Italy; nadia.mulinacci@unifi.it Correspondence: urska.vrhovsek@fmach.it (U.V.); fu *
Correspondence: urska.vrhovsek@fmach.it (U.V.); fulvio.mattivi@unitn.it (F.M.) Academic Editor: Roberto Fabiani Received: 14 November 2019; Accepted: 11 December 2019; Published: 18 December 2019 Abstract: To differentiate extra virgin olive oils (EVOO) according to the origin of purchase, such as
monocultivar Italian EVOO with protected denomination of origin (PDO) and commercially-blended
EVOO purchased in supermarkets, a number of samples was subjected to the analysis of various lipid
species by liquid chromatography/mass spectrometry (LC-ESI-MS/MS, LC-ESI-IT-MS) and proton
nuclear magnetic resonance analysis (1H-NMR). Many putative chemical markers were extracted as
differentiators by uni- and multivariate statistical analysis. Commercially-blended EVOO contained
higher concentrations of the majority of minor lipids, including free fatty acids, their alkyl (methyl
and ethyl) esters, monoglycerides, and diglycerides, which may be indicative of a higher degree
of triglyceride lipolysis in these than in monocultivar PDO EVOO. Triterpenoids and particular
TAG species were also found in higher proportions in the samples from the commercially-blended
EVOO class, suggesting a possible influence of factors such as the cultivar and geographical origin. The largest differences between the classes were determined for the concentrations of uvaol and
oleanolic acid. The results of the analysis by isotopic ratio mass spectrometry (IRMS) were reasonably
consistent with the information about the geographical origin declared on the labels of the investigated
EVOOs, showing considerable variability, which possibly also contributed to the differences in lipid
composition observed between the two investigated classes of EVOO. Keywords: extra virgin olive oil; lipids; LC-MS/MS; NMR; IRMS; PDO molecules molecules Molecules 2020, 25, 4; doi:10.3390/molecules25010004 1. Introduction Extra virgin olive oil (EVOO) is appreciated among consumers because of its specific flavor and
nutritional properties. Due to its economic importance, EVOO is among the most common commodities
subject to fraud and mislabeling, and for this reason it is protected by regulation. The international
trade standard issued by the International Olive Council (IOC) [1] and the corresponding umbrella
regulation in the European Union (EU) [2] include a set of analytical and sensory methods to test and
confirm the quality grade and authenticity of olive oil. In EU, EVOO can be additionally protected Molecules 2020, 25, 4; doi:10.3390/molecules25010004 www.mdpi.com/journal/molecules Molecules 2020, 25, 4 Molecules 2020, 25, 4 2 of 20 by protected denomination of origin (PDO) [3]. PDO EVOOs are produced according to a set of
specific rules set by the holder of a designation in a specification document, governing aspects such
as olive cultivars used, cultivation, harvest and processing conditions, and oil physico-chemical and
sensory characteristics. In our recent case study conducted on the Italian market it has been shown that oils labelled by
the highest quality category grade (EVOO), despite meeting basic regulatory requirements, can differ
significantly in qualitative terms [4]. Monocultivar PDO EVOOs purchased on family farms were found
to be superior to those offered at the same time in supermarkets with respect to their volatile profiles
and sensory quality. Such large heterogeneity within the EVOO category can certainly influence and
distort consumers’ perception of EVOO quality and in a way discredit the reputation of EVOO in
general. Having in mind that the heterogeneity of oils within the EVOO category with respect to
origin of purchase is certainly among the less studied topics in the ever-growing scientific area of
olive oil traceability and quality, more studies are needed to find reliable chemical markers able to
discriminate EVOO based on this criterion. Such findings would significantly contribute in clarifying
the interrelationship between EVOO origin, overall quality and price, and would as well provide a
basis for designing additional measures of protection of the PDO EVOO class in general, which is most
likely target of fraud by mislabeling due to its large economic importance [5]. y
g
y
g
g
p
Triglycerides (triacylglicerols—TAGs), which are basically esters of glycerol and fatty acids
(FAs), are the main neutral lipid component of olive oil (ca. 98%) [6]. 1. Introduction Olive oil TAGs contain
primarily oleic (C18:1), palmitic (C16:0), linoleic (C18:2n−6), stearic (C18:0), palmitoleic (C16:1), and
linolenic (C18:3n−3) acids, while others occur in minor amounts. Monounsaturated FAs (MUFAs)
and essential polyunsaturated FAs (PUFAs) are among the most important nutritional elements of
EVOO. The consumption of MUFAs has been associated with decrease of several cardiovascular risk
factors [7], while EVOO linoleic and linolenic acids are an important source of essential FAs in human
nutrition [8]. The percentage of TAGs with equivalent carbon number 42 (ECN 42) in total TAGs, where
ECN is the sum of the number of carbon atoms in three constituent FAs in TAG molecule subtracted
by 2 × total of double bonds, can be used as a marker for the detection of the presence of seed oils in
olive oil [2]. In combination with other olive oil constituents, TAGs have been successfully utilized
as markers of varietal [9–11] and geographical origin of EVOO [11]. In virgin olive oils, diglycerides
(DAGs) are present in a range of 1% to 3% in the form of 1,2- and 1,3-isomers, whose ratio has been
used as a marker of olive oil “freshness” [12]. The percentage of total free FAs (FFAs or acidity) is
one of the parameters which is evaluated for the purposes of olive oil quality categorization [1,2]. The composition of olive oil total FA (the sum of those bound with glycerol in TAGs and the FFA
forms) is usually determined by gas chromatography with flame-ionization or mass spectral detection
after TAG hydrolysis and methylation [2] and may provide important information about olive oil
nutritional quality (level of FA unsaturation) and purity. In the last years, proton nuclear magnetic
resonance (1H-NMR) spectral analysis of olive oil is often used to determine not only the % molar
ratio of fatty acyl chains in TAG but also the relative amount of DAGs and, eventually, to detect the
presence of peroxidized acyl chains in TAGs [13]. Several results have also proved the usefulness of
FA composition and distribution on the glycerol moiety for the establishment of EVOO cultivar or
geographical origin [14–16]. The concentration of alkyl esters of free FAs (FAAE), specifically ethyl
esters, is included among the criteria for olive oil quality grade evaluation [1,2]. 1. Introduction These markers
originate mostly from inappropriate handling of olive fruit and oil [17,18] so their concentrations may
be used to detect fraudulent mixtures of EVOO with lower quality oils, including deodorized ones. It is general opinion that the standard profiling of TAGs, DAGs, and total FFAs has limited
discriminative power to differentiate olive oils according to various criteria [19]. However, it was
assumed that recent analytical developments and novel sensitive methods could be able to provide new,
more specific data with more information on olive oil lipids that could be useful for EVOO differentiation. y
p
p
more specific data with more information on olive oil lipids that could be useful for EVOO differentiation. In this work, we applied a multi-methodological approach based on several potent analytical
techniques in order to find new reliable markers able to discriminate EVOO based on the origin p
p
In this work, we applied a multi-methodological approach based on several potent analytical
techniques in order to find new reliable markers able to discriminate EVOO based on the origin Molecules 2020, 25, 4 3 of 20 of purchase. A method was developed based on liquid chromatography with triple quadrupole
mass spectrometric detection (LC-ESI-MS/MS) for the simultaneous quantification of minor lipids,
including the profiling of FFAs, which, to our knowledge, has been studied rather scarcely. As well,
the method provided a more detailed composition of FA alkyl esters occurring in olive oil in relation
to previous studies, supplemented by particular MAGs and triterpenoids. On the other hand, liquid
chromatography with quadrupole ion-trap mass spectrometry (LC-ESI-IT-MS) was utilized for the
profiling of major TAGs, but also aimed to the targeted detection of particular trace TAG species,
such as C50:4, C50:3, and C56:3, as well as those containing FAs with odd number of carbon atoms,
which, to our knowledge, have not been studied extensively until now. In order to provide more
detailed and yet complementary data to those obtained by the other techniques mentioned above,
all the samples were subjected to 1H-NMR quantitative analysis to obtain both the distribution among
lipid species (TAG/DAG/FFA) and a reliable distribution of acyl chains unsaturation (saturated FA
(SFA)/MUFA/PUFA). The latter parameter also allowed establishing the unsaturation index (UI) and
the iodine value (IV), two useful chemical parameters in EVOO quality control. 1. Introduction p
q
y
Besides quality in general, the most important aspect that defines a given PDO and drives the
consumers’ preferences towards this class of EVOO is in fact the authenticity of its geographical origin. One of the most useful techniques to prove and authenticate the geographical origin of EVOO is
stable isotope ratio analysis by isotope ratio mass spectrometry (IRMS) [20]. For example, the stable
isotope ratio of C (13C/12C, expressed as δ13C) of palmitic, oleic, and linoleic FAs was successful in
differentiating olive oils according to the country or region of provenience [20,21]. Both the δ13C and
18O/16O (δ18O) ratios determined for bulk olive oils from various countries were found to change
according to the latitude, the distance from the sea and the environmental conditions during growing
of the plants [22,23]. The δ13C and δ2H (2H/1H) of n-C29 alkanes were significantly more positive
in olive oils from the southern compared with northern Mediterranean countries [24]. As for Italian
EVOOs, works carried on δ13C and δ18O [25,26], also in combination with δ2H [27,28], proved that
it wass possible to distinguish samples from different Italian macro areas, as well as Italian from
other Mediterranean olive oils. The three isotopic ratios, in particular δ2H and δ18O, were found to
be correlated to the climatic (mainly temperature) and geographical (mainly latitude and distance
from the coast) characteristics and to the δ18O and δ2H of the surface waters as well to the year of
production [25–28]. The δ2H values significantly distinguished olive oils produced on the Adriatic
from those from the Tyrrhenian coast of Italy in each year [29]. The combination of isotopic analysis
with 1H-NMR profiling achieved optimal discrimination between Greece, Spain, Italy, Turkey, Crete,
France, and between Italy and Tunisia, the country from which the largest amount of olive oil is
imported in Europe [30]. In this study, it was assumed that IRMS would be able to provide relevant
information on the three isotopic ratios in the two investigated EVOO classes that could be useful for
the confirmation of geographical origin declared on their labels, and possibly for their differentiation. The aim of this study was dual. In the first part, sensitive analytical methods based on complementary
LC-MS and NMR techniques were applied to detect less known chemical markers among various lipid
species able to differentiate Italian monocultivar PDO EVOOs obtained on family farms from those
purchased in supermarkets. 1. Introduction The second goal was to verify the declared geographical origin of the EVOOs
from the both classes by IRMS analysis. It was considered that such findings would significantly contribute
to EVOO diversification on the market, and would help to clarify the interrelationship between EVOO
origin, quality, and price, and in this way support the growth of the niche in the market segment of
consumers informed and interested in healthy, quality products with remarkable diversity and clear identity. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids Validation parameters for the method of determination of minor lipid compounds in EVOO by
LC-ESI-MS/MS are shown in Tables S3 and S4. All the calibration curves exhibited good linearity 4 of 20 Molecules 2020, 25, 4 (r2 values from 0.95 to 1.00). Limits of quantification ranged from 0.2 to 40 µg/L depending on the
compound. The linearity data were used to assess the percentage of matrix effect (% ME), which was
reported in Table S3. The matrix effect was found to be insignificant because the obtained variability
was close to %RSD repeatability values [31]. Thus, curves prepared in solvent were selected for the
quantification. The coefficients of variation (CV%) did not exceed 15% for intra-day assay and 20% for
inter-day assay. The average recovery was in the range from 65% to 125% with %RSD less or equal 20%,
which was considered satisfactory. The recovery values obtained surpassed 90% for 14 compounds,
were between 80% and 90% for 4 compounds and between 70% and 80% for 3 compounds, with %RSD
values between 1% and 11%. This indicated good accuracy, recovery, and precision of the method. It is worth mentioning that several lipids for which the method was also validated (Table S1), such as
carnitines, glycerophospholipids, and sphingolipids, were not detected in the samples of this study,
since their concentrations were below the determined limits of detection (LOD). In all the investigated EVOO samples 20 minor lipids were identified, including 10 free fatty acids
(FFAs), six FFA methyl and ethyl esters, two monoglycerides (MAGs), and two triterpenoids (Table 1). The most abundant among FAAs was oleic (C18:1) followed by palmitic (C16:0), linoleic (C18:2), stearic
(C18:0), and palmitoleic (C16:1) acids, which corresponded to the natural distribution of total FAs
(esterified in TAGs + FFA) in EVOO in general [6]. The methyl and ethyl esters of the most abundant
FFAs, that is oleates, palmitates, and linoleates, dominated the alkyl ester composition, while oleic and
linoleic acids were a structural part of the only two identified MAGs (Table 1). Table 1. Concentrations (µg/g) of minor lipids in monocultivar protected designation of origin (PDO)
and commercially-blended extra virgin olive oils obtained by LC-ESI-MS/MS analysis. An asterisk (*)
in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and
least significant difference (LSD) test. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids Table 1. Concentrations (µg/g) of minor lipids in monocultivar protected designation of origin (PDO)
and commercially-blended extra virgin olive oils obtained by LC-ESI-MS/MS analysis. An asterisk (*)
in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and
least significant difference (LSD) test. Minor Lipids
Origin/Class
Monocultivar PDO
Commercially-Blended
Free fatty acids
Palmitic acid (C16:0)
285.41
362.95
Palmitoleic acid (C16:1)
10.58
16.57
Stearic acid (C18:0)
27.41
43.39
Oleic acid (C18:1)
809.53
1045.52
Linoleic acid (C18:2)
70.52
93.10
Linolenic acid (C18:3)
5.67
9.76 *
Arachidic acid (C20:0)
8.53
11.42
Behenic acid (C22:0)
8.52
9.45
Erucic acid (C22:1)
0.06
0.05
Lignoceric acid (C24:0)
21.85
27.04
Total free fatty acids
1248.09
1619.27
Free fatty acid esters
Methyl oleate
4.02
7.09 *
Methyl linoleate
0.05
0.24 *
Ethyl palmitate
0.10
1.01 *
Ethyl stearate
0.00
0.32 *
Ethyl oleate
2.29
8.18 *
Ethyl linoleate
0.38
1.04 *
Total free fatty acid esters
6.83
17.87 *
Monoglycerides
1-Oleoyl-rac-glycerol
30.11
53.29 *
1-Linoleoyl-rac-glycerol
8.77
12.84 *
Total monoglycerides
38.88
66.13 *
Triterpenoids
Oleanolic acid
26.71
50.13 *
Uvaol
4.58
14.04 *
Total triterpenoids
31.28
64.17 * Minor Lipids
Origin/Class
Monocultivar PDO
Commercially-Blended 5 of 20 Molecules 2020, 25, 4 FFAs in olive oil derive from the breakdown of TAGs by lipolysis. There are many factors which
can affect the degree of TAG lipolysis, including anomalies during biosynthesis, microbial activity,
and environmental factors. Infestation by the olive fly (Bactrocera oleae) is a major cause of high
FFA content in olives. Damaged olive fruits, delayed fruit processing, and storage in inappropriate
conditions result in increased lipolysis rates, while olive oil extraction which is not properly conducted
(e.g., prolonged contact between oil and vegetation water) may also result in high FFA values [6,32]. Therefore, the content of FFA is directly related to the quality of olive oil and reflects the care taken
from blossoming and fruit set to the eventual sale and consumption of the oil [33]. The FFA content,
also known as acidity, is one of the main criteria used to establish different categories of olive oil:
according to the European community, EVOO, as the highest quality category, must have FFA content
below or equal to 0.8% (as oleic acid, w/w), as obtained by the standard titration method [2]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids In this work,
the average total FFA concentration obtained by LC-ESI-MS/MS analysis did not exceed 0.2% in neither
of the two investigated EVOO classes (Table 1). Although a tendency towards higher concentrations in
commercially-blended than in PDO EVOO was noted for the majority of FFAs, statistically significant
differences were found only for linolenic acid. Such a result was, to some extent, in accordance
with a previous study in which low-priced EVOO samples were found to contain more FFAs than
EVOOs of higher price [34]. FFA content was previously shown to increase during olive oil storage
and aging [35,36]. In this work, in contrast to the monocultivar PDO EVOOs which were analyzed
relatively fresh, the age of commercially-blended EVOOs was not declared by the producers/sellers
and it was practically unknown. It was possible that the samples from the latter class were fully or
partially composed from oils obtained in harvests prior to 2016, and that the increased concentrations
of particular FFAs partially resulted from TAG chemical hydrolysis during aging. Despite the possible
differences with respect to the EVOO age, it must be kept in mind that all the EVOOs included in this
study were carefully selected and sampled at the same time, and were therefore valid and authentic
representatives of the both classes of EVOOs offered on the market at that given moment. The content of fatty acid alkyl esters (FAAEs) was principally introduced among the chemical
parameters controlled in olive oil quality evaluation [2] to detect blends including low quality olive
oils with weak organoleptic defects [17,18]. FAAEs are formed by esterification of short-chain
alcohols methanol and ethanol with FAAs yielding methyl and ethyl esters, respectively, although
transesterification with triglycerides or partial glycerides may also be a source [37]. They are generally
considered indicators of lower olive oil quality and their high concentration often indicate the use of
olive fruits with fermentative alterations [17,38–40]. In fact, it was demonstrated that FAAE formation
was not limited mainly by the content of FAA, but it appeared to be strongly related to the concentration
of free alcohols in oil, among which ethanol can be produced exclusively by fermentation [37]. However,
evidence exists that the content of FAAE can be relatively high even in high quality EVOO, and vice
versa [41]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids In this study, the average total concentration of fatty acid ethyl esters (FAEEs) and the
total FAAE concentration were below the maximum limit of 35 mg/kg prescribed by the European
Commission regulation for EVOO [2]. Higher concentrations of all the identified FAAE/FAEEs were
found in commercially-blended EVOOs (Table 1), which indicates the possibility that the olives used
for the production of particular samples from this class were overripe or of lower quality suffering
from fermentative alterations. Such results are in agreement with our previous report generated
from a study with the same sample set, where commercially-blended olive oils were characterized by
lower sensory quality on the average, with a number of samples having a sensory defect, including
fusty/muddy sediment, vinegary/winey, or musty [4] which could have originated from undesirable
fermentative processes, as reported earlier [38,42]. FAAE concentration was previously shown to
increase during storage [41,43], which is another possible cause of the higher concentration found in
commercially-blended EVOOs, which were possibly not fresh at the moment of sampling. y
p
y
p
g
Similar to diglycerides (DAGs), the presence of MAGs in olive oil is a result of either incomplete
biosynthesis of TAGs or their later hydrolysis during processing and storage [12,44]. In virgin olive
oil, DAGs are present in the range of 1–2.8%, while MAGs are found in amounts lower than 0.25%, Molecules 2020, 25, 4 Molecules 2020, 25, 4 6 of 20 with a much higher proportion of those containing a single fatty acid on position 1 than on position 2
of glycerol moiety [45,46]. The identification of only two 1-MAG species in this work confirmed this
phenomenon (Table 1). Both compounds, 1-oleoyl- and 1-linoleoyl-rac-glycerol were found in higher
concentration in commercial–blended EVOO, confirming the possibility that a higher degree of TAG
hydrolysis occurred in these than in PDO EVOOs. The largest portion of triterpenoids in olive fruit is located in its epicarp. Triterpenoid concentration
in olive oil can be increased by longer malaxation durations and higher malaxation temperatures
during olive processing, depending on the compound and olive cultivar [47]. High levels of particular
triterpenoids may indicate the presence of olive pomace oil in EVOO, and the percentage of the sum
of triterpene diols uvaol and erythrodiol with respect to total sterols is in fact included among the
criteria which are evaluated in testing EVOO authenticity in EU [2]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides
and Triterpenoids Higher concentrations of the
triterpenoids identified in this study, oleanolic acid and uvaol, were found in commercially-blended
EVOO (Table 1). Although a possibility should not be neglected that the malaxation and processing
parameters were the cause, it must be kept in mind that the content of triterpenoids strongly depends
on cultivar origin [47,48], which is therefore another possible source of the observed difference. 2.2. LC-ESI-IT-MS Analysis of Triglycerides Relative proportions (%) of triglycerides (TAGs) obtained by LC-ESI-IT-MS analysis in
monocultivar PDO and commercially-blended EVOO are reported in Table 2. As expected, TAGs
consisting of the most abundant naturally occurring FAs in olive oil, the species 54:3, 52:2, 54:4, and 52:3,
dominated the profiles in both classes of EVOO. The obtained profiles did not fully coincide with those
obtainable by the official EU method [2], with some TAGs not reported and some additionally identified,
which suggests the method applied in this study could be used as a complementary approach to the
standard one for obtaining additional information. Table 2. Relative proportions (%) of triglycerides (TAGs) in monocultivar protected designation of
origin (PDO) and commercially-blended extra virgin olive oils obtained by liquid chromatography with
quadrupole ion-trap mass spectrometry (LC-ESI-IT-MS) analysis. An asterisk (*) in a row represents
significant differences between mean values at p < 0.05 obtained by ANOVA and least significant
difference (LSD) test. TAG Species †
TAG Chains ‡
Origin/Class
Monocultivar PDO
Commercially-Blended
TAG 50:1
18:1
16:0
16:0
5.83
5.44
TAG 50:2
18:1
16:1
16:0
3.06
2.84
TAG 50:3
-
-
-
0.63
0.70
TAG 50:4
-
-
-
0.07
0.08
TAG 52:1
18:1
18:0
16:0
2.32
2.47
TAG 52:2
18:1
18:1
16:0
19.10
19.06
TAG 52:3
18:2
18:1
16:0
10.36 *
9.64
TAG 52:4
18:3
18:1
16:0
3.38
3.13
TAG 52:5
-
-
-
0.46
0.42
TAG 52:6
-
-
-
0.05 *
0.03
TAG 53:2
18:1
18:1
17:0
0.42
0.44
TAG 53:3
18:1
18:1
17:1
0.68
0.70
TAG 53:4
-
-
-
0.12
0.14
TAG 54:1
-
-
-
0.68
0.80 *
TAG 54:2
18:1
18:1
18:0
6.37
7.34 *
TAG 54:3
18:1
18:1
18:1
25.40
26.59
TAG 54:4
18:2
18:1
18:1
11.86
11.56
TAG 54:5
18:3
18:1
18:1
4.55
4.47
TAG 54:6
-
-
-
0.74
0.70
TAG 56:1
-
-
-
0.16
0.18
TAG 56:2
20:0
18:1
18:1
1.47
1.51
TAG 56:3
20:1
18:1
18:1
1.63
1.53 7 of 20 Molecules 2020, 25, 4 Table 2. Cont. 2.2. LC-ESI-IT-MS Analysis of Triglycerides TAG Species †
TAG Chains ‡
Origin/Class
Monocultivar PDO
Commercially-Blended
TAG 56:4
-
-
-
0.43
0.38
TAG 58:1
-
-
-
0.06
0.06
TAG 58:2
22:0
18:1
18:1
0.38
0.39
TAG 58:3
-
-
-
0.11
0.10
TAG peroxides §
-
-
-
0.77
0.72
† Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ number of carbon atoms:
double bonds in each of the three fatty acids in the structure of the corresponding TAG; § proportion (%) of the sum
of 52:2, 52:3, 54:3, 54:4, and 54:5 TAG peroxides in total TAGs. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ number of carbon atoms:
double bonds in each of the three fatty acids in the structure of the corresponding TAG; § proportion (%) of the sum
of 52:2, 52:3, 54:3, 54:4, and 54:5 TAG peroxides in total TAGs. The differences between the two EVOO classes with respect to average TAG composition were
not large (Table 2). TAG composition is not evaluated among the parameters related to EVOO
sensory quality, while a part of EVOO nutritional value linked to TAGs, related mainly to the FA
unsaturation level, depends mostly on cultivar, geographical origin and fruit ripening degree [9–11,34]. The differences between the two classes of EVOO, observed for a relatively small number of TAG
species, could be primarily ascribed to the abovementioned factors. TAGs 52:3 and 52:6 occurred in
a higher average percentage in monocultivar PDO EVOO, while TAGs 54:1 and 54:2 stood out with
higher values in commercially-blended EVOO (Table 2). The proportions of the TAG species that could
possibly be associated with particular alterations in production with possible repercussions on olive oil
quality, such as species that include FAs with odd number of carbon atoms (53:2 and 53:3) and TAG
peroxides, did not differ between the two classes. The proportions of particular minor TAG isomers, not included in the official methods [2] and
investigated rather scarcely in olive oil up to date, are reported in Table 3. Significant differences
between the two EVOO classes were found only for the relative proportions of TAG 50:4 I and II
species. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atom
double bonds in each of the three fatty acids in the structure of the corresponding TAG. Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ N
double bonds in each of the three fatty acids in the structure of the corresponding TAG. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atoms:
double bonds in each of the three fatty acids in the structure of the corresponding TAG 2.3. H-NMR Analysis of Lipids The lipid (essentially TAG) composition of EVOO samples was established by measurement and
analysis of the corresponding 1H-NMR spectra as described in Section 3.4. The main features of the
spectra are outlined in Figure 1 reporting also one of the main TAG species present in olive oils (TAG
54:4, 18:1/18:1/18:2) as a model. The data reported in Table 4 were obtained by area peak integration
and simple equations relating them to the number of protons at a given position. Figure 1. 400 MHz proton nuclear magnetic resonance (1H-NMR) spectrum of a monocultivar protected
designation of origin (PDO) extra virgin olive oil sample in CDCl3 at 300 K. Figure 1. 400 MHz proton nuclear magnetic resonance (1H-NMR) spectrum of a monocultivar protected
designation of origin (PDO) extra virgin olive oil sample in CDCl3 at 300 K. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra
virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences
between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra
virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences
between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra
virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences
between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Lipids
Origin/Class
Monocultivar PDO
Commercially-Blended
Total triglycerides (TAGs)
99.38
99.05
Total saturated fatty acids (SFA)
15.83
15.52
Total monounsaturated fatty acids (MUFA)
74.95
75.77
Linoleic acid in TAG (C18:2)
7.92
7.61
Linolenic acid in TAG (C18:3)
1.30 *
1.10
Unsaturation index (UI)
0.95
0.94
Iodine value (IV)
82.33
84.10 *
Total 1,2-diacylglycerols (1,2-DAGs)
0.56
0.72 *
Estimated free fatty acids and minor lipids
0.07
0.26 * In particular, the ratio of the peaks area F/H represents the best way to validate the approximations
used in the approach for the analysis of edible oils relying on the large dominance of TAG species [49]. 2.2. LC-ESI-IT-MS Analysis of Triglycerides Although the source of the observed differences remained unexplained at this stage, and it
could only be assumed that factors such as cultivar and geographical origin, respectively, could have
had a significant effect, the results obtained are certainly intriguing and imply the need to further
investigate the significance of the trace TAG species in olive oil. Table 3. Relative proportions (%) of minor triglycerides (TAGs) and particular TAG isomers in
monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils
obtained by HPLC-HRMS analysis. An asterisk (*) in a row represents significant differences between
mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. TAG Species †
TAG Chains ‡
Origin/Class
Monocultivar PDO
Commercially-Blended
TAG 50:4 isomers
TAG 50:4 I
18:2
16:1
16:1
24.54
31.20 *
TAG 50:4 II
18:3
16:1
16:0
75.46 *
68.80
total
-
-
-
100.00
100.00
TAG 50:3 isomers
TAG 50:3 II
18:2
16:1
16:0
66.56
67.55
TAG 50:3 III
18:3
16:0
16:0
33.44
32.45
total
18:1
18:1
16:0
100.00
100.00
TAG 56:3 isomers
TAG 56:3 I
20:1
18:1
18:1
71.63
71.96
TAG 56:3 II
20:0
18:2
18:1
28.37
28.04
total
-
-
-
100.00
100.00
TAG 53 isomers
TAG 53:4
-
-
-
10.12
10.41
TAG 53:3
18:1
18:1
17:1
56.17
54.79
TAG 53:2
18:1
18:1
17:0
33.71
34.80
total
18:1
18:1
18:0
100.00
100.00
† Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atoms:
double bonds in each of the three fatty acids in the structure of the corresponding TAG. 8 of 20 Molecules 2020, 25, 4 2.3. H-NMR Analysis of Lipids Although the averaged UI (0.941 in the first set versus 0.950 in the second
set) and iodine value (84.0 versus 84.5, respectively) of the two mentioned sets of commercially-blended
EVOO were quite similar, the second set was characterized by significantly higher relative amounts of
SFA and PUFA and lower amount of MUFA (oleic chain, essentially). The differences between the two classes of the investigated EVOO with respect to the 1H-NMR
data can be seen in Table 4. Both classes were characterized by relatively similar major lipid parameters. Monocultivar EVOOs were distinguished by a higher level of linolenic acid and lower iodine value (IV),
while a significant difference for unsaturation index (UI) was not found, meaning an unambiguous
general conclusion about the difference between the two classes of EVOO with respect to the level of
unsaturation could not be made at this point. Level of saturation of acyl chains in olive oil TAGs may
depend on various factors, including geographical position and climate, as well as varietal origin [50]. It is possible that these were among the main sources of both intra- and inter-class variability of lipid
composition observed in this study. Stereospecific distribution of FAs in DAG is known to be affected by several factors. 1,2-DAG
isomers are commonly attributed to the incomplete biosynthesis of TAGs in olive fruit, whereas
1,3-DAGs are considered to derive mainly from enzymatic or chemical hydrolysis of TAGs before
or during oil extraction [12]. It was shown that 1,2-, 1,3-, and total DAG concentrations in olive oil
significantly increase as a result of alterations during processing, including, for example, prolonged
storage of piled olives before processing [12,51]. During storage 1,2- species isomerize to more stable
1,3-DAGs, making the ratio of 1,3-/1,2-DAG a useful criterion indicative of olive oil age [12,44,51]. In this study, a higher proportion of 1,2-DAG fraction was found in commercially-blended than in
PDO EVOO (Table 4), while 1,3-DAG isomers were not identified. Considering the contents of the
other tentative indicators of olive oil age evaluated in this study, such as FFAs and FAAEs, it was
tentatively assumed that commercially-blended EVOO were at least partially composed of olive oils
obtained during harvests prior to 2016, meaning their age was older, on the average, than that of the
PDO ones. 2.3. H-NMR Analysis of Lipids Its value should be exactly 1.500 in an oil containing only TAG species, since the signal F (δH ≈2.30 brt,
-CH2 in α-position in the acyl chains) represents six protons and the signal H (δH ≈4.29 dd and
δH ≈4.14 dd, -CH2 from sn-1,3 TAG) represents four protons. F/H values higher than 1.500 can be
explained by the presence of DAG, MAG, and/or FFA which give their contribution to F but do not
contribute to the H peak area. As much as the F/H ratio diverges from 1.500 the contribution of 9 of 20 Molecules 2020, 25, 4 DAG, MAG, and FFA becomes higher, but within the range 1.450 ≤F/H ≤1.550 the approach is still
considered reliable. Thus, the F/H ratio indicates whether the approximations are correct and therefore
produce trustworthy analytical data for the % molar fraction of SFA, MUFA, and PUFA fatty acyl chains
in a targeted olive oil. In this work, the average F/H value of all the analyzed EVOO was 1.512 with a
very small relative standard deviation of 0.5%, confirming the calculations were valid and reliable. y
g
A certain degree of intra-class heterogeneity was observed within both classes of investigated
EVOO with respect to the relative proportions of total SFA, MUFA, and PUFA. Concerning the relative
amount of the lipid acyl chains, a bimodal distribution of PDO EVOOs was noted, with a major
set (14 of 20 PDO samples) showing a classical distribution of SFA/MUFA/PUFA = 15.1 ± 1.5/76.3 ±
1.4/8.6 ± 0.9, whilst the remaining lead to the averaged distribution values lower in MUFA, such as
SFA/MUFA/PUFA = 16.1 ± 0.8/72.6 ± 0.8/10.4 ± 0.5. Worth of note, particularly unexpected distributions
were observed in particular samples, such as in Ottobratico cultivar PDO EVOO from Reggio Calabria
with SFA/MUFA/PUFA = 19.0 ± 0.3/70.8 ± 0.3/10.2 ± 0.2 (richer in SFA and PUFA), and in Taggiasca
cultivar PDO EVOO from Imperia with SFA/MUFA/PUFA = 12.5 ± 0.1/80.0 ± 0.2/7.5 ± 0.1 (richer in
MUFA). For commercially-blended EVOO a similar intra-class differentiation was observed, with the
most populated set (19 of 25 samples) centered at average molar fractions SFA/MUFA/PUFA = 15.0 ±
0.9/76.9 ± 1.9/8.1 ± 15 and a minor set (6 of 25) centered at average molar fractions SFA/MUFA/PUFA =
17.1 ± 0.5/72.1 ± 1.2/10.8 ± 1.5. 2.4. Multivariate Statistical Analysis Principal component analysis (PCA) separated the samples belonging to the two classes of
investigated EVOO according to the origin of purchase relatively successfully (Figure 2). Although
monocultivar PDO EVOOs were produced from different olive cultivars grown in different geographical
areas in Italy, they were grouped much closer to each other than the commercially-blended ones,
suggesting a greater level of intra-class homogeneity with respect to the profile of lipids. It is possible
that the presumed differences between the average age of the EVOOs from the two classes, and still a
relatively homogenous geographical origin of Italian PDO in comparison to possibly heterogeneous
provenience of the commercially-blended EVOOs (Italy and other EU countries), were among the
causes. Several markers were found to be related to the commercially-blended EVOOs, including all
the minor lipid species, such as FFAs, FAAEs, MAGs, and DAGs, and also particular TAG species and
iodine value, which corresponded completely to the one-way ANOVA results. As mentioned above,
the positions of the commercially-blended EVOO samples on Cartesian plane were rather dispersed,
pointing to the very heterogeneous composition of minor lipids and potential quality of these samples. Molecules 2019,
10 of 20 Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to
the origin of purchase in two-dimensional space defined by the first three principal components, PC1,
PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO
purchased on family farms, while red cycles represent commercially-blended EVOO purchased in
supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of
various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1,
PC2, and PC3. Relati ely
ood e a atio
obtai ed by hie a
hi al lu te i
a aly i
o fi
ed that the t
o
Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according
to the origin of purchase in two-dimensional space defined by the first three principal components,
PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO
purchased on family farms, while red cycles represent commercially-blended EVOO purchased in
supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of
various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1,
PC2, and PC3. Figure 2. 2.3. H-NMR Analysis of Lipids Knowing that the concentration of 1,2-DAGs decreases during storage, it was expected
that the presumably older commercially-blended EVOO would be characterized by lower amounts in
relation to PDO EVOO, but this was not the case. Nevertheless, the possibility cannot be rejected that
the commercially-blended samples contained higher average concentration of 1,2-DAGs already at the
moment of production and/or release on the market, which later decreased but were still higher than
that found in monocultivar PDO EVOOs. The differences observed between the average estimated levels of FAA and other minor lipids
found in the two classes of EVOO (Table 4) correspond well to those determined for particular FAAs, 10 of 20 Molecules 2020, 25, 4 FAAEs, and MAGs by the LC-ESI-MS/MS method (Table 1). Commercially-blended EVOOs were
characterized by higher levels, which was possibly mainly a result of an increased degree of TAG
lipolysis, although the contribution of other factors, such as different cultivars and geographical origin,
as well as EVOO age and storage conditions, should not be completely excluded. 2.4. Multivariate Statistical Analysis (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to
the origin of purchase in two-dimensional space defined by the first three principal components, PC1,
PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO
purchased on family farms, while red cycles represent commercially-blended EVOO purchased in
supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of
various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1,
PC2, and PC3. Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according
to the origin of purchase in two-dimensional space defined by the first three principal components,
PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO
purchased on family farms, while red cycles represent commercially-blended EVOO purchased in
supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of
various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1,
PC2, and PC3. 11 of 20 Molecules 2020, 25, 4 Molecules 2020, 25, 4 Relatively good separation obtained by hierarchical clustering analysis confirmed that the two
investigated classes of EVOO differed notably with respect to the composition of lipids (Figure 3). Most of the conclusions were similar to those obtained by the PCA analysis: PDO EVOOs formed a more
heterogeneous class, characterized by a smaller number of markers, while the commercially-blended
EVOOs exhibited rather diverse lipid composition. Molecules 2019,
11 of 20 Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar
protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and
commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated
using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent
lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of
lipids across different samples. The color gradient, ranging from dark blue through white to dark red,
represents low middle and high abundance of lipid species
Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar
protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and
commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated
using 21 most significant compounds (the highest Fisher ratios). 2.4. Multivariate Statistical Analysis The rows in the heatmap represent
lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of
lipids across different samples. The color gradient, ranging from dark blue through white to dark red,
represents low, middle, and high abundance of lipid species. Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar
protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and
commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated
using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent
lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of
lipids across different samples. The color gradient, ranging from dark blue through white to dark red,
e
e e t lo
iddle a d hi h abu da
e of li id
e ie
Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar
protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and
commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated
using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent
lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of
lipids across different samples. The color gradient, ranging from dark blue through white to dark red,
represents low, middle, and high abundance of lipid species. PLSDA allowed a rather good differentiation of the two classes of investigated EVOO according
to the origin of purchase (Figure 4). Interestingly, the highest variable importance in projection (VIP)
scores were attributed to the triterpenoids, such as uvaol and oleanolic acid, which turned out to be
the most important differentiators. Such a result confirmed once again the potential of the
compounds from the olive oil unsaponifiable fraction to serve as markers according to various
criteria. Besides triterpenoids, the 15 most important lipids according to PLSDA included particular
FAAE and other minor lipid species abundant in commercially-blended EVOO, while certain TAGs
fi
d
l
d
l i
PDO EVOO
PLSDA allowed a rather good differentiation of the two classes of investigated EVOO according
to the origin of purchase (Figure 4). 2.4. Multivariate Statistical Analysis Interestingly, the highest variable importance in projection (VIP)
scores were attributed to the triterpenoids, such as uvaol and oleanolic acid, which turned out to be
the most important differentiators. Such a result confirmed once again the potential of the compounds
from the olive oil unsaponifiable fraction to serve as markers according to various criteria. Besides
triterpenoids, the 15 most important lipids according to PLSDA included particular FAAE and other
minor lipid species abundant in commercially-blended EVOO, while certain TAGs were confirmed as
related to monocultivar PDO EVOO. Molecules 2020, 25, 4
M l
l
2019 12 of 20
f 12 of 20
12 f 20 Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the
origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green
cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family
farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b)
variable importance in projection (VIP) scores of the variables (lipids) most useful for the
differentiation of monocultivar PDO EVOO and commercially-blended EVOO. Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the
origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green
cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms,
while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable
importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of
monocultivar PDO EVOO and commercially-blended EVOO. fi
f
h
l
b
(
) Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the
origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green
cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family
farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b)
variable importance in projection (VIP) scores of the variables (lipids) most useful for the
differentiation of monocultivar PDO EVOO and commercially-blended EVOO. Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the
origin of purchase in two-dimensional space by partial least squares discriminant analysis. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS)
2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) f
f
g
p
g
y
p
p
y
The average values of δ13C, δ2H, and δ18O in monocultivar PDO and commercially-blended
EVOO are reported in Table 5. Statistically significant differences were determined for δ2H and δ18O,
with lower values found in monocultivar PDO EVOO. According to the literature [30], the isotopic
values of olive oil increase with decreasing latitude. It is possible that the contribution of Italian
monocultivar PDO EVOO originating from the orchards located further from the sea and at higher
latitudes with colder climate (e.g., Brescia, Verona, and Garda PDOs) prevailed and significantly
decreased the average δ2H and δ18O isotopic values in monocultivar PDO EVOO, the same as non-
Italian commercial EVOO originating from lower latitudes in warmer EU Mediterranean countries
possibly had a notable influence on increasing the average δ2H and δ18O values determined in
The average values of δ13C, δ2H, and δ18O in monocultivar PDO and commercially-blended EVOO
are reported in Table 5. Statistically significant differences were determined for δ2H and δ18O, with lower
values found in monocultivar PDO EVOO. According to the literature [30], the isotopic values of
olive oil increase with decreasing latitude. It is possible that the contribution of Italian monocultivar
PDO EVOO originating from the orchards located further from the sea and at higher latitudes with
colder climate (e.g., Brescia, Verona, and Garda PDOs) prevailed and significantly decreased the
average δ2H and δ18O isotopic values in monocultivar PDO EVOO, the same as non-Italian commercial
EVOO originating from lower latitudes in warmer EU Mediterranean countries possibly had a notable
influence on increasing the average δ2H and δ18O values determined in commercially-blended EVOO. mmercially-blended EVOO. Table 5. Average values of stable isotopic ratios obtained for monocultivar protected designation of
origin (PDO) and commercially-blended extra virgin olive oils obtained by isotope ratio mass
Table 5. Average values of stable isotopic ratios obtained for monocultivar protected designation
of origin (PDO) and commercially-blended extra virgin olive oils obtained by isotope ratio mass
spectrometry (IRMS). An asterisk (*) in a row represents significant differences between mean values at
p < 0.05 obtained by ANOVA and least significant difference (LSD) test. ometry (IRMS). An asterisk ( ) in a row represents significant differences between me
.05 obtained by ANOVA and least significant difference (LSD) test. 2.4. Multivariate Statistical Analysis Green
cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms,
while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable
importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of
monocultivar PDO EVOO and commercially-blended EVOO. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS)
2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) Stable Isotopic Ratios
Origin/Class
Monocultivar PDO Commercially-Blended
δ13C
−29.65
−29.44
δ2H
−151.28
−144.96 *
δ18O
23 89
26 10 *
Stable Isotopic Ratios
Origin/Class
Monocultivar PDO
Commercially-Blended
δ13C
−29.65
−29.44
δ2H
−151.28
−144.96 *
δ18O
23.89
26.10 * By correlating the two parameters more linked to geographical origin, i.e., δ2H and δ18O, it was
possible to visualize different groupings (Figure 5). As already observed [27], Garda PDO EVOO
(Casaliva cultivar) was characterized by the lowest δ2H and δ18O values, most probably due to the
production area (far from the sea, higher latitude) and climate (colder than the Mediterranean one). The commercial non-Italian EU EVOO showed the highest δ2H and δ18O values, overlapping only
with those of Ragusa PDO (Tonda Iblea cultivar), because the geographical and climatic
characteristics of Sicily are similar to those of other European Mediterranean countries, as observed
previously [30]. The commercially-blended EVOOs of Italian origin had δ2H and δ18O values
By correlating the two parameters more linked to geographical origin, i.e., δ2H and δ18O, it was
possible to visualize different groupings (Figure 5). As already observed [27], Garda PDO EVOO
(Casaliva cultivar) was characterized by the lowest δ2H and δ18O values, most probably due to the
production area (far from the sea, higher latitude) and climate (colder than the Mediterranean one). The commercial non-Italian EU EVOO showed the highest δ2H and δ18O values, overlapping only
with those of Ragusa PDO (Tonda Iblea cultivar), because the geographical and climatic characteristics
of Sicily are similar to those of other European Mediterranean countries, as observed previously [30]. The commercially-blended EVOOs of Italian origin had δ2H and δ18O values overlapping with those 13 of 20
13 of 20 Molecules 2020, 25, 4
Molecules 2019, of Italian monocultivar PDO with the exception of Garda PDO EVOO, which was as expected because
the areas of production overlapped as well. overlapping with those of Italian monocultivar PDO with the exception of Garda PDO EVOO, which
was as expected because the areas of production overlapped as well. Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin
olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian
origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. Figure 5. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS)
2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin
olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian
origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. 3 Materials and Methods Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin
olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian
origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin
olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian
origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. 3. Materials and Me
3.1. EVOO Samples 3.1. EVOO Samples
After preliminary selection from a larger group of high quality monocultivar EVOOs with PDO,
samples that were produced from olives of Italian cultivars harvested in 2016 were collected from
different geographical areas in Italy (price range from 20 to 30 €/L), including Reggio Calabria
(cultivar: Ottobratica; n = 3), Perugia (cultivar: Moraiolo; n = 3), Ragusa (cultivar: Tonda Iblea; n = 3),
Grosseto (cultivar: Frantoio; n = 3), Imperia (cultivar: Taggiasca; n = 1), Brescia (Garda Bresciano PDO,
cultivar: Moraiolo; n = 1), Verona (Garda Orientale PDO, cultivar: Leccino; n = 1), and Riva del Garda
(Garda Trentino PDO, cultivar: Casaliva; n = 5). Furthermore, 25 commercially-blended EVOOs were
selected according to Nielsen data (New York, NY, USA 2016) as among the most consumed during
2016 in Italy (price range from 3 to 12 €/L) and were purchased from Italian grocery stores
(supermarkets), consisting of seven samples with Italian and 18 samples with EU origin declared on
their labels. All the samples were stored in dark glass bottles at a controlled temperature of 15 °C
After preliminary selection from a larger group of high quality monocultivar EVOOs with PDO,
samples that were produced from olives of Italian cultivars harvested in 2016 were collected from
different geographical areas in Italy (price range from 20 to 30 €/L), including Reggio Calabria (cultivar:
Ottobratica; n = 3), Perugia (cultivar: Moraiolo; n = 3), Ragusa (cultivar: Tonda Iblea; n = 3), Grosseto
(cultivar: Frantoio; n = 3), Imperia (cultivar: Taggiasca; n = 1), Brescia (Garda Bresciano PDO, cultivar:
Moraiolo; n = 1), Verona (Garda Orientale PDO, cultivar: Leccino; n = 1), and Riva del Garda (Garda
Trentino PDO, cultivar: Casaliva; n = 5). Furthermore, 25 commercially-blended EVOOs were selected
according to Nielsen data (New York, NY, USA 2016) as among the most consumed during 2016 in Italy
(price range from 3 to 12 €/L) and were purchased from Italian grocery stores (supermarkets), consisting
of seven samples with Italian and 18 samples with EU origin declared on their labels. All the samples
were stored in dark glass bottles at a controlled temperature of 15 ◦C before analysis, and gaseous N2
was added in the headspace to prevent oxidation each time the bottles were opened. 3.3. LC-ESI-MS/MS Analysis The samples were prepared by weighing 500 mg of oil in a 10 mL flask, brought to volume with a
2-propanol solution and internal standard (stearic acid d3 at 1 mg/L). The final solutions were filtered
through 0.22 µm filters and transferred into 2 mL vials [52]. LC-ESI-MS/MS analysis of FFA and other
lipids was carried out using a UHPLC Dionex 3000 (Thermo Fisher Scientific, Dreieich, Germany),
coupled to an API 5500 triple-quadrupole mass spectrometer (Applied Biosystems/MDS Sciex, Toronto,
ON, Canada) equipped with an electrospray source. Five microliters of sample were injected into
the LC-ESI-MS/MS system using an autosampler (Dionex Thermo Fisher Scientific, Germany) kept at
10 ◦C. A reversed phase column Ascentis Express C18 (150 mm × 2.1 mm, 2.7 µm; Sigma, Milan, Italy)
set at 55 ◦C was used for the compound separation. Flow-rate was 0.26 mL/min and the composition
of mobile phases was: solvent A (CH3CN 40% in water, NH4COOH 10 mM and HCOOH 0.1%) and
solvent B (CH3CH(OH)CH3 90%, CH3CN 10%, NH4COOH 10 mM and HCOOH 0.1%). Separation
was carried out following a 30 min multistep linear gradient, according to the method reported by
Della Corte et al. [53]. Selected chemical standards were used to construct calibration curves and
data were expressed as mg/kg after normalization on the basis of the internal standard stearic acid d3. The targeted lipids were detected under multiple reaction monitoring (MRM) mode and the compounds
were identified based on their reference standards, retention times, and qualifier and quantifier ions
(Table S2). The chromatographic system and data acquisition were managed by Analyst™software
version 1.6.1 (Applera Corporation, Norwalk, CT, USA). pp
p
For the method validation, the US Food and Drug Administration (FDA) recommendations
for a bioanalytical method were followed [54]. The validation included the evaluation of linearity,
sensitivity, variability, recovery, accuracy, and precision based on calibration standards and quality
control (QC). Calibration curves were made in 2-propanol and lipid matrix [53,55] in order to evaluate
the percentage of matrix effect (%ME) for each compound. The values were determined by comparing
the equality in the slope ratio between the curves in solvent and matrix, using the following formula:
%ME = 100% × (1 −slope solvent/slope matrix) [56]. The regression line was created with the least
square fit, and the determination coefficient (r2) was also calculated. before analysis, and gaseo
bottles were opened.
3.2. Standards and Solvents 3.2. Standards and Solvents
The solvents used for the analysis of lipids in EVOO were LC-MS grade methanol, hexane,
isopropanol and formic acid, purchased from Honeywell Riedel-de Haën (Seelze, Germany) and all
aqueous solutions, including the HPLC mobile phase, were prepared with water purified using a
The solvents used for the analysis of lipids in EVOO were LC-MS grade methanol, hexane,
isopropanol and formic acid, purchased from Honeywell Riedel-de Haën (Seelze, Germany) and all
aqueous solutions, including the HPLC mobile phase, were prepared with water purified using a
Milli-Q system (Millipore, Vimodrone, Milan, Italy). All the analytical standards used for identification
and calibration are listed in Table S1. 14 of 20 Molecules 2020, 25, 4 14 of 20 3.3. LC-ESI-MS/MS Analysis The linearity was evaluated by
preparing different levels of independent calibration and adding increasing concentrations of each lipid
in different concentration ranges. The sensitivity of the method was evaluated with limits of detection
(LOD) and limits of quantification (LOQ) at the concentration in which the quantizer transitions
showed a signal to noise ratio (S/N) of >3 and >10, respectively. To estimate the analytical variability,
intra-day and inter-day parameters were calculated by injecting 10 times a middle concentration level
QC sample on the same day and re-injecting it for six consecutive days. Intra-day and inter-day
variability were evaluated by the coefficients of variation (CV%). The recovery test was carried out
to verify the applicability of the LC-ESI-MS/MS technique, and it was determined as the average of
the “measured value”/“the expected value” ratio (%). The precision values were calculated as relative
standard deviation (%RSD) among the measures replicated in the QC sample. They were obtained
by analyzing the same sample 10 times. Since the precision can vary with the concentration, it was
appropriated to analyze at least three samples at different concentrations (low, medium, and high)
with respect to the calibration range for each analyte. The accuracy was calculated as the difference
between the calculated value and the theoretical value divided by the theoretical value, reported as the
relative error percentage (%RE). 3.4. H-NMR Analysis of Lipids All the EVOO samples were prepared by addition and suitable mixing of 700 µL of deuterated
solvent (CDCl3) to 200 µL of oil (solution about 200 mM) in a 5 mm NMR tube. All the 1H-NMR spectra
were acquired at 300 K on a Bruker-Avance 400 MHz NMR spectrometer (Bruker, Bremen, Germany)
by using a 5 mm BBI probe with 60◦hard pulse length of 6.6 µs at a transmission power of 0 db. For the
acquisition, 32 K complex points were recorded, the spectral width was set to 10 ppm, the frequency
offset was set to 4.8 ppm, the relaxation delay was set to 15 s, the acquisition time was 8.2 s, the number 15 of 20 Molecules 2020, 25, 4 of scans was set to 32, and the number of dummy scans was equal to 2. The total experimental time
was 13 min. All spectra were acquired without spinning. The chemical shift scale was calibrated
by using the residual proton signal of the deuterated solvent (CHCl3 signal at 7.260 ppm). The data
were acquired using the software Topspin 2.1 (Bruker Biospin, Rheinstetten, Germany). The resulting
spectra were processed manually and automatically with the software MestreNova 12.0.0 (Mestrelab
Research SL, Santiago de Compostela, Spain) taking care to achieve good symmetry on all peaks. The baseline was corrected using a polynomial function. The integral data extracted from the spectra
were analyzed using standard software (Microsoft Office Excel 2016). The ratio of the peaks area F/H
(Figure 1) was tested to validate the approximations used in this study for calcuation of various lipid
species, as suggested earlier [49]. The average F/H value of all the EVOO analyzed in this work was
1.512 with a very small relative standard deviation of 0.5%, confirming the approximations of the
calculations were fulfilled. The data reported were obtained by the following procedures. The % molar
fraction of α-linolenic acid (18:3) was obtained by the ratio of the peak area of ω-3 Me (δH = 0.97 t) with
respect to the peak area of F (×2/3), the % molar fraction of linoleic acid (18:2) by the ratio of the peak
area of bis-allylic protons (δH = 2.77 brt) with respect to the peak area of F minus the contribution of the
previously evaluated % molar fraction of α-linolenic acid (i.e., %18:2 = %PUFA −%18:3). 3.5. LC-ESI-IT-MS Analysis of Triglycerides LC-ESI-IT-MS analysis of the olive oils was performed on a Hewlett-Packard Model 1100 Series
liquid chromatograph coupled both to an Agilent 1100 Series DAD (Photo Diode-Array Detector)
(Hewlett–Packard Development Company, L.P., Palo Alto, CA, USA), and to a Bruker Esquire-LC
quadrupole ion-trap mass spectrometer equipped with atmospheric pressure ESI+ interface (ESI-IT-MS). Isocratic elution was applied with a flow of 0.3 mL/min by using a Kinetex C18 column (2.6 µm 100A
100 × 2.1 mm) (Phenomenex, Sydney, Australia) as stationary phase, and isopropanol:methanol 10/90
(v/v), 10 mM in ammonium acetate, as mobile phase. Samples were prepared by diluting 1:200 (5 mM)
each EVOO with a solution of MeOH:CHCl3 8/2 (v/v), and 4 µL were injected. Relative quantitation
of TAG species was established by peak area integration of the MS extracted ion currents of the
corresponding major ions produced by ESI ionization by assuming the same response time for all the
TAGs species. 3.4. H-NMR Analysis of Lipids Finally, MUFA
(16:1 + 18:1, essentially) was evaluated by the peak area of allylic protons (δH = 2.01 brt) with respect to
the peak area of F minus the contribution of the previously evaluated % molar fraction of PUFA, whilst
SFA (16:0 + 18:0 essentially) was evaluated from total peak area of methyl protons (δH = 0.97 + δH =
0.89) with respect to the peak area of F (×2/3) minus the contribution of PUFA and MUFA. The relative
contribution of 1,2-DAG was given by the integration of the peak at δH = 3.71 brd attributable to the
-CH2 from sn-1,2-DAG, always present in minor amount in olive oils. From these data the average
unsaturation index (UI) and the iodine value (IV) of the acyl chains in TAG were evaluated. Worth
of note, the standard deviations of all the mentioned measurements, calculated from three technical
replicates (ex novo acquisition and data analysis) of a given EVOO sample, were quite low (<1%) for
SFA, MUFA, linoleic and linolenic fatty acyl chains, giving good reliability to the approach applied in
this study. 3.6. IRMS Analysis The analysis of the stable isotope ratios of H, C and O was performed on the bulk olive oil. 13C/12C (δ13C) was measured (around 0.5 mg of oil) using an isotope ratio mass spectrometer IsoPrime
(Isoprime Limited, Manchester, UK) following total combustion in an elemental analyzer (VARIO
CUBE, Elementar, Hanau, Germany). 18O/16O (δ18O) and 2H/1H (δ2H) were measured (around 0.3 mg
of oil) using an IRMS (Finnigan DELTA XP, Thermo Scientific, Bremen, Germany) coupled with a
pyrolyzer (Finnigan TC/EA, high temperature conversion elemental analyzer, Thermo Scientific). For δ2H and δ18O analysis, the weighed samples were stored in a desiccator above P2O5 for at least
four days before analysis, then put into an auto-sampler equipped with a suitable cover. During Molecules 2020, 25, 4 16 of 20 measurement, dryness was guaranteed by flushing nitrogen continuously over the samples. Before
determining the δ2H values, the H3+ factor was verified to be lower than 8, as suggested in the
instrumental manual. The values were denoted in delta in relation to the international V-PDB (Vienna-Pee Dee Belemnite)
for δ13C and Vienna-standard mean ocean water (V-SMOW) for δ18O and δ2H, according to the following
general equation: δi E = (i RSA −i RREF), where i is the mass number of the heavier isotope of element
E, RSA is the respective isotope ratio of the sample and RREF is the relevant internationally recognized
reference material [57]. The delta values were multiplied by 1000 and expressed in units “per mil”
(%). The δ13C and δ2H values were calculated against two international reference materials (Icosanoic
Acid Methyl Esters USGS70, δ13C value: −30.53% and δ2H value: −183.9% and USGS71, δ13C value:
−10.5% and δ2H value: −4.9%), through the creation of a linear equation. δ18O was calculated against IAEA 601 (benzoic acid δ18O = +23.3%) and 602 (benzoic acid δ18O
= +71.4%), through the creation of a linear equation. Data were therefore reported relative to V-PDB
on a scale normalized to LSVEC-NBS19 for δ13C, and relative to the V-SMOW-SLAP scale for δ2H
and δ18O. The uncertainty (2 s) of measurements, calculated following the Nordtest approach, which
combines within-laboratory reproducibility standard deviation and laboratory bias using PT data [58],
was < 0.3% for δ13C analysis, < 0.5% for δ18O and < 3% for δ2H. 3.7. Statistical Data Elaboration Data obtained by the LC-ESI-MS/MS analysis of minor lipids, LC-ESI-IT-MS profiling of TAGs,
1H-NMR analysis of major lipid parameters, and IRMS analysis in the investigated EVOO were
subjected to one-way analysis of variance (ANOVA) and the average values were compared by least
significant difference (LSD) test at the level of p < 0.05. The data were further processed by principal
component analysis (PCA) in order to better visualize the differences between the two classes of EVOO
and explain them on the basis of the content and composition of various lipid species. Prior to PCA,
the original datasets were reduced to include only the lipids and parameters for which statistically
significant difference between the two classes was determined by one-way ANOVA. Partial least
squares discriminant analysis (PLSDA) was performed to extract the most useful variables among
lipids for the differentiation of the two investigated classes of EVOO: variable importance in projection
(VIP) scores for lipids were determined as the weighted sums of the squares of the weight in the
PLSDA. Hierarchical clustering was conducted and a heatmap was generated by Ward algorithm and
Euclidean distance analysis. Multivariate statistical elaboration was performed on mean-centered
data. ANOVA and PCA data elaboration was performed using Statistica v. 13.2 software (StatSoft
Inc., Tulsa, OK, USA), while PLSDA and cluster analysis was conducted using MetaboAnalyst v. 4.0
(http://www.metaboanalyst.ca) created at the University of Alberta, Canada [59]. 4. Conclusions LC-MS and NMR techniques were found to be potent tools to study the variability of various
lipid species in EVOO. Their outputs were shown to be relatively complementary and their combined
use successfully extracted several chemical markers useful for the differentiation of the two classes
of EVOO with respect to the origin of purchase: monocultivar PDO EVOO from family farms vs. commercially-blended EVOO from supermarkets. Considering that the EVOO samples from both
classes were characterized by known (for PDO) and declared/presumed (for commercially-blended)
geographical and pedoclimatic heterogeneity and large variations in olive growing and oil producing
parameters, the extracted markers could be considered relatively robust. Commercially-blended
EVOO contained higher concentrations of the majority of minor lipids, including FAAs, FAAEs,
MAGs, and DAGs, which may be indicative of a higher degree of TAG lipolysis in these than in
monocultivar PDO EVOO. However, triterpenoids and particular TAG species were also found
in higher concentrations/proportions in the samples from the commercially-blended EVOO class,
suggesting a possible influence of other factors, including diverse cultivar and geographical origin, 17 of 20 Molecules 2020, 25, 4 17 of 20 respectively. The results of IRMS analysis were reasonably consistent with the information about the
geographical origin declared on the labels of the investigated EVOOs, which showed considerable
variability. The results of this study undoubtedly confirmed the heterogeneity of oils which are sold
declared as EVOO in Italy in terms of their lipid composition and geographical origin. In that sense,
the obtained findings could significantly contribute to EVOO diversification on the market, and could
help to clarify the interrelationship between EVOO origin, quality, and price, and in this way support
the growth of the niche in the market segment of consumers informed and interested in healthy, quality
products with remarkable diversity and clear identity. Supplementary Materials: The following are available online, Table S1: standards of minor lipids used in the
LC-ESI-MS/MS method development. Table S2: mass transitions (MRM) and instrumental parameters optimized
for each metabolite for the analyses by LC-ESI-MS/MS. Table S3: method validation parameters for each metabolite
for the analyses by LC-ESI-MS/MS - part I. Table S4: method validation parameters for each metabolite for the
analyses by LC-ESI-MS/MS - part II. Author Contributions: Conceptualization, F.M., I.L., N.M., and U.V.; funding acquisition, F.M., U.V., and F.C.,
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https://openalex.org/W2807364799 | https://jfootankleres.biomedcentral.com/track/pdf/10.1186/s13047-018-0262-5.pdf | English | null | UK podiatrists’ experiences of podiatry services for people living with arthritis: a qualitative investigation | Journal of foot and ankle research | 2,018 | cc-by | 7,705 | McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27
https://doi.org/10.1186/s13047-018-0262-5 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27
https://doi.org/10.1186/s13047-018-0262-5 Open Access UK podiatrists’ experiences of podiatry
services for people living with arthritis:
a qualitative investigation Louise McCulloch1*
, Alan Borthwick1, Anthony Redmond2, Katherine Edwards3, Rafael Pinedo-Villanueva3,
Daniel Prieto-Alhambra3, Andrew Judge3, Nigel K. Arden3 and Catherine J. Bowen1 Abstract Keywords: Arthritis, Podiatry, Footcare, Service provision * Correspondence: L.A.McCulloch@soton.ac.uk
1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK
Full list of author information is available at the end of the article * Correspondence: L.A.McCulloch@soton.ac.uk
1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK
Full list of author information is available at the end of the article * Correspondence: L.A.McCulloch@soton.ac.uk
1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK
Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Background: Provision of podiatry services, like other therapies in the UK, is an area that lacks guidance by the
National Institute for Health and Care Excellence. Many individuals living with arthritis in the UK are not eligible to
access NHS podiatry services. The primary aim of this investigation was to understand the views of podiatry clinicians
on their experiences of referral, access, provision and treatment for foot problems for patients who have arthritis. Methods: Focus groups were undertaken to explore, in-depth, individual views of podiatrists working in the UK to gain
feedback on experiences of barriers and facilitators to referral, access, provision and treatment for foot problems for
individuals living with arthritis. A purposive sampling strategy was adopted and two, semi-structured, focus group
interviews conducted, involving 12 podiatrists from both NHS and independent sectors. To account for geographical
variations one focus group took place in each of 2 predetermined ‘zones’ of the UK; Yorkshire and Hampshire. Thematic analysis was employed to identify key meanings and report patterns within the data. Results: The key themes derived from the podiatry clinician focus groups suggest a variety of factors influencing
demand for, and burden of, foot pain within the UK. Participants expressed frustration on having a service that accepts
and treats patients according to their condition, rather than their complaint. Additionally, concern was conveyed over
variations in the understanding of stakeholders’ views of what podiatry is and what podiatrists aim to achieve for patients. Conclusion: Podiatrists interviewed believed that many individuals living with arthritis in the UK are not eligible to access
NHS podiatry services and that this may be, in part, due to confusion over what is known about podiatry and access
criteria. Essentially, podiatrists interviewed called for a timely renaissance of current systems, to newer models of care that
meet the foot care needs of individual patients’ circumstances and incorporate national multi-disciplinary guidance. Through this project, we have formulated key recommendations that are directed towards improving what other
stakeholders (including GPs, commissioners and users of podiatry services) know about the effectiveness of podiatry and
also to futureproof the profession of podiatry. Background emailed a brief overview of the study through the
Colleges’ newswire. Those interested in joining the study
were emailed an information sheet, along with the
contact details of the primary investigator (LMc). Inter-
ested podiatrists then contacted the primary investiga-
tor (LMc) for additional information, to have any
further questions answered and be screened against the
project’s criteria. g
Provision of podiatry services, like other health therapies
in the UK, is an area that lacks guidance by the UK
National Institute for Health and Care Excellence. There
is a perceived lack of understanding of how to access
treatment for foot problems, and limited understanding
of what podiatry services can offer, by both patients and
non-podiatric clinicians [1–6]. Many podiatry depart-
ments have recently felt themselves unsettled by job cuts
and recent changes in how services are commissioned
has shifted focus towards management of acute wounds,
specifically for the management and prevention of limb
loss associated with diabetes [7, 8] The consequent im-
pact of podiatry services reconfiguration of skill mix and
services, away from management of foot pain associated
with other chronic conditions such as rheumatoid arth-
ritis and osteoarthritis, is not known. General Practi-
tioners (GPs) are consulted by 15% of the reported 20
million people in the United Kingdom (UK) with symp-
toms of rheumatic disease each year, forming up to 25%
of a GPs workload [9]; with nearly 30% of the older
population in chronic pain due to ‘arthritis’ [10] or a
lessened quality of life [11], rheumatological disability is
predicted to be a major public health concern in the
coming years [12]. This loss of podiatry services from
the UK NHS potentially puts the most frail and vulner-
able people at risk of mobility loss [13, 14]. The primary
aim of this investigation was to understand the views of
podiatrists
on
their
experiences
of
referral,
access,
provision and treatment for foot problems for patients
who have arthritis. Arthritis was selected as the long-term
condition to scrutinise due to feedback from our patient
and public involvement (PPI) consultations as the one that
caused the most confusion over access to foot-care. p
j
A
purposive
sampling
strategy
was
undertaken,
consistent with the qualitative study design adopted. Procedure Each focus group was conducted by the main researcher
(LMc) supported by a
second investigator (KE in
Yorkshire; AB in Hampshire) as note-taker to aid with
reflection, transcription and subsequent coding. General
topics
for
discussion
were
identified
with
pre-
determined ‘topic guide’ questions written prior to the
focus groups. The topic guide was informed by, and con-
structed from, the findings from analysis of a systematic
review of the literature relative to evidence for podiatry
and foot care conducted by the team [19]. Digital audio-recordings were transcribed, anonymised
and imported into a data analysis package (N-Vivo 11). Using this and manual methods, codes were generated
by noting recurring comments and used to categorise re-
sponses by the researcher (LMc). The codes were re-
fined, compared and grouped into similar features which
served as potential themes. Thematic analysis was iden-
tified as a suitable method to search for patterns related
to podiatrists’ views on podiatry services for individual’s
living with arthritis [16, 18]. Emerging themes were dis-
cussed by the wider research team (LMc, AB, CB) for
verification, identification of any additional areas of
interest and consensus via discussion of patterns across
the data. Potential themes were repeatedly discussed by
the research team to identify any alternative interpreta-
tions. The process of verifying themes as a team pro-
vided a more rigorous approach, different perspectives
and agreement on final themes. Background Participants were selected according to time since quali-
fication, employer (NHS, independent or academia) and
experience of managing foot health for individual’s living
with
arthritis,
to
ensure
the
study
would
capture
insightful and meaningful data from a diversity of ex-
perience, employments and perspectives. To enable a
‘snapshot’ of 2 representative areas of the UK, 2 zones
were established; Yorkshire (North England) and Hamp-
shire (South England) and a focus group interview was
held in each of the zones. Methods A qualitative research study design was employed to en-
able a deep exploration of podiatrists’ views, to gain feed-
back on experiences of barriers and facilitators to referral,
access, provision and treatment for foot problems for indi-
viduals living with arthritis. Focus groups were chosen as
the most appropriate approach to capture a large amount
of information in a relatively short period of time [15] and
allowed us to not only to identify the issues that the podia-
trists’ raised, but also allowed for the observation of how
podiatrists discussed the issues in a ‘natural’ social setting. The methods adopted reflected existing standards for ro-
bustness in qualitative research, deploying triangulation of
data, respondent validation and data saturation, which
guided the final sample size [16–18]. © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 2 of 8 Page 2 of 8 Theme 2: ‘Condition vs Complaint’ This is confounded by an inherent frustration at a
continuing dearth of understanding, of the scope, depth
and
value
of
podiatric
practice,
by
non-podiatrists
including patients: This theme presents podiatrists’ unease on how podiatry
varies within current healthcare systems, with inconsist-
ent approaches causing inequality, discrimination and
discrepancy. An over reliance on tick boxes, and appar-
ent detriment of clinical autonomy, means that people
who are not currently ‘at risk’ (but could potentially be
in the future) are able to access podiatry services, how-
ever those who have high podiatric risk, but by tick box
standards are not classified as such, are thus ‘ineligible’. Table 1 Key themes emergent from focus group interviews
Themes with key quote
Subthemes
Theme 1: Evolving Professional Culture
“Historically the commissioner’s never
quite got around to finishing off writing
the specification”
AHPs understanding
of Podiatry
Commissioning
Patients understanding
of Podiatry
Theme 2: ‘Condition vs Complaint’
“Is it about the patient who’s got diabetes
or is it that they’ve got diabetic lower limb
complications? Because the two are
quite different.”
Inequalities and eligibility
Private sector versus NHS
The current bandwagon
Importance of Podiatry
in Arthritis
Theme 3: Transforming and Sustaining
Podiatry
“We really need to go to the top and make
podiatry the same as dental care, the same as
eye care, the same as hearing, audiology, you
know, we’re just off the radar.”
Equipping Podiatrists
Building Podiatry
Proposals for future
shape of Podiatry Table 1 Key themes emergent from focus group interviews
Themes with key quote
Subthemes
Theme 1: Evolving Professional Culture
“Historically the commissioner’s never
quite got around to finishing off writing
the specification”
AHPs understanding
of Podiatry
Commissioning
Patients understanding
of Podiatry
Theme 2: ‘Condition vs Complaint’
“Is it about the patient who’s got diabetes
or is it that they’ve got diabetic lower limb
complications? Participants The study recruited 12 participants in total, six to each
focus group. Of the clinical podiatrists interviewed, three Participants were recruited through their membership of
the College of Podiatry UK. Potential participants were McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 3 of 8 Page 3 of 8 “[HB1]: I think it’s still fairly common, from feedback
from staff for …the start of the consultation with a
new patient is actually getting them to understand
why you want to know this.” You know, “what’s the
medication got to do with you” et cetera. And that can
actually take up some of the initial time that actually
when explaining about why it’s important and
actually you know “the feet are actually attached to
the rest of your body”, that type of conversation. were solely NHS employed, three were solely in private
practice, six worked in a variety of settings (including
three working part-time in academia). NHS bandings
(where applicable) ranged from 5 to 8. Fifteen codes
were initially identified from the 2 focus group inter-
views. Key themes were constructed via abductive ana-
lysis, and are presented in Table 1 with the subthemes
and one exemplar quote. An abridged summary, with
excerpts of data drawn from the transcripts, is presented
below. Quotes are allocated alphabetical codes where re-
quired, for differentiation. [HG2]: That’s the “what’s that got to do with my feet?” [HB1]: “Yes… a big sum of that time is actually about
just starting to drill down and set the scene with the
patient about what we’re trying to achieve. And then
on to what they want to achieve. With a bit more
understanding why we’re taking medical history and
how it’s relevant to what’s happening in their feet.” Theme 1: Evolving professional culture This theme presents clinical podiatrist’s perceptions on
how podiatry has become shaped historically. Whilst
current podiatry services are well received and valued,
participants vocalised a perception that procurement of
services can be based on sketchy knowledge and absent
evidence: And recent changes and streamlining of NHS manage-
ment structures was discussed: “I know with my locality, the proposal that was sent by
the CCG, it was decided that actually they lacked the
understanding about podiatry. And so it was, we
would buy our local level and then send back to them,
because otherwise they didn’t quite comprehend what
we did. And so we were able to divide it into our
separate areas, like nail surgery, routine care, diabetes
and then send it back to them so that they had more
of an understanding of what we actually did. So that
is a problem.” [Podiatrist: LB1] “We’ve lost a lot of that middle-management podiatry
managers, we haven’t got anybody really fighting for
our service at the moment. And just replying to the
comment about NHS practitioners, I’ve never, in the
whole time that I’ve practiced podiatry, ever seen such
disillusionment. I think that everybody’s burnt out at
work, I think that they’re being managed by people
that don’t actually understand what’s happening.” [LG1] Theme 2: ‘Condition vs Complaint’ Because the two are
quite different.”
Inequalities and eligibility
Private sector versus NHS
The current bandwagon
Importance of Podiatry
in Arthritis
Theme 3: Transforming and Sustaining
Podiatry
“We really need to go to the top and make
podiatry the same as dental care, the same as
eye care, the same as hearing, audiology, you
know, we’re just off the radar.”
Equipping Podiatrists
Building Podiatry
Proposals for future
shape of Podiatry Theme 1: Evolving Professional Culture
“Historically the commissioner’s never
quite got around to finishing off writing
the specification” “I’m really reluctant to do that because a) you’ve got
people with multi-pathologies and b) is it about the
patient who’s got diabetes or is it that they’ve got
diabetic lower limb complications? Because the two
are quite different. And you know again it’s about back
to ‘we shouldn’t just be providing services to people
with diabetes, it’s about services for people with lower
limb complications’… back to what I said earlier about
some services that have got severe restrictions, you
know you could be a 27 year old with diabetes playing
rugby but you could technically get service because Theme 2: ‘Condition vs Complaint’
“Is it about the patient who’s got diabetes
or is it that they’ve got diabetic lower limb
complications? Because the two are
quite different.” Theme 3: Transforming and Sustaining
Podiatry Page 4 of 8 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 you’ve got diabetes as opposed to actually having a
need.” [HB1] people who see the patients when they present with
those conditions…“and I’ve got sore feet” you know…
“and actually got sore hands too”. But then it’s about
getting the training of podiatrists as well, you know, they
not just looking at the feet. If there are some red flags
that come up like they do with diabetes…what do they
do in class about diagnosing arthritis? We all should
be...we shouldn’t just be doing the squeeze test to feet, we
should be doing the squeeze test on the hands.” [HG1] The introduction of access criteria in practice is re-
ported to have created a culture of exclusion to many
vulnerable people, with podiatric clinicians alluding to
cultures of ‘condition over complaint’ and ‘postcode lot-
tery’. Podiatrists refer to an unmet need of foot-care and
the consequential risk of foot-health deterioration. Theme 2: ‘Condition vs Complaint’ Con-
fusion was felt to exist, around non-podiatrists’ under-
standing what a status of high or low risk means. And
with non-standardised criteria in use (‘pain’, ‘diabetes’ or
specific long-term health conditions) eclectic podiatric
services are being provided across the country. If eligibility systems are used, they should be set
nationally, evidenced, agreed across professional groups
and used consistently, whilst embracing expert clinical
discretion. “We need care pathways … You know, I think we need
to subdivide all the things that podiatry offers and
have a tick box assessment sheet that we can actually
offer to somebody that’s diagnosed with arthritis and
make sure that there is an effective referral system…for
that patient to know what care is available and what
they can expect if they're presenting with certain
conditions.” [LG1] “They tend to put the commissioned service versus
service level agreements. So, a lot of diabetes services
are commissioned. So they ‘have’ to provide that
service, so even though we, in the acute trust run, you
know, quite a full rheumatology foot service, as soon
as we’re a man down in diabetes, people get pulled
from arthritis clinics, from rheumatology, to cover
diabetes. And that is just based on, purely
commissioned services versus service level agreements. We have a service level agreement to provide
treatment for Rheumatology patients…” [HG1] Clinicians suggested a preference for access to podiatry
services being more person-centred, tailored to individuals: “I think there certainly needs to be evidence to show
that there should be a pathway whereby all these
patients get some sort of similar assessment to identify
what their initial needs are. And maybe on an annual
basis or even a three-yearly basis or something, just to
ensure that then things can be identified early on to
start actually taking place, whether it be footwear,
whether it be on education or whether they need to
change medication or whatever else... It has to be put
up the agenda.” [LG1] Theme 3: Transforming and sustaining podiatry
This theme captures practising clinicians’ views for the
future shape of podiatry in modern healthcare: “It {resolving current constraints to podiatric access}
is multifaceted; it is conversations with the commissioners
about getting specification rights in the first place. Theme 2: ‘Condition vs Complaint’ It is
discussions internally within health trusts around
priorities and in some ways protecting what we’ve got …
So the only way we can get around that {current
constraints to podiatric access}, as I can see, is raising
the profile of the profession. Raising the knowledge and
raising the value of what we do and the cost efficiency
of what we do.” [HB1] They propose a more multidisciplinary, coordinated
approach to patient services, specifically requesting that
arthritis and other long term health conditions have
models of access and guidelines comparable to those for
diabetes: Podiatrists want to see inequalities in service provision
eliminated, offering a shift in the priorities of podiatric
services to incorporate more long term conditions: “Pathways. Referral pathways, just like diabetes ...a bit
more streamlined and a bit more easy to access.” [HG3] “Pathways. Referral pathways, just like diabetes ...a bit
more streamlined and a bit more easy to access.” [HG3] Evolving professional culture Notably, podiatrists expressed key concerns of frustra-
tion that, although podiatry has evolved as a profession,
there remains a sense of misunderstanding, by non-
podiatrists and patients, of the scope of practice and
ability of podiatrists in what they do. The revelation that
podiatrists believe their scope of practice is limited by
the profile and image of the profession is not a new one. Earlier work has identified the hierarchical nature of the
health professions [21] and the way in which podiatry
has perceived itself as less visible and more misunder-
stood than other comparable professions [22–24]. In our
investigation, advances in scope of practice and a grow-
ing presence in multi-disciplinary team (MDT) working
were clearly considered important factors in raising the
profile of the podiatry profession, however were per-
ceived more evident in specific fields, such as diabetes
foot care, and much less clear in primary care which is
also evidenced widely in the literature [25]. They reported a need to work with other professionals
to drive changes for more long term conditions: “And it's not just our profession that’ll link with them
[public health], for the benefit of our patients because,
you know, podiatry is one of them, you could have
ENT in there, you could have physio in there, you’ve
got other disciplines in there. They can all push this
agenda forward and start saying, yes, here’s another
one, it's a long-term condition that we need to be doing
more for.” [LG1] Clinicians believed access to podiatry services should
be transformed to fit modern healthcare needs, to meet
the needs of patients within an evolving healthcare sys-
tem, which incorporates building in onward referral to
private sector podiatrists, into the NHS service: Key leaders in the profession, locally and nationally, were
lauded for the development of services in the past and
concern was voiced over the increasing trend for managers
responsible for defending, promoting and commissioning
podiatry services in today’s healthcare practices, to be non-
podiatrists with limited knowledge of the scope of practice
of the profession. The vital role of key, charismatic charac-
ters in podiatry has been previously reported in the
literature as being fundamental in developing and augment-
ing the profession in specialisms such as diabetes [26],
podiatric surgery [27] and rheumatology [28]. “Can I, can I bring something in there that’s quite
important? “Pathways. Referral pathways, just like diabetes ...a bit
more streamlined and a bit more easy to access.” [HG3] “Podiatry provides an opportunity to pick up long term
conditions in the early stages, so we know that
mechanically, arthritis in the foot is the second most
common site for presentation so podiatrists can be a
guard responsible for aiding, for new diagnosis for a
patient and show them …you know some red flags for
podiatry to go in, because they’re likely to be the “Make it more equal over the UK rather than just
dependant on personality, and really that sums up
what people said – going through more pathways,
focussing on multidisciplinary teams.” [HG4] “If we had a more multidisciplinary coordinated
approach it would be better for the patient. I know Page 5 of 8 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 that we have access to all these other professions but
sometimes those communications, are blocked, not
blocked but they are strained because you’ve got to
write a letter, and that’s got to go off, then someone’s
got to sign it and… whereas if you had a better,
multidisciplinary approach like we do in terms of
diabetes then those patients would go through proper
routes a lot quicker” [HG1] ‘foot care’ and embedding evidence within national and
local guidelines [19–22]. The resultant key themes con-
structed from our investigation are discussed below: ‘Condition vs Complaint’ Whilst the podiatrists interviewed in this study believe
that their services are valued and appreciated by their
patients, they express concern that only certain people
can access NHS podiatry care in the UK. Interestingly,
despite the evidencing of outcomes, cost effectiveness
and quality of services being currently so important in
the procurement and commissioning of NHS services,
there continues to be a paucity of published evidence to
show the ‘value’ that patients attribute to UK podiatry
services and the interventions that podiatrists use, both
in respect to its significant importance amongst health-
care delivery and its impact upon patients’ quality of life. Patients who can afford it may choose to seek foot care
expertise from the private sector, yet this excludes many. The implications are made clear. In the UK, the majority
of NHS podiatry care is initiated from within the pri-
mary care sector through referral from GPs [7]. Podiatric
clinicians in this investigation suggested that Clinical Evolving professional culture We actually have a good NHS private
practice working relationship in our area, the culture
that we historically have had is that when a patient is
deemed no longer eligible for treatment, that they’re
discharged to the third sector. And you know, if you
actually have a dentist, and the NHS can't meet your
dental needs, you’re recommended that you can seek
dentistry privately, the same with seeing an optician.”
[LG1] Discussion Using focus group methodology and a thematic ap-
proach to data analysis, this study has provided unique
insights into UK podiatrists’ (based in 2 distinct regions
of the UK, Yorkshire and Hampshire) perceptions of
barriers and facilitators to referral, access, provision and
treatment for foot problems for individuals living with
arthritis. Our overarching findings indicate that podia-
trists experience frustration about the role and status of
podiatric services, the inequalities in service provision
(between regions and between individuals) and the loss
of clinical autonomy – fuelling an ethos of ‘condition
over complaint’. The literature relating to foot healthcare
supports the need to transform and shape podiatry by
promoting the scope of practice, taking ownership of McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 6 of 8 Page 6 of 8 Commissioning Groups (CCGs), comprising primary
care GPs, were much less well informed about the po-
tential health gains to be made through referral to
podiatry than perhaps other services, or in diabetes care,
where MDT working enhances professional profiles. As
a result, podiatrists in this investigation noted that com-
munity referral to podiatry is less well targeted than it
might be, given the lack of understanding of the roles
and skills of modern podiatrists [29] among GPs and
other commissioners in primary care. This is reflective
of recent analysis of GP referral patterns for foot pain,
which found that the majority went to orthopaedics [30]. Interestingly
this
reflects
the
cultural
and
socio-
historical context of the allied health professions, which
occupied a lesser position within a complex health
division of labour throughout most of the twentieth cen-
tury [23, 31]. services to ‘cope’. Alternative foot health providers were
broached, including charitable organisations and ‘nail
bars’, where concerns were aired from both NHS and
private sector practitioners, as were the incongruities of
jointly managing patients between multiple providers. This echoes the views of other experts advocating
podiatric intervention for those with foot health vulner-
ability and pathology due to long term health conditions
[36–39]. This, in turn, synchronises with NHS England’s
(2014) 5 Year Forward View [40] for a healthcare system
that demonstrates improvements in service outcomes,
improves preventative care, enables the frail and elderly
to stay healthy, independent and access individualised,
person centred care. Discussion Frustration was reported over the prioritisation of UK
NHS service provision according to the contract type,
with commissioned services having priority over service
level agreements, often prioritising one patient group, or
clinic,
over
another. Furthermore
confusion
was
expressed, by podiatrists in our investigations, on behalf
of service users not eligible to access podiatry services
when acquaintances were. Feedback from people who
have chronic conditions is consistent with this, indicat-
ing that patients are not accessing foot healthcare [1–3,
41] and that they are confused over referral pathways to
podiatry services [2, 42, 43]. A sense of frustration was consistent through the dis-
cussions on the disparity across the UK of accessibility
to NHS podiatry services and the inequity between
areas, patient groups and commissioning bodies. Eligibil-
ity criteria, and the use of ‘tick box’ access, in combin-
ation with a national public health drive, appears to have
resulted in open eligibility to podiatry services for some
patients, but limited or barred access for other patient
groups who may have an equal or greater podiatric need. A sense of frustration was consistent through the dis-
cussions on the disparity across the UK of accessibility
to NHS podiatry services and the inequity between
areas, patient groups and commissioning bodies. Eligibil-
ity criteria, and the use of ‘tick box’ access, in combin-
ation with a national public health drive, appears to have
resulted in open eligibility to podiatry services for some
patients, but limited or barred access for other patient
groups who may have an equal or greater podiatric need. Whilst this is positive and inclusive for ‘eligible’
people, it excludes others. This allows access to podiatry
services for people who may not need specialist podiatric
intervention at the time, yet are able to access care be-
cause they have a specific condition, albeit not affecting
their feet. This, in turn appears to be causing inequities
of condition over complaint. Barriers towards accessing
podiatry care for individuals who have arthritis have
been previously highlighted in other countries [32–34]. This is consistent with findings that the provision of foot
care for people with rheumatoid arthritis is not driven
by foot health characteristics such as foot pain or foot
related disability [32, 35] and indicates that the role of
podiatry in the prevention of deterioration of foot health
is partially, but not fully, recognised. Transforming & sustaining podiatry Since the inception of podiatry in the early part of the
twentieth century, podiatry models of care within the
UK NHS have remained fairly static and the model of
access and care within private practice has remained
stable within the realms of financial accessibility [7]. Despite that, demand has shifted towards acute levels of
care within the UK NHS. Changes to service access in
the 1990s has led to resource allocation, guidance and
prioritisation for patients with complex acute care needs,
predominantly diabetes [19]. Provision of podiatry services for individuals with arth-
ritis is an area that lacks guidance. Whilst participants of
this study acknowledged the presence of some foot
health guidelines for people with arthritic conditions, re-
ferring specifically to the Arthritis and Musculoskeletal
Alliance (ARMA) and NICE guidelines [44] for people
with arthritis, they reported little recognition of, nor suf-
ficient emphasis placed on, the use of these relevant
guidelines by non-podiatry health professions or pa-
tients. The deficiency in specific guidance for foot health
for people arthritis conditions appears to be in contrast
to the vast plethora of guidance available for foot care
services and intervention for people with diabetes [19]. Indeed, current literature suggests existing foot health
guidelines for people with arthritic conditions are not
being utilised to their fullest advantage and there is a Alone, medical or podiatric pathology can place a per-
son at mild, moderate or severe podiatric risk status. With comorbidities, this risk increases, in some cases
significantly [36, 37]. Podiatrists are aware of the risk
status and vulnerability of patients who do not have
their podiatric needs met, including those who are ineli-
gible for NHS care but cannot afford private sector care. From the concerns podiatrists expressed on behalf of
their service users, came some consideration of alterna-
tive foot care options that the public access. Private
practice was represented positively in providing valuable
services, from both private sector and NHS practi-
tioners,
including
suggestion
that
it
enables
NHS McCulloch et al. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Conclusion The burden of foot pain for individuals living with arth-
ritis in the UK is not insubstantial, yet many cannot ac-
cess NHS podiatry services [7, 51]. The key themes
derived from the podiatry clinician focus groups suggest
that there are a variety of factors influencing demand
for, and burden of, foot pain within the UK. Primarily,
participants expressed frustration on having a service
that accepts and treats patients according to their condi-
tion, rather than their complaint. Secondly, concern was
conveyed over variations in stakeholders’ understanding
of what podiatry is and what podiatrists aim to achieve
for patients. Essentially, podiatrists interviewed called for
the reform of the current accessibility to services to one
that matches the foot care needs of individual patients. Availability of data and materials
h d
h
h f d
f The data that support the findings of this study are available from the
corresponding author upon reasonable request. Transforming & sustaining podiatry Journal of Foot and Ankle Research (2018) 11:27 Page 7 of 8 Page 7 of 8 Page 7 of 8 Clinicians are keen to explore alternative ways to pro-
mote podiatry services for procurement and new models
of service provision, to be more reflective of people’s in-
dividual circumstances and believe that setting and
implementing nationally set guidance is the optimal way
to inform commissioning of podiatry services towards a
more inclusive service provision. recognised need to improve the implementation of such
guidance [45]. Whilst new models of foot care for indi-
viduals who have inflammatory arthritis have been pro-
posed [43, 46, 47] the recognition, development and
implementation of guidance and pathways for other long
term conditions that affect the feet (including osteoarth-
ritis) is necessitated in a similar format to those for
people with diabetes. Abbreviations
h Podiatrists in this investigation considered that current
UK health recommendations on recognition, transform-
ation, sustainability and public health [40, 48] to be a
timely opportunity for the profession to promote and re-
establish podiatry’s full scope of practice to all stake-
holders (patients, service managers, commissioners and
other health professionals). They too encourage the de-
velopment of new care models for podiatry, to meet the
burden of foot pain in the UK and demands of modern
healthcare. Podiatry
has
long
been
encouraged
to
become more versatile and involved in preventative
healthcare [7, 49] and this now coordinates with recom-
mendations for all AHPs [48]. Podiatrists interviewed
believed change was needed, to sustain the provision of
services and profession. Abbreviations
ARMA: Arthritis and Musculoskeletal Alliance; GP: General Practitioner;
NICE: National Institute for Health and Care Excellence Abbreviations
ARMA: Arthritis and Musculoskeletal Alliance; GP: General Practitioner;
NICE: National Institute for Health and Care Excellence Strengths and potential limitations This study examined the perceptions of podiatrists in
two regions of the UK, as a potentially representative
snapshot. By using the experiences of 2 diverse groups
of podiatrists from two disparate regions, rich text and
themes have been generated. Limitations are acknowl-
edged as both are in England, therefore data may not be
wholly representative of the four home UK nations
(England, Scotland, Wales and Northern Ireland) mean-
ing proposed themes may be more or less significant in
other areas. This may, however, align with high degrees
of variation in specialist rheumatology service provision
across the UK, wherein podiatry remains a notably
poorly represented profession [50]. Author details
1 1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic &
Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics,
Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. 1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic &
Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics,
Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. 1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic &
Musculoskeletal Medicine Leeds UK 3Nuffield Department of Orthopaedics 1Faculty of Health Sciences, University of Southampton, Highfield Campus
Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic &
3 Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics,
Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. Received: 21 March 2018 Accepted: 6 May 2018 Competing interests Dr. Alan Borthwick is Editor UK and Prof Catherine Bowen is the Deputy
Editor UK of the Journal of Foot and Ankle Research. It is journal policy that
editors are removed from the peer review and editorial decision-making
processes for papers they have co-authored. The remaining authors declare
no conflicts of interest in relation to this work. Ethics approval and consent to participate Full ethical approval was gained (IRAS: 15/SW/0251). All participants provided
written informed consent. Governance for the study was approved by the
Faculty of Health Sciences, University of Southampton Ethics Committee via
the ERGO (Ethics and Research Governance Online) online approval system. Acknowledgements g
The authors would like to thank all the participants of the study and Andy
Stow and Adam Thomas from the College of Podiatry who helped with
study recruitment. Authors’ contributions CB, AB, AR, RP, DP, AJ and NA conceived the study. KE led on the systematic
review of evidence for podiatry that underpins the topics for this study. LMc
conducted the focus groups and extracted and produced the first draft. KE
and AB collected notes and observed participants within the focus groups. LMc, AB, CB, analysed the data. LMc, AB, AR, KE, RP, DP, AJ, NA and CB
critically reviewed the academic content and participated in producing the
final draft. All authors read and approved the final manuscript. Funding This study was supported by a project grant from the College of Podiatry. CB is currently being supported to undertake Fellowship from The National
Institute for Health Research. The views and opinions expressed herein are
those of the authors and do not necessarily reflect those of National Institute
for Health Research, NHS or the Department of Health. References
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https://openalex.org/W4386631839 | https://www.researchsquare.com/article/rs-3326201/latest.pdf | English | null | Diffraction separation and imaging based on curvelet domain cascade filter | Research Square (Research Square) | 2,023 | cc-by | 7,965 | Diffraction separation and imaging based on
curvelet domain cascade ¦lter Zongnan Chen
China University of Mining and Technology (Beijing)
Jingtao Zhao Zongnan Chen
China University of Mining and Technology (Beijing)
Jingtao Zhao Diffraction separation and imaging based on curvelet domain cascade
filter
Zongnan Chen1, Jingtao Zhao1,Suping Peng2 1 College of Geoscience and Survey Engineering, China University of Mining and Technology
(Beijing), Beijing, China. E-mail: zlczn1995@163.com, diffzjt@163.com;
2 State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and
Technology (Beijing), Beijing, China. E-mail: psp@cumtb.edu.cn. Right Running Head: Curvelet-domain diffraction separation method
di
h
i
h
il diff j
6 Corresponding author: Jingtao Zhao E-mail: diffzjt@163.com Research Article License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Additional Declarations: No competing interests reported. Version of Record: A version of this preprint was published at Pure and Applied Geophysics on April 2nd,
2024. See the published version at https://doi.org/10.1007/s00024-024-03456-6. Curvelet-domain diffraction separation method ABSTRACT Diffraction separation plays an important role in high-resolution imaging of small-scale
discontinuous geological bodies. These discontinuities or nonuniformities are related to the oil
and gas migration path and reservoir space, and they are also common geological hazard factors
in engineering. In the common offset domain, diffractions are hyperbolic, while reflections are
mostly linear. The difficulty of diffraction separation technology is to suppress the reflected
energy while retaining the diffraction energy. Curvelet is a sparse transformation with angle
classification. Reflections are distributed in a few coefficient matrices after curvelet
transformation, whereas diffractions are the opposite. Based on the significant difference between
reflections and diffractions in the curvelet domain, a method of diffraction separation using
cascaded filters in the curvelet domain is proposed. Cascade filters in the curvelet domain include
high-pass filters and median filters. The adaptive high-pass filter can suppress the low-frequency
part of reflections, and the median filter is used to suppress the high-frequency part of reflections. Numerical experiments show that the proposed method has good performance in eliminating tilt 1 1 Curvelet-domain diffraction separation method and horizontal reflections, as well as the ability to retain the polarity reversal characteristics of
diffractions and more energy. Field application further verifies the potential value of this method
in solving the identification of complex stratigraphic structures and small-scale discontinuities. and horizontal reflections, as well as the ability to retain the polarity reversal characteristics of
diffractions and more energy. Field application further verifies the potential value of this method
in solving the identification of complex stratigraphic structures and small-scale discontinuities. Keywords: diffraction separation, curvelet transform, median filter, high-pass filter 1. Introduction In resource and engineering geophysical exploration, it is a very meaningful task to locate
the small-scale distributed geologic bodies such as micro-faults, pinches, fractures, and string
beads (Lanbach et al 2000). During the propagation of seismic waves, distributed geologic bodies
will become new sources and generate diffractions. Therefore, diffractions can indicate the
position of faults in the seismic wavefield (Krey 1952) and contain valuable information
regarding both the structure and composition of seismic media (Belfer et al 1998). However, the
energy of diffraction is usually an order of magnitude lower than that of reflection, making it
difficult to use diffraction in conventional seismic data processing flow (Landa and Keydar
1998). Independent diffraction imaging can avoid the shielding of specular reflection energy and
improve the resolution of discontinuous geological bodies in seismic profiles (Khaidukov et al
2004). There are two types of diffraction imaging techniques. The first method uses the geometric
difference between reflection and diffraction to separate the wavefield in various gathers, and
then image the separated diffraction. Landa et al (1987) proposed that diffraction and reflection
had obvious geometric differences in the common offset domain, and used travel-time correlation
to extract diffraction. Fomel (2002) used the dominant local slope estimated by plane-wave
destruction (PWD) filters to suppress linear signals. Since then, PWD has become the most
widely used diffraction separation method in areas such as diffraction velocity analysis. 2 Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method (Gonzalez et al 2016; Yu et al 2017a; Lin et al 2018; Decker et al 2017). The Hilbert transform
was used to locate the diffraction points, and the diffraction was extracted from both sides of the
diffraction point using a double-branch Radon transform (Li et al 2018). Zhao et al (2019) used
the spacing-varying median filter in the flattened shot domain to separate diffraction. Chen et al
(2021) built a sparse inversion model based on Radon transform and Curvelet transform to
separate diffractions in the common offset domain. Bakhtiari Rad et al (2018) used the width of
the projected Fresnel zone to augment the filter, and then identify diffractions from reflections. With the extensive application of artificial intelligence in seismic exploration, the convolutional
neural network is applied to diffraction separation (Sheng and Zhao 2022). Another method of diffraction imaging is to achieve diffraction separation and imaging by
modifying the migration operator during the imaging process. Fomel et al (2007) performed
diffraction velocity analysis in the post-stack domain to achieve high-resolution imaging. Berkovitch et al (2009) used a new local time correction formula to parameterize the diffraction
travel time curve and achieve the flattening and focusing of diffraction events. Karimpouli et al
(2015) proposed an apex-shifted Radon transform (ASRT) method to image diffractions in pre-
stack data. The ASRT method used a diffraction hyperbolic trajectory similar to pre-stack time
migration to locate the diffraction bodies and estimate their corresponding background velocity. To predict the reflection, Yu et al (2017b) focused on the pre-stack diffraction residual near the
first Fresnel aperture and proposed a regularized L2-norm model with a smooth constraint on the
local slope. Li et al (2020). used a Mahalanobis-based and phase-based attenuation function to
modify the Kirchhoff migration formula in the full-azimuth dip-domain to realize diffraction
separation. In this paper, we separate diffraction and reflection in the Curvelet domain, which is a sparse
transform that is more suitable for curve characteristics (Shan et al 2009). In the common offset
domain, reflections are mostly smooth linear events, whereas diffractions are still hyperbolic. We 3 Curvelet-domain diffraction separation method transform seismic data into the curvelet domain and then apply a cascade of median filter and
frequency high-pass filter. 2. Method The basic theory of the proposed curvelet-domain diffraction separation method is to apply a
cascade filter along the scale and angle parameters of the curvelet domain, which is effective in
suppressing reflections and preserving weak diffractions. The proposed method is composed of
the following elements. 2.1. Curvelet transform Curvelet-domain diffraction separation method The high pass filter is used to suppress the majority of the low-
frequency energy of the reflection event, while the median filter is used to suppress the high-
frequency linear energy of the reflection edge. Following the inverse curvelet transform, the
diffraction retained by the cascade filter is restored to the data domain. This method utilizes the
geometric differences between diffraction and reflection in the common offset domain, and
belongs to the first type of diffraction separation method. Compared to current diffraction
separation methods, it can better protect diffraction energy during the separation process. The
diffraction separation and imaging effect of synthetic and field data confirm the method's
feasibility and efficiency. This method of cascaded filter diffraction extraction based on Curvelet
transform can obtain higher image quality for small-scale geological bodies and improve the
resolution of seismic exploration. 2.1. Curvelet transform The Curvelet transform was proposed by Candes and Demanet (2003). It introduces a new
compact curve frame sparse representation Fourier integral operator, and its fast discretization
algorithm is realized by Candes et al (2006). Curvelet transform can accurately express seismic
signals with the smallest coefficient and has a better-focusing effect on curve events (Ma and
Plonka 2009). Therefore, it has many applications in denoising and wavefield separation
(Demanet and Ying 2007; Cao et al 2015; Hu et al 2019; Zhang and Langston 2020). We use the
curvelet theory introduced by Candes et al (2006) to describe the Curvelet transform. 4 4 Curvelet-domain diffraction separation method Let x be the spatial variable, be the frequency variable, r and be the polar coordinate
parameters in the frequency domain. Two window functions W( )r and V( )r are established,
which are called "radial window function" and "angle window function" respectively. They are
smooth, non-negative, and real-valued. The window functions comply with the following
conditions: (
)
(
)
2 2
=1,
3 4,3 2
j
j
W
r
r
=−
(1)
(
)
(
)
2
1,
1 2,1 2
l
V
t
l
t
=−
−
=
−
(2) (1) (
)
(
)
2
1,
1 2,1 2
l
V
t
l
t
=−
−
=
−
(2) (2) for all scales with
0
j
j
, the frequency window function in the Fourier domain is defined as: for all scales with
0
j
j
, the frequency window function in the Fourier domain is defined as: (
)
(
)
2
3
4
2
,
2
2
2
j
j
j
j
U
r
W
r V
−
−
=
(3) (3) where
2
j
is the downward rounding of
2
j
. The support of
j
U is a polar wedge. In order to
obtain the real value curvelet, the symmetrical form
(
)
(
)
,
,
j
j
U
r
U
r
+
+
of equation (3) is
used. where
2
j
is the downward rounding of
2
j
. The support of
j
U is a polar wedge. 2.1. Curvelet transform In order to Define the “mother” curvelet
( )
j x
by Fourier transform. Define the “mother” curvelet
( )
j x
by Fourier transform. ( )
( )
j
j
U
=
(4) (4) In this way, all curvelets on the 2
j
− scale can be obtained by rotating and translating from
( )
j x
: ( )
j x
: 1. Defines an isometric sequence of rotation angles
2
2
2
j
l
l
−
=
, where
0,1,2... l =
, 0
2
l
; 0
2
l
; 2. and the sequence of translation parameters
(
)
2
1
2
,
k
k k
=
. with
these
notations,
the
curvelet
at
scale
2
j
−
,
orientation
l
and
position 2. and the sequence of translation parameters
(
)
2
1
2
,
k
k k
=
. with
these
notations,
the
curvelet
at
scale
2
j
−
,
orientation
l
and
position (
)
(
)
,
1
2
1
2
2 ,
2
l
j l
j
j
kx
R
k
k
−
−
−
=
is defined by: (
)
(
)
,
1
2
1
2
2 ,
2
l
j l
j
j
kx
R
k
k
−
−
−
=
is defined by: (
)
(
)
,
1
2
1
2
2 ,
2
l
j l
j
j
kx
R
k
k
−
−
−
=
is defined by: Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method ( )
(
)
(
)
(
)
,
, ,
l
j l
j l k
j
k
x
R
x
x
=
−
(5) (5) where R is the rotation by radians. 2.1. Curvelet transform Thus, the curvelet coefficient of a function
(
)
2
2
f
L
R
is simply defined by itself and a curvelet
, ,
j k l
with parameters: is simply defined by itself and a curvelet
, ,
j k l
with parameters: (
)
( )
( )
2
, ,
, ,
, ,
:
,
j l k
j k l
R
c j l k
f
f x
x dx
=
=
(6) (6) according to equations (4) and (6), the curvelet domain represented by the curvelet coefficient is
essentially a space-time domain. The curvelet tiling of space and frequency is completely displayed by Ma and Plonka
(2010). Because our focus is on diffraction separation, we will not repeat the graph of the curvelet
in this paper meticulously. However, to understand the application scenario of curvelet
transformation, we designed a toy model and showed its wavefield and the corresponding
curvelet domain expression (curvelet coefficient), as shown in Figure 1. 2.2. Cascade filter In the curvelet domain, the reflection events still behave linearly and only a few flat angles
contain them. On the contrary, diffraction contains more angle information because of hyperbolic
characteristics, so more curvelet coefficients are needed to describe diffraction. We only need to
filter those angles containing reflection on each scale to suppress reflection. Only a few angles of
diffraction and reflection coincide, in other words, only the curvelet coefficients in these angles
need to be separated (such as Figure 1d). Curvelet transform, on the other hand, provides us with
an angle classification filter to protect diffraction energy. In the curvelet domain, the interior of
the reflection is low frequency, while the edge is high frequency. We use a high pass filter to
suppress the low-frequency part and a median filter to suppress the high-frequency part of the
reflection edge. The two filters are described below. The mathematical formulation of the high-pass filtering is as follows: Perform two-dimensional discrete Fourier transform on the curvelet domain coefficient
matrix
,
1
2
( ,
)
j l
c
k k
with scale = j and angle = l : 1 1
2 2
1
1
2 (
)
1
2
,
1
2
0
0
(
,
)
( ,
)
K k
K k
M
N
i
M
N
j l
C K K
c
k k e
−
−
−
+
=
(7) (7) In order to suppress the reflection frequency as much as possible, we use ideal high-pass
filtering
1
2
(
,
)
H K K
as follows: 1
2
0
1
2
1
2
0
0
(
,
)
(
,
)
1
(
,
)
D K K
D
H K K
D K K
D
=
(8) (8) 7
where D is the distance from the column sorting to the middle line in the C matrix,
0
D is set to
one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: 7
where D is the distance from the column sorting to the middle line in the C matrix,
0
D is set to
one-sixth of the total number of columns in the C matrix. [Figure 1 is here] Fig 1 (a) 2D reflectance model containing a scatter and a horizontal reflector. (b) Synthetic
data from the Kirchhoff forward modeling. (c) The curvelet coefficients of synthetic data. (d) Specific Curvelet domain coefficient matrix, when scale = 5 and angle = 8 Figure 1(a) presents a 2D geologic model in which a scatter is covered by a horizontal at a
depth of 1km. The velocity of the background medium is 2 km/s. The synthetic data in Figure
1(b) is generated using Kirchhoff integral method and Ricker wavelet with the dominant
frequency of 30Hz. There are 1000 receivers and shots with a space interval of 2m in the zero-
offset data. The time length of synthetic data is 2 seconds. In Figure 1 (b), the hyperbolic event at
1km shows the response of scattering points respectively. The amplitude of horizontal events is
about ten times that of hyperbolic diffraction. According to equation 6, we get the curvelet
coefficient of Figure 1(b), as shown in Figure 1(c). In Figure 1(c), the coefficient close to the
image center represents the low-frequency scale, and the coefficient far from the image center 6 6 Curvelet-domain diffraction separation method represents the high-frequency scale. It should be noted that there is no angle information in the
curvelet coefficient of the smallest scale. We select a scale and angle parameter representing
diffraction and reflection curvelet coefficients as a specific example, as shown in Figure 1(d). 2.2. Cascade filter represents the high-frequency scale. It should be noted that there is no angle information in the
curvelet coefficient of the smallest scale. We select a scale and angle parameter representing
diffraction and reflection curvelet coefficients as a specific example, as shown in Figure 1(d). 2.2. Cascade filter 2.2. Cascade filter High-pass filtering effect by: where D is the distance from the column sorting to the middle line in the C matrix,
0
D is set to
one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: where D is the distance from the column sorting to the middle line in the C matrix,
0
D is set to 7
one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: xth of the total number of columns in the C matrix. High-pass filtering effect by: Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method 1
2
1
2
1
2
(
,
)
(
,
)
(
,
)
H
C
K K
C K K
H K K
=
(9) 1
2
1
2
1
2
(
,
)
(
,
)
(
,
)
H
C
K K
C K K
H K K
=
(9) 1
2
1
2
1
2
(
,
)
(
,
)
(
,
)
H
C
K K
C K K
H K K
=
1
2
1
2
1
2
(
,
)
(
,
)
(
,
)
H
C
K K
C K K
H K K
=
(9) the two-dimensional inverse Fourier transform is performed on
1
2
(
,
)
H
C
K K
to obtain the curvelet the two-dimensional inverse Fourier transform is performed on
1
2
(
,
)
H
C
K K
to obtain the curvelet coefficient matrix
,
1
2
( ,
)
H
j l
c
k k
after high pass filtering. [Figure 2 is here] Fig 2 (a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest
frequency; (b) The shape of the ideal high pass filter, we set it as a rectangular window; (c)
Spectrum after ideal high pass filtering; (d) Curvelet coefficient matrix after high pass filtering Figure 2 shows an example of a high-pass filtering process using Figure 1d. Figure 2(a)
shows the spectrum of Figure 1(d). As we can see, there are low-frequency reflections in the
center of the spectrum, as well as relatively high-frequency diffraction on both sides of the image
center line. Therefore, we improve the circular structure of the traditional high-pass filters. A
rectangular high-pass filter (Figure 2(b)) can better suppress reflection and retain diffraction on
the spectrum. The Curvelet coefficient matrix
,
1
2
( ,
)
H
j l
c
k k
obtained by high-pass filtering is shown
in Figure 2(d). After removing the low frequency, the high frequency caused by reflection
remains. Although they only appear in a small range of the spectrum, the linear high frequency
caused by the reflection edge will bring the "ringing" phenomenon. We use a median filter to
solve this trouble. The following is the mathematical principle of median filtering. ,
,
,
1
arg min
b
p q
A
H M
j l
b
a
c
C
a
c
c
c
=
=
−
(10) (10) where
,
,
H M
j l
c
denotes the output value of the median filter for the current location point
,
p q
x
;
,
,
1
2
{ ,
,
,
}
p q
p q
A
C
c c
c
=
,
,p q are the position index in a 2-D dimension, ,a b are indices in the
filtering window. The symbol A means the fixed length of the filtering window. The curvelet
coefficient matrix after median filtering is shown in Figure 3(a). where
,
,
H M
j l
c
denotes the output value of the median filter for the current location point
,
p q
x
;
,
,
1
2
{ ,
,
,
}
p q
p q
A
C
c c
c
=
,
,p q are the position index in a 2-D dimension, ,a b are indices in the
filtering window. The symbol A means the fixed length of the filtering window. transform 2.3. Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Inverse curvelet transform is carried out in the curvelet domain after cascade processing of
the high pass filter and median filter. We have completed the separation of diffraction from the
space-time domain(Figure 3(b))so far. [Figure 2 is here] The curvelet
coefficient matrix after median filtering is shown in Figure 3(a). where
,
,
H M
j l
c
denotes the output value of the median filter for the current location point
,
p q
x
; 8 Fig 3 (a) Figure 2 (d) after median filtering. (b) The diffraction obtained by inverse curve Fig 3 (a) Figure 2 (d) after median filtering. (b) The diffraction obtained by inverse curvelet [Figure 3 is here] [Figure 3 is here] [Figure 4 is here] Fig 4 The workflow of curvelet domain cascade filter diffraction separation method Fig 4 The workflow of curvelet domain cascade filter diffraction separation method One contribution of this method is to apply a cascade filter based on the curvelet transform,
which makes it possible to separate diffraction in common offset gathers. Compared with other
diffraction separation methods, it no doubt has inherent advantages as the diffractions in common
offset gathers are distributed at multiple angles. Therefore, the curvelet domain has good
performance in distinguishing geometric forms of reflection and diffraction. Selecting a specific
curvelet domain for filtering can protect the amplitude of the two branches of diffraction. 2.3. Curvelet-domain diffraction separation method In the proposed curvelet-domain diffraction separation method, a combined operation of the
high-pass filtering and median filtering is used to extract curvelet coefficient matrixes of
diffractions. The forward transform and inverse transform of the curvelet is used to switch
seismic data in the common offset domain and curvelet domain. The whole method framework
(Figure 4) is outlined as follows: 1. Convert the common offset domain data to curvelet domain; 1. Convert the common offset domain data to curvelet domain; 2. Adaptively select the coefficient matrix according to the scale coefficient of the curvelet
domain, which contains reflections and diffractions at the same dip angle; 3. Applying the two-dimensional discrete Fourier transform to the selected curvelet
coefficient matrix; 4. Using the frequency domain ideal high-pass filter to suppress the low-frequency signal
in the curvelet domain; 5. Applying the two-dimensional inverse discrete Fourier transform to obtain the curvelet
coefficient matrix with diffraction coefficients; 6. Cascading the median filter to suppress the residual reflection edge and the "ringing" 9 Curvelet-domain diffraction separation method generated by the ideal high-pass filter; generated by the ideal high-pass filter; 7. Convert the curvelet domain to the common offset domain. 7. Convert the curvelet domain to the common offset domain. 3. Synthetic example The 2D fault model shown in Figure 5(a) is used to generate synthetic seismic data, which
includes multiple faults and a horizontal reflector (reflection coefficient is 1). The media velocity
is set to 1.5 km/s. The six faults with fault distances ranging from 80m to 180m are located in the
transverse positions of 2.3km and 3.8km respectively. The specular reflection on both sides of the
depression has different inclination, which can be used to test the proposed method's suppression
effect on the inclined formation reflection events. The numerically synthetized Kirchhoff
algorithm is used to generate 2D synthetic data with a dominant 30Hz Ricker wavelet. The
surface observation system we designed is used to generate zero offset data, which includes 600
shots and receivers with a 10m space interval. The number of time samples is 1100, with a time
interval of 2ms. The synthetic data in Figure 5(b) includes 20 edge diffractions and 10 reflections. The two branches of edge diffractions have opposite polarity. 10
[Figure 5 is here] 10
[Figure 5 is here] 10 10 Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Fig 5 (a) Graben reflectance model including inclined strata and fault edges. (b) The synthetic
seismic wave field forward simulated by Kirchhoff integral method Based on the curvelet transform, we can obtain curvelet coefficients of synthetic data. The
angle quantity division of the curvelet coefficient is based on scale, and the number of scales is
related to the size of input data. For the synthetic data we used, curvelet transform divides it into
seven scales. In practical terms, the mesoscale parameters of the curvelet transform start from 0,
but the computer can only start from 1 when calculating and saving. In this paper, we use the
scale code displayed on the computer. We choose the "first" scale without angle parameters and
the fifth scale divided into 64 angles as the presentation of cascade filtering in the curvelet
domain (Figure 6). [Figure 6 is here] [Figure 6 is here] Fig 6 (a) Curvelet coefficient matrix of "first" scale; (b) The "first" scale curvelet coefficient
matrix after cascade filtering; (c) 16 continuous angle windows on the fifth scale of curvelet
domain; (d) The fifth scale after cascade filtering 11
Figure 6(a) shows the first scale curvelet coefficients obtained from the curvelet
transformation of synthetic data. There is the same but fuzzy distribution pattern as the seismic
data in the Spatio-temporal domain because the first scale of curvelet transform is the lowest
frequency range representing the image contour. The proposed cascade filtering is applied to the
first scale curvelet coefficient to obtain the diffraction curvelet coefficient as shown in Figure
6(b). Although the spatial shape of the wavefield is fuzzy in the curvelet domain, the hyperbolic
shape of diffraction is better preserved than that of reflection. Figure 6(c) shows the coefficient
matrix of 16 consecutive angular windows of the synthetic data on the fifth scale of the curvelet
domain. As we can see, both reflections and diffractions are concentrated in different angle
windows according to the inclination range. In curvelet transform, the number of angle windows
will double for every two scales. So, we design an adaptive operator based on scale change to 11 Curvelet-domain diffraction separation method select part of the angle window for filtering. Figure 6(d) shows the results of cascade filtering. In
the filtered coefficient matrix, the reflected curvelet coefficient is suppressed and the diffraction
coefficient is retained. Moreover, in the coefficient matrixes, those are not selected for filtering,
the curvelet coefficients representing the distal end of the diffraction two branches are all retained
for the recovery of the diffraction wavefield. [Figure 7 is here] [Figure 7 is here] Fig 7 (a) Diffractions separated by cascade filtering method in curvelet domain; (b) Diffractions
separated by traditional PWD method; (c) Curvelet domain cascade filtering method separates
reflections; (d) Reflections separated by traditional PWD method; (e) Migration imaging of (a); (f)
Migration imaging of (b) The separated diffraction wavefield is obtained by inverse curvelet transform using the
curvelet coefficients after cascade filtering, as shown in Figure 7(a). Both horizontal and oblique
reflections are well suppressed. The traditional PWD diffraction separation method is applied to
synthetic data. The diffraction wavefield separated by the PWD method is shown in Figure 7(b). As we can see, the proposed method can better suppress the inclined reflection energy and retain
the polarity reversal characteristic of edge diffraction. In order to illustrate the superior
performance of the proposed method in protecting diffraction amplitude, we show the reflection
separated by the curvelet domain cascade filtering method (Figure 7(c)) and PWD method
(Figure 7(d)) respectively. The proposed method performs very well in the index of diffraction
energy protection. In addition to the reflection wavefield of the PWD method, Chen et al (2021)
also showed their reflection separation results, which contained significantly more diffraction
than the proposed method. The migration imaging of the curvelet method and PWD method are
shown in Figure 7(d) and (e), respectively. 12
The numerically synthetized example demonstrates the good performance of the proposed
curvelet-domain diffraction separation method in eliminating strong reflections and separating 12 Curvelet-domain diffraction separation method diffractions. The diffraction image can accurately depict the fault edge, and therefore play a
significant role in studying the Geological disaster causing factors and oil and gas migration
pathway. diffractions. The diffraction image can accurately depict the fault edge, and therefore play a
significant role in studying the Geological disaster causing factors and oil and gas migration
pathway. Fig 8 Nankai DMO stacked data Fig 8 Nankai DMO stacked data Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD
method [Figure 9 is here] Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD 4. Field data application It is necessary to carry out diffraction imaging in field seismic data because diffraction
carries the information of underground small-scale scatterers and discontinuities. The Nankai
deep-water field data with well-developed diffraction and variable reflection inclination is often
used to test the performance of diffraction separation methods (Decker et al 2017, Chen et al
2021, Sheng et al 2022). The dip-moveout correction (DMO) stacked profile (Figure 8) is used to
verify the availability of the proposed method. Due to the multi-stage geological structure, the
wavefield is very complex. The migration imaging velocity is from Decker et al (2017). We can
see that reflection and diffraction constitute shallow events. Due to the existence of a steep dip
stratum, the energy of some diffraction is strong. Some weak diffraction will be masked by strong
reflection in the 7.5-second part of the data. [Figure 8 is here] [Figure 11 is here] [Figure 11 is here] Fig 11 (a) The migration imaging comes from the diffractions separated by the proposed method;
(b) Full wavefield migration imaging method We apply the proposed method to the field data, diffractions separated from the DMO
stacked profile is shown in Figure 9(a). Figure 9(b) shows the same profile after applying the
PWD method. We use red and yellow arrows respectively to indicate the difference between
diffraction and reflection in the separated wavefield. It can be seen that the proposed method has
more advantages than the traditional PWD method in suppressing steep angle reflection and 13 Curvelet-domain diffraction separation method protecting diffraction energy. In order to show the protection of diffraction amplitude by the two
methods when separating the wavefield, the separated reflections are shown in Figure 10(a) and
(b), respectively. There are fewer diffractions eliminated in the left figure. The reflection results
demonstrate that the proposed method only filters part of curvelet domains, which protects the
energy at the far end of the diffraction. The retention of diffraction amplitude highlights the
location of small-scale discontinuous objects in seismic imaging, which is the basis for high-
resolution imaging. [Figure 10 is here] [Figure 10 is here] Fig 10 (a) The reflections separated by the proposed method; (b) Reflections separated by the
PWD method Figure 11(a) shows the time migration of the diffractions separated by the proposed method. Compared with the full wavefield migration imaging (b), the discontinuous geological bodies at
7.5 seconds are effectively revealed, and the special structures with strong reflection interference
between 6.5 and 7 seconds are highlighted. The field stacked data application verifies the good
performance of the proposed curvelet-domain cascade filtering diffraction separation method for
eliminating strong reflections and separating weak diffractions. It opens a possibility for
performing the separation of diffractions in the common-offset domain. The revealed micro faults
and discontinuous geological bodies further show its potential value in high-resolution imaging
research. 5. Discuss and conclusion Separating diffraction in the common offset domain is an important step to improve the 14 Curvelet-domain diffraction separation method spatial resolution of diffraction imaging. Diffraction and reflection show completely different
geometric forms in the common offset domain, in which most of the reflection is linear and the
diffraction is hyperbolic. The conventional common offset domain diffraction separation method
not only suppresses the reflected energy but also weakens the originally weak diffraction energy. The proposed curvelet domain cascade filter diffraction separation method provides a new
method for diffraction separation in the common offset domain, which can maintain the
diffraction amplitude and the polarity reversal of edge diffraction. spatial resolution of diffraction imaging. Diffraction and reflection show completely different
geometric forms in the common offset domain, in which most of the reflection is linear and the
diffraction is hyperbolic. The conventional common offset domain diffraction separation method
not only suppresses the reflected energy but also weakens the originally weak diffraction energy. The proposed curvelet domain cascade filter diffraction separation method provides a new
method for diffraction separation in the common offset domain, which can maintain the
diffraction amplitude and the polarity reversal of edge diffraction. The advantage of this method is that the curvelet transform can transform the energy of the
space-time domain in different angle ranges to their own independent curvelet domain. Therefore,
it can separate diffraction with more accurate reflection suppression. Through the cascade of the
high pass filter and median filter, we suppress the low-frequency energy inside the reflection and
the high-frequency energy at the edge of the reflection in the curvelet domain. The inverse
curvelet transform can transform the filtered curvelet domain data into seismic diffraction
wavefield, so as to realize diffraction separation imaging. We use a toy model to show the implementation process of the proposed method. The
effectiveness and advantages of this method in diffraction separation are verified by examples of
synthetic data and field data. This method can improve the resolution of discontinuous geological
bodies in seismic data. We also conducted some interesting tests. For example, cascade filtering is directly applied
to the data. It is found that cascade filtering cannot adapt to complex wavefields, and the
diffraction energy loss is large in the separation process. We believe that the curvelet transform
and its inverse transform provide a "working area" of cascade filtering, which is a key step to
protect the diffraction vibration amplitude. Declarations Conflict of interest The authors declared that they have no conflicts of interest in this work. Conflict of interest The authors declared that they have no conflicts of interest in this work. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in Conflict of interest The authors declared that they have no conflicts of interest in this work. Conflict of interest The authors declared that they have no conflicts of interest in this work. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. 5. Discuss and conclusion In addition, we apply the median filter and high pass
filter respectively in the curvelet domain, rather than their cascade. When median filtering is used
in the curvelet domain, the separation effect is the worst. A large number of reflections are 15 Curvelet-domain diffraction separation method retained in the data and cannot be separated. The reason is that even after curvelet transformation,
the reflection is still a relatively low-frequency signal. The median filter is essentially a low-pass
filter, so it cannot separate the wavefield. When high pass filtering is used in the curvelet domain,
most of the reflected energy is suppressed. However, the edge part of the reflection cannot be
removed. The reason is that the frequency of the reflection edge coincides with the diffraction
and cannot be removed by frequency domain filtering. Acknowledgments This work is supported by the National Natural Science Foundation of China (Grant No. 42022031),
National
Key
Research
and
Development
Program
of
China(Grant
No.2020YFE0201300), Fundamental Research Funds for the Central Universities (Grant No. grant no. 2021JCCXMT0, 2602020RC130). We thank Peng Research Group in CUMTB for
support of this work. We express great appreciation to the anonymous reviewers and editors for
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Figure 1
a) 2D re§ectance model containing a scatter and a horizontal re§ector. (b) Synthetic data from the
Kirchhoff forward modeling. (c) The curvelet coe¨cients of synthetic data. (d) Speci¦c Curvelet domai
coe¨cient matrix, when scale = 5 and angle = 8 Figure 1 (a) 2D re§ectance model containing a scatter and a horizontal re§ector. (b) Synthetic data from the
Kirchhoff forward modeling. (c) The curvelet coe¨cients of synthetic data. (d) Speci¦c Curvelet domain
coe¨cient matrix, when scale = 5 and angle = 8 Figure 2
(a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest frequency; (b) The
shape of the ideal high pass ¦lter, we set it as a rectangular window; (c) Spectrum after ideal high pass
¦ltering; (d) Curvelet coe¨cient matrix after high pass ¦ltering Figure 2 (a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest frequency; (b) The
shape of the ideal high pass ¦lter, we set it as a rectangular window; (c) Spectrum after ideal high pass
¦ltering; (d) Curvelet coe¨cient matrix after high pass ¦ltering Figure 3
(a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform Figure 3 (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform Figure 4
The work§ow of curvelet domain cascade ¦lter diffraction separation method Figure 4 The work§ow of curvelet domain cascade ¦lter diffraction separation method Figure 5
(a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave
¦eld forward simulated by Kirchhoff integral method Figure 5 (a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave
¦eld forward simulated by Kirchhoff integral method (a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave
¦eld forward simulated by Kirchhoff integral method Figure 6
(a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascad
¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after
cascade ¦ltering Figure 6 (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade
¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after
cascade ¦ltering (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade
¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after
cascade ¦ltering (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade
¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after
cascade ¦ltering Figure 7
(a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffrac
traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§e
Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Mi
(b) Figure 7
(a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by
traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d)
Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of
(b) Figure 7 (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by
traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d)
Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of
(b) (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by
traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d)
Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of
(b) (b) Figure 8 Nankai DMO stacked data Nankai DMO stacked data Figure 9
(a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method Figure 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method Figure 10 Figure 10 Figure 10 (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method Figure 11
(a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full
wave¦eld migration imaging Figure 11 (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full
wave¦eld migration imaging (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full
wave¦eld migration imaging (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full
wave¦eld migration imaging |
https://openalex.org/W3201844608 | https://bjbabs.org/index.php/bjbabs/article/download/53/43 | English | null | The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review | Baghdad journal of biochemistry & applied biological sciences/Baghdad journal of biochemistry and applied biological sciences | 2,021 | cc-by | 7,468 | Keywords ACE2, COVID-19, gene polymorphism, gender, SARS-CoV-2 Keywords ACE2, COVID-19, gene polymorphism, gender, SARS-CoV-2 SYSTEMATIC
REVIEW
BAGHDAD JOURNAL OF BIOCHEMISTRY AND
APPLIED BIOLOGICAL SCIENCES
2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915
https://doi.org/10.47419/bjbabs.v2i03.53
The impact of ACE2 genetic polymorphisms
(rs2106809 and rs2074192) on gender susceptibility to
COVID-19 infection and recovery: A systematic review
Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3
1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq
2The Presidency of the University of Anbar, Ramadi, Iraq
3College of Education for Pure Science, University of Anbar, Ramadi, Iraq SYSTEMATIC
REVIEW
BAGHDAD JOURNAL OF BIOCHEMISTRY AND
APPLIED BIOLOGICAL SCIENCES
2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915
https://doi.org/10.47419/bjbabs.v2i03.53
The impact of ACE2 genetic polymorphisms
(rs2106809 and rs2074192) on gender susceptibility to
COVID-19 infection and recovery: A systematic review
Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3
1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq
2The Presidency of the University of Anbar, Ramadi, Iraq
3College of Education for Pure Science, University of Anbar, Ramadi, Iraq SYSTEMATIC
REVIEW
BAGHDAD JOURNAL OF BIOCHEMISTRY AND
APPLIED BIOLOGICAL SCIENCES
2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915
https://doi.org/10.47419/bjbabs.v2i03.53
The impact of ACE2 genetic polymorphisms
(rs2106809 and rs2074192) on gender susceptibility to
COVID-19 infection and recovery: A systematic review
Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3
1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq
2The Presidency of the University of Anbar, Ramadi, Iraq
3College of Education for Pure Science, University of Anbar, Ramadi, Iraq 2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915
https://doi.org/10.47419/bjbabs.v2i03.53 ABSTRACT Copyright: © 2021 Ahmed A. Suleiman, Tamadher A. Rafaa,
Ali M. Al-Rawi, Mustafa F. Dawood Copyright: © 2021 Ahmed A. Suleiman, Tamadher A. Rafaa,
Ali M. Al-Rawi, Mustafa F. Dawood ABSTRACT Background: Epidemiological studies revealed there is a difference in susceptibility
to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
because of differences in gender with age and males being more inflicted. There is a
clear indication that deaths caused by coronavirus disease 2019 (COVID-19) in
males appeared at a higher rate than females across 35 nations. The implication of
associated disease-risk genes, involved in the susceptibility of COVID-19 such as the
angiotensin-converting enzyme 2 (ACE2), has recently received considerable
attention due to their role in severe injury of lung and mediated SARS-CoV-2 entry
as a host receptor. Received 09-06-2021
Revised 04-09-2021
Accepted 07-09-2021
Published 23-09-2021
Corresponding Author
Ahmed A. Suleiman
ahmed.suleiman@uoanbar.edu.iq Objectives: Herein, we aimed to systematically review how two main genetic
polymorphisms of ACE2 (rs2106809 and rs2074192) can affect the gender
susceptibility to SARS-CoV-2 infection. Objectives: Herein, we aimed to systematically review how two main genetic
polymorphisms of ACE2 (rs2106809 and rs2074192) can affect the gender
susceptibility to SARS-CoV-2 infection. Department of Biotechnology,
College of Science, University of
Anbar, Ramadi, Iraq Methods: To conduct this systematic review, a literature search in PubMed, Google
Scholar, ScienceDirect, and Nature was made for the period 2004 to 2020. We
searched for the impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192)
on gender susceptibility.f DOI https://doi.org/10.47419/
bjbabs.v2i03.53
Pages: 167-180
Distributed under
the terms of the Creative
Commons
Attribution-NonCommercial 4.0
International (CC-BY-NC 4.0),
which permits use for any
non-commercial purpose,
distribution, and reproduction in
any medium, provided that the
original work is properly cited. DOI https://doi.org/10.47419/
bjbabs.v2i03.53
Pages: 167-180
Distributed under
the terms of the Creative
Commons
Attribution-NonCommercial 4.0
International (CC-BY-NC 4.0),
which permits use for any
non-commercial purpose,
distribution, and reproduction in
any medium, provided that the
original work is properly cited. Results: We noticed that there was a differential genotype distribution between
males and females in various global populations whereas mutant variants were
common in males compared to wild-type variants among females which may reflect
differences in gender susceptibility to infection with SARS-CoV-2. Females are less
susceptible to coronavirus as compare to males because of the expression of ACE2
receptor. It has a double role in favour of COVID-19 and against COVID-19. Conclusions: Male mortality is greater than female mortality, which might be
attributed to the ACE2 deficiency in women. Epidemiological studies have shown
that the differences in sex and age have different susceptibility to SARS-CoV-2
infection. INTRODUCTION Coronaviruses, a family of disease-causing viruses, responsible for diseases that threaten
the humans on the earth such as severe acute respiratory syndrome (SARS),1 Middle
East Respiratory Syndrome (MERS),1,2 and the recently declared coronavirus disease 2019
(COVID-19);3 and all are ranging from the mild to very severe pneumonia. The severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-
19, is single strand RNA (ssRNA) virus comprmised of glycoprotein spikes, mediating the
virus to enter in host cells.4 Recently, both epidemiological5 and experimental6 features of
COVID-19 patients have been defined. In hypertensive patients, diabetics, obese, and the
elderly, recent researches have shown a greater risk of infection.7 However, little evidence
on the impact of ACE2 genetic polymorphisms on gender susceptibility to infection and the
rate of COVID-19 are available. Phylogenetic research has led scientists to explore the host entry process of SARS-CoV-2
and found that it enters into the host cell by binding to ACE2 membrane receptors.8 Body
parts including the respiratory tract, stomach, small intestine, skin, thymus, spleen, liver,
bone marrow, and blood vessels are all vulnerable to COVID-19 infection due to an abun-
dance of ACE2.9 In lung alveolar epithelial cells, ACE2 is expressed in larger amounts. Thus,
it contributes in damaging the lungs in acute respiratory distress syndrome (ARDS) and
pneumonia.10 SARS-CoV-2 has also been shown to form an association with the renin-
angiotensin-aldosterone system (RAAS) via (ACE2) enzyme.11 Angiotensinogen is a key substrate for RAAS, which made in the liver, and split to pro-
duce angiotensin 1 (also called pro-angiotensin), by the renin. The body has vasodilatory,
anti-inflammatory and antioxidant properties attributed to the ACE2.12 The ACE2 catalytic
domain is the extracellular portion of the cell, which can be destroyed, followed by the
release of ADAM17 (metallopeptidase and disintegrin) into the blood Figure 1.13 The asso-
ciation between ACE2 and SARS-CoV-2 has an important involvement and relationship to
the severity of infection developing in the human body Figure 2.14 Furthermore, SARS-CoV-2-mediated infection has been shown to vary according to dif-
ferences in age. For instance, elder patients are more vulnerable than children to COVID-
19. Knowing this relationship will pave a way for inventors and investigators to develop
better options, assisting in the treatment of COVID-19. How to cite this article: Suleiman AA, Rafaa TA, Alrawi AM, Dawood MF. The impact of ACE2 genetic polymorphisms
(rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review. Baghdad
Journal of Biochemistry and Applied Biological Sciences, 2021;2(03):167-180. doi: bjbabs.v2i03.53 167 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION A study points out the possible
sources of improved confrontation to COVID19 in youngsters compared to grownups due
to ACE2 expression components, the double role of ACE2 in defending lesions (inflam-
matory) along with detrimental effects of ACE2 which act as a molecular aim in promot-
ing the virus entry. The objective of the authors is to provide evidence on the activities
of the ACE2 enzyme in contradiction of or in service of the progression of COVID-19
to demonstrate the complexity of ACE2 enzyme behaviour during illness, this facilitates
researchers’ chance to create safe vaccines and solutions for therapeutics. In turn, the study
of the roles of ACE2 in different age groups, will also promote clarity, and study the receptor
behavior in the present situation.15 The ACEs is one of the exopeptidases, which might be
common to several peptides. It is predominantly found in the cell membrane, and firstly Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 168 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Figure 1 The enzymaticflow of the renin-angiotensin system (RAS) depicts the main receptor systems,
the biological activities of angiotensin 2 and Ang-(1-7), and the stability of ACE and ACE2. 7 A). RAS
system showing the angiotensin peptide metabolic pathway as the initiator compound cleaved by renin
(kidney) to form Ang 1 followed by ACE’s followed by Ang 2 to Ang (1 to 7) facilitated cleavage of ACE2. Ang 2 functions on the receptors of AT1 and AT2, while Ang (1 to 7) operates on the receptors of Mas and
antagonizes the activities of the axis of Ang2/AT1R. B) Curbed ACE2 levels result in a balance change in
the RAS to the Ang 2/AT1R (activator) axis, promoting the progression of the infection. Improved levels of
ACE2 change the balance to the Ang (1 to 7)/MasR axis (inhibitor) via rhACE2, ACE2 activators, resulting
in defence from viral infection. Figure 1 The enzymaticflow of the renin-angiotensin system (RAS) depicts the main receptor systems,
the biological activities of angiotensin 2 and Ang-(1-7), and the stability of ACE and ACE2. 7 A). RAS
system showing the angiotensin peptide metabolic pathway as the initiator compound cleaved by renin
(kidney) to form Ang 1 followed by ACE’s followed by Ang 2 to Ang (1 to 7) facilitated cleavage of ACE2. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION Ang 2 functions on the receptors of AT1 and AT2, while Ang (1 to 7) operates on the receptors of Mas and
antagonizes the activities of the axis of Ang2/AT1R. B) Curbed ACE2 levels result in a balance change in
the RAS to the Ang 2/AT1R (activator) axis, promoting the progression of the infection. Improved levels of
ACE2 change the balance to the Ang (1 to 7)/MasR axis (inhibitor) via rhACE2, ACE2 activators, resulting
in defence from viral infection. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 169 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 Figure 2 Way of the entrance of the SARS-CoV-2 to host cell. 7 The protein S of the virus attaches to the
human ACE2 receptor, when receptor-binding domain, human proteases triggered. It makes its way into
the cell via the endosomal path. Then, viral RNA is translation and cytoplasm of ORF1a and considered to
generate pp1a in additional pp1ab polyproteins. RTC proteases cleave these proteins, which promote the
expansion of full length (−) RNA copies and RNA replicas and function as for full length (+) RNA genomes
templates. A collection sub-genomic RNAs formed by fragmented transcription, with frequent open reading
frames, Only the nearest (5′ end) is translated in this case. After the synthesis of viral structural proteins, the
nucleocaspids are assembled in the cytoplasm. After that, there’s endoplasmic reticulum and Golgi apparatus
budding through the lumen of the intermediate compartment. This is accompanied by releasing virions from
the infested cell-mediated by exocytosis. Figure 2 Way of the entrance of the SARS-CoV-2 to host cell. 7 The protein S of the virus attaches to the
human ACE2 receptor, when receptor-binding domain, human proteases triggered. It makes its way into
the cell via the endosomal path. Then, viral RNA is translation and cytoplasm of ORF1a and considered to
generate pp1a in additional pp1ab polyproteins. RTC proteases cleave these proteins, which promote the
expansion of full length (−) RNA copies and RNA replicas and function as for full length (+) RNA genomes
templates. A collection sub-genomic RNAs formed by fragmented transcription, with frequent open reading
frames, Only the nearest (5′ end) is translated in this case. After the synthesis of viral structural proteins, the
nucleocaspids are assembled in the cytoplasm. After that, there’s endoplasmic reticulum and Golgi apparatus
budding through the lumen of the intermediate compartment. INTRODUCTION This is accompanied by releasing virions from
the infested cell-mediated by exocytosis. reported in the year 2000.16 This discovery gave the angiotensin 2 attention, a dynamic
peptide often referred to as angiotensin-(1-8). This is the basic cause of facilitating events
including increased vasoconstriction, pro-inflammatory action, pro-fibrosis, and stimula-
tion of aldosterone secretion by binding to angiotensin 1 (AT1) receptor. ACE2 works by
deactivating angiotensin 2 and then converting it to angiotensin.17 Similarly, this active peptide inhibits angiotensin 2’s activity. Moreover, aminopeptidases
enzyme is shown to deactivate angiotensin 2, it regulates the conversion of angiotensin 2 into
angiotensin 3, resulting in activities like with angiotensin 2 receptors and an affinity of 30
times greater than that of AT1 receptors,17 resulting in effects such as increased natriuresis Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 170 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. and bradykinin, besides a vasodilation.18 and bradykinin, besides a vasodilation.18 and bradykinin, besides a vasodilation.18 y
These components form an integral part of the process of renin-angiotensin aldosterone,
consisting of pathways for initialization and prevention. Here the forthcoming consists of
the receptor pathway for angiotensin 2 or angiotensin 1 or ACE1 or aldosterone, while the
latter consists of the receptor pathway for angiotensin (1-7) or ACE2 or Mas, where the
preventer pathway act as a blocker for the action of angiotensin 2 in the way for the initia-
tor. Furthermore, ACE2 has been discovered to interact with AT1 receptors, angiotensin 2
receptor blockers have targeted these receptors, which are mediated by angiotensin 2, are
opposed to the actions caused by this receptor, thus occupying the angiotensin 2 interac-
tion site. This in turn, stimulates angiotensin 2 liberation, this is accompanied by enhanced
ACE2 enzyme expression in the body. As indicated by sex-disaggregated information incor-
porated by worldwide scientists, there is a clear indication that coronavirus-related deaths
with males appeared at a higher rate than females across 35 nations (Worldwide Health
50/50). For example, the extent of deaths among people adds up to·13.3\7.4 in Italy, 4.7\2.8
in China, 8.4\4.7 in Spain, 10.6\6.6 in The Netherlands), and 4.0\1.7 in Ireland. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION It is hypothesized that, for example, Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 171 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. by encouraging coronavirus binding, the 2nd X chromosome may shield women from lethal
polymorphisms that make COVID-19 more violent in men. Certainly, in a current report,
weaker results in elder COVID-19 patients were due to the existence of lower ACE-2 levels
and subsequent upregulation of proinflammatory pathways of angiotensin II (Ang II) in the
body, which may render patients more vulnerable to systemic ’deleterious’ Ang II effects.14
In almost a yin/yang phase, ACE and ACE2 are produce, Ang II and Ang-1-7 are connected
to one other after there is a vice versa relationship in their quantity one increases another
decrease.25 Viruses enter into host cells due to ACE2, however, over expression can defend against
harm (by decreasing Ang II and forming Ang-1-7). And, ACE2 exhibits metalloproteinase
17 (ADAM17) can ”shed” ACE2 from endothelial cells, This causes the release of bioactive
and catalytic ectodomains into the circulation. Therefore, the ACE/ACE2 ratio is changed in
different tissues, membrane-bound soluble, and the role of ACE2 is complicated. For exam-
ple, it has been suggested that by restricting its attachment to cellular ACE2.26 Coronavirus
could be reduced by soluble ACE2. However, Sama and colleague showed that in patients
with heart failure (HF), males are associated with higher ACE2 plasma levels.27 Neverthe-
less, the authors agree that there is no proof that there is a connection between membrane-
bound ACE2 levels and shedding enzymes in the two genders. In fact, with preserved and
reduced ejection, HF contains a higher amount of soluble ACE2 ejection fraction.28 Also,
the expression of ACE2 tends to be decreased in postmenopausal women.29 Stimulatingly,
transgender men subjected to treatments show substantially high (ACE2) levels expression
and a high amount of Sertoli cells communicating ACE2 in the testis. Estrogens and andro-
gens are declining by the passage of time,30 this weakening is likely to lead to a decrease
in ACE2 expression with ageing in both genders. INTRODUCTION Gender
equality index finding revealed also that women are at a greater risk of infection than males
due to multiple factors: women commute via public transport, do grocery shopping, and
sometimes dominate many professions Epidemiology studies revealed different gender and
age have different susceptibility to contagion with SARS-CoV-2 with males and older age
being the most inflicted.19 The implication of associated disease risk genes involved in the
susceptibility of COVID-19 such as the ACE2 has recently received good attention due to
its role in the acute injury of lungs.20 The genetic variants of ACE2 showed to be correlated
with mixing angiotensin-(1-7) stages in females suffering from high blood pressure.21 ACE2
was made to work as a SARS-CoV-2 receptor. The gene ACE2 showed effective genetic
polymorphisms among a different population around the globe which may influence the
susceptibility to infection and/or disease progression to COVID-19.20 In this regard, this
study sought to explore whether the genetic polymorphism in the ACE2 gene, particularly
rs2106809 and rs2074192 would explain the genetic differences between males and females
toward infection with SARS-CoV-2 in various parts of the world. The sex variations can be
explained by multiple X-linked genes. fAmongst the main savouries of the lethality of the
virus are cardiovascular comorbidities. The number of non-genetic, sex-independent fac-
tors to alter vulnerability and mortality is enormous, with many others consisting on gender
and cultural habits from various countries, should be considered. There are a few women
dying, (young and elderly) than males (age-fellow). Actually, a series of possible methods
can enlighten that why women are less susceptible toward serious COVID-19 infections. This is because the involvement of two factors including the transmembrane protease ser-
ine 2 and ACE2, may be considered first of all.22
Although the receptor for the S protein of coronavirus is ACE2. The organs that are Although the receptor for the S protein of coronavirus is ACE2. The organs that are
mainly targeted by SAR-CoV-2 contain ACE2. ACE2 has been suggested as a modulator of
SARS-CoV-2 exposure in both sexes.23 The location of ACE2 is the X chromosome and in
sites commonly escaping the inactivation of one X chromosome.24 It is also possible that
this plays a significant role in women’s defence system. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION It is not so far clear whether the deadliness of
SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated
inflammatory response.36 Numerous additional genes linked to X and Y can also explain
gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify
inferior virus-related loads and inflammation to decrease in women as compared to men.38 inferior virus related loads and inflammation to decrease in women as compared to men. The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo-
some controls the immune system. These can be high-regulated in females and the response
to both virus-related contagions and vaccines can be calculated. To recognize a precise
gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net-
work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif-
ferences in immune response, strong-minded by genetic factors, and hormones,37 can play
a significant role. The number of CD4 + T cells also varies between genders, with women
with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent
features can change vulnerability and death is huge, numerous additional factors, including
gender and cultural behaviours, are likely to be considered in different countries. For exam-
ple, there was a high in females because of social and religious activities (Report on the Epi-
demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus-
tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking
ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have
been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable
entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19
in smokers, at least in part.41 This study attempted to provide an answer for the variable
infection and mortality rates of the SARS-CoV-2 between males and females worldwide INTRODUCTION It is not so far clear whether the deadliness of
SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated
inflammatory response.36 Numerous additional genes linked to X and Y can also explain
gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify
inferior virus-related loads and inflammation to decrease in women as compared to men.38
The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo-
some controls the immune system. These can be high-regulated in females and the response
to both virus-related contagions and vaccines can be calculated. To recognize a precise
gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net-
work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif-
ferences in immune response, strong-minded by genetic factors, and hormones,37 can play
a significant role. The number of CD4 + T cells also varies between genders, with women
with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent
features can change vulnerability and death is huge, numerous additional factors, including
gender and cultural behaviours, are likely to be considered in different countries. For exam-
ple, there was a high in females because of social and religious activities (Report on the Epi-
demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus-
tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking
ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have
been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable
entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19
in smokers, at least in part.41 This study attempted to provide an answer for the variable
infection and mortality rates of the SARS-CoV-2 between males and females worldwide by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in
men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded
from the outcome of extreme COVID-19. We must understand, however, that there are
variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be
affected by exercise and medical conditions. INTRODUCTION It is not so far clear whether the deadliness of
SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated
inflammatory response.36 Numerous additional genes linked to X and Y can also explain
gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify
inferior virus-related loads and inflammation to decrease in women as compared to men.38
The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo-
some controls the immune system. These can be high-regulated in females and the response
to both virus-related contagions and vaccines can be calculated. To recognize a precise
gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net-
work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif-
ferences in immune response, strong-minded by genetic factors, and hormones,37 can play
a significant role. The number of CD4 + T cells also varies between genders, with women
with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent
features can change vulnerability and death is huge, numerous additional factors, including
gender and cultural behaviours, are likely to be considered in different countries. For exam-
ple, there was a high in females because of social and religious activities (Report on the Epi-
demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus-
tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking
ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have
been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable
entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19
in smokers, at least in part.41 This study attempted to provide an answer for the variable
infection and mortality rates of the SARS-CoV-2 between males and females worldwide by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in
men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded
from the outcome of extreme COVID-19. We must understand, however, that there are
variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be
affected by exercise and medical conditions. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION The study of 2017 showed there are no
differences in the two genders in the activity of serum of ACE and ACE2, although lower
serum activity of ACE2 was observed in newer relative to older women.31 Overall, differ-
ences in ACE and ACE2 expression can tend to specific to organs and age-dependent in both
genders, in animals32 and humans with a less obvious function in soluble ACE226. It is a
matter of investigation whether the level of ACE2 in the lungs are linked to the vulnerabil-
ity and harshness of COVID-19.33 It was stated in a preprint red-top that monomers may
have advanced ACE2 expression in the lungs compared to women,34 with potentially sig-
nificant implications for COVID-19 infections, as the SARS-CoV-2 enter via respirational
tract. However, enlarged permeability of capillary, clotting, fibrosis, and death of alveo-
lar cells observed in both SARS and COVID-19.Explained by polymorphisms in ACE and
ACE2 genes.35 Lung damage and respiratory failure can be explained by these effects. The
role of ACE2 in COVID-19 is not completely clear but most evidence suggests that it may
be advantageous to have a low membrane-bound ACE/ACE2 ratio. Certainly, ACE may
be pro-inflammatory and pro-oxidant, whereas antioxidant and anti-inflammatory effects
can be mediated by ACE2. In HF, soluble ACE2 is higher; it is not yet clear whether this is
defensive or harmful or is just an epiphenomenon. Nevertheless, by controlling the activ-
ity of the ADAM17 enzyme, inhibition of ACE2 shedding has been advised as a possible
beneficial solution for heart failure.28 As the ACE2 expression on chromosome X affected Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 172 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in
men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded
from the outcome of extreme COVID-19. We must understand, however, that there are
variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be
affected by exercise and medical conditions. Quality assessment The quality of the included studies was checked independently by two authors (AAS and
MFD) using a set of pre-defined criteria such as quality of research design, and completeness
of extractable information. MATERIALS AND METHODS
Literature search and strategy A systematic literature search was conducted on September 2020 in reputed literature
databases and search engines (PubMed, Google Scholar, ScienceDirect, and Nature) by
applying these keywords: (ACE), (ACE2), (COVID-19), (Polymorphism), (SNP), we con-
ducted research and extracted the data that was relevant to research topic. A total of 150 research paper were retrieved from all the above-mentioned databases. From all these 150 publications, 30 research paper were closely related to our research topic
after reading the paper’s title and abstract. It is not yet known whether this differential rate of susceptibility between genders to
infection/mortality of SARS-CoV-2 is attributed to the genetic variants of the main host Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 173 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 receptor ACE2 in various ethnic populations. Therefore, two main genetic polymorphisms
(rs2106809 and rs2074192) were screened and analyzed using previously published papers. All reviews, reports, opinions, commentaries, and non-full length research papers were
excluded. Data extraction and quality evaluation The screening process was conducted independently by (title, abstract, full-text and data
extraction) by three authors (AAS, TAR, and AMA), and in the event of a discrepancy
between the three authors, the MFD is referred to as a co-creator of the consensus. The
authors reviewed the full text of the article for further information and clarification when
there is insufficient data. Data from eligible studies were extracted and summarized in an
excel spreadsheet. The following information was extracted for each of the included studies:
district name, study design, study area/city, study period, study design, sample types, study
population, number of study participants. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 RESULTS AND DISCUSSION A total of 150 items were collected from all the databases mentioned previously. From
these publications, 30 papers closely related to the topic of our study were selected. It was
found that 6 researches2,5,6,39,42,43 match the objective of our study. The rest of the researches
were only neglected for several reasons, including the small number of study participants,
lack of focus on race, and non-full length articles. By analyzing public data, it was found that the two SNPs (rs2106809 and rs2074192) were
expressed at variable proportions among different ethnic population around the world11. A summary of these findings as outlined in Table 1. The prevalent genotypes of rs2074192
among Caucasian males were almost dominated by TT mutant genotypes whereas CC or CT
genotypes were common in females. On the other hand, the genotype trend was changed
in the Asian female population as CC or CT (no mutant genotypes were observed) with no
considerable difference among males than those observed with Caucasian. A similar pattern
for the rs2106809 genotypes particularly among females in the Middle East and India. Taken
together for both genetic polymorphisms, it appeared that males had a mutant genotype Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 174 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 compared to either wild or heterozygous mutant in females. Considering the limitation of
sample size number, these data may suggest that the mutant genotype among males could
contribute to the severity of infection in males compared to females around the world but
the absence of such variants in females may explain the low infectivity/mortality rate seen
among them. ABBREVIATIONS ACE2, angiotensin-converting enzyme; ARDS, acute respiratory distress syndrome;
CDC, Disease Control and Prevention; HF, heart failure; NA, not available; RAAS,
renin-angiotensin-aldosterone system; SARS, severe acute respiratory syndrome; ssRNA,
single-stranded ribonucleic acid. CONCLUSIONS Many factors may affect COVID-19 infection and recovery such as immune response,
smoking, and genetic alteration in many genes including ACE2. Females are less affected
as compared to males because ACE2 gene is located on X chromosome and females have
two copies of ACE2. This research is all about ACE2 and its impact on the gender suscep-
tibility to infection and rate of recovery COVID-19. Patient body parts e.g. lungs, small
intestine, stomach, liver blood vessels, bone marrow, skin, oral, nasal mucosa and kid-
ney are most affected due to the presence of ACE2 which is the receptor of COVID-19. RAAS has been made in the liver and split into renin for angiotensin1 development which
activated angiotensin 2 by ACE. ACE2 counters vasoconstrictions and pro-inflammatory
activities which are opposed by ACE result. Elder patients are more vulnerable than chil-
dren to COVID-19. Epidemiology studies showed different gender and age have dif-
ferent susceptibility to contagion with SARS-CoV-2. ACE2 exhibited a high degree of
genetic polymorphisms among a different population around the world. Both rs2106809
and rs2074192 would explain the genetic differences between males and females toward
COVID-19. TMPRSS2 splits the S-protein preferring virus attachment to the cell mem-
brane. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 Data availability Author is only responsible for the data in this script which may not reflect the opinion or
policy of the journal. Ethical approvals Not applicable for systematic reviews. Funding resources This work didn’t receive any fund. Conflict of interest Not declared. Authors’ contributions All the author looks on the original idea and contributed to data collection, analysis, and
interruptions. ACKNOWLEDGEMENTS The authors would like to express deep thanks to the University of Anbar, College of Science,
Department of Biotechnology for their support in access for articles. The authors would like to express deep thanks to the University of Anba Department of Biotechnology for their support in access for articles. 175 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Table 1 Genotype distribution of ACE2 (rs2106809 and rs2074192) genetic polymorphisms among the different world population
SNP
Reference
Genotype
Most frequent genotype
Country
Race
Wild type
Hetero
Homo mutant
M
F
rs2106809
2
CC (M: 35.1%,
F: 21.7%)
CT (M: NA, F:
56.5%)
TT (M: 64%, F:
50%)
TT
CT
Egypt
Middle Eastern
42
CC (M: NA, F:
85%)
CT (M: NA, F:
10%)
TT (M: NA, F:
5%)
NA
CC
India
Asia
rs2074192
5
CC (M: 57.1%,
F: 34%)
CT (M: NA, F:
44.7%)
TT (M: 42.9%, F:
21.4%)
CC/TT
CT
Australia
Caucasian
6
CC
CT
TT (M: 24.7%, F:
43.9%)
NA
TT
Canada
Caucasian
39
CC
CT
TT (M: 47%, F:
46.8%)
TT
TT
Canada
Caucasian
43
CC (M: NA, F:
38.7%)
CT (M: NA, F:
41.1%)
TT (M: NA, F:
19.8%)
NA
CC/CT
China
Asia Table 1 Genotype distribution of ACE2 (rs2106809 and rs2074192) genetic polymorphisms among the different world popu
SNP
Reference
Genotype
Most frequent genotype
Wild type
Hetero
Homo mutant
M
F
rs2106809
2
CC (M: 35.1%,
F: 21.7%)
CT (M: NA, F:
56.5%)
TT (M: 64%, F:
50%)
TT
CT
42
CC (M: NA, F:
85%)
CT (M: NA, F:
10%)
TT (M: NA, F:
5%)
NA
CC
rs2074192
5
CC (M: 57.1%,
F: 34%)
CT (M: NA, F:
44.7%)
TT (M: 42.9%, F:
21.4%)
CC/TT
CT
6
CC
CT
TT (M: 24.7%, F:
43.9%)
NA
TT
39
CC
CT
TT (M: 47%, F:
46.8%)
TT
TT
43
CC (M: NA, F:
38.7%)
CT (M: NA, F:
41.1%)
TT (M: NA, F:
19.8%)
NA
CC/CT
F, female; M, male. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53
176 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 176 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 DECLARATIONS DECLARATIONS
Authors’ contributions
All the author looks on the original idea and contributed to data collection, analysis, and
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https://openalex.org/W2473725799 | https://jag.journalagent.com/z4/download_fulltext.asp?pdir=pajes&plng=eng&un=PAJES-68725 | English | null | Utilization of RFID data to evaluate characteristics of private car commuters in Middle East Technical University campus | Mühendislik bilimleri dergisi/Mühendislik bilimleri dergisi | 2,016 | cc-by | 4,622 | Abstract Analyzing travel behavior of Middle East Technical University (METU)
campus users via traditional survey approach requires great effort. However, using Radio Frequency IDentification (RFID) system installed
at all the campus entry gates provided a cheaper and an effective
approach to determine basic characteristics of the campus private car
commuters. The RFID data combined with traveler details enabled the
study of the arrival and departure car-based commute behavior of
academic personnel, administrative personnel and students, separately. The results revealed that campus car-based travel demand is mainly
active between 07:00 to 22:00. While the majority of the private car
commuters arrive during 08:00-09:00, the evening peak is distributed
over a much longer period from 15:00 to 19:00. Administrative
personnel have sharper evening departures between 17:00-18:00, while
academic ones show a more scattered pattern lasting longer. Car-
traveler students mostly arrive later during 09:00-10:00 and start
leaving the campus as early as 15:00 lasting until late evenings. Stay
time of vehicles on campus revealed that 43% of all trips to campus
lasted less than 15 minutes, especially during morning and evening
peaks, suggesting that a high number of RFID card holders pass through
the campus, possibly for pick-ups or drop-offs. A small reverse commute
pattern occurred due to the trips generated by family members of those
living in on-campus housing units. Orta Doğu Teknik Üniversitesi (ODTÜ) kampüs kullanıcılarının seyahat
davranışını geleneksel anket yaklaşımı ile analiz etmek büyük çaba
gerektirmektedir. Ancak, tüm kampüs giriş kapılarında kurulu radyo
frekansı ile tanımlama sistemi (RFID) sistemi, yerleşkedeki düzenli özel
araç kullanıcılarının temel özelliklerinin belirlemek için daha ucuz ve
etkin bir yaklaşımın geliştirilmesine imkan sağlamaktadır. RFID
verisinin kullanıcı bilgileriyle birlikte incelenmesi, akademik personel,
idari personel ve öğrencilerin yolculuklardaki geliş ve gidiş
davranışlarının ayrı ayrı çalışılmasına olanak sağlamıştır. Sonuçlar,
özel araç tabanlı yolculuk talebinin 07.00-22.00 arasında aktif olduğu
göstermektedir. Düzenli yolculuk yapanların çoğunluğu 08.00-09.00
arasında yerleşkeye giriş yaparken, akşam zirve saati 15.00’dan 19.00’a
kadar daha uzun periyoda dağılmıştır. İdari personel akşamları
belirgin bir şekilde 17.00-18.00 arasında çıkarken akademik personel
araç çıkışı daha dağınık ve uzun süren bir profil göstermektedir. Özel
araç kullanan öğrenciler çoğunlukla 09.00-10.00 saatleri arasında
gelmekte ve çıkışları 15.00’dan itibaren gece geç saatlere kadar
sürmektedir. Araçların yerleşke içinde kalma süreleri, özellikle sabah ve
akşam zirve saatler boyunca, %43’ünün 15 dakikadan daha az kaldığını
göstermektedir; bu da birçok taşıt pulu sahibinin büyük olasılıkla
eş/çocuk alma/bırakma için yerleşkeden geçtiğini düşündürmektedir. Abstract Zirve saatlerde tespit edilen ters yönlü düzenli bir yolculuk akımı,
kampüs içinde yaşayanların aile bireyleri tarafından gerçekleştirilen
yolculuklardan kaynaklanmaktadır. Keywords: Commute travel, Travel demand, Travel behavior Anahtar
kelimeler:
Düzenli
yolculuklar,
Yolculuk
talebi,
Yolculuk davranışı Yolculuk davranışı (a nursery, an elementary and a high school) for the children of
campus workers, which contribute to the commute travel
behavior, as well. (a nursery, an elementary and a high school) for the children of
campus workers, which contribute to the commute travel
behavior, as well. doi: 10.5505/pajes.2015.68725
Research Article/Araştırma Makalesi doi: 10.5505/pajes.2015.68725
Research Article/Araştırma Makalesi Received/Geliş Tarihi: 16.10.2014, Accepted/Kabul Tarihi: 28.01.2015
* Corresponding author/Yazışılan Yazar Öz Orta Doğu Teknik Üniversitesi yerleşkesindeki düzenli özel araç
kullananların karakteristiklerinin değerlendirilmesinde RFID verisi
kullanımı Oruç ALTINTAŞI1*, Hediye TÜYDEŞ YAMAN1 1Department of Civil Engineering, Faculty of Engineering, Middle East Technical University, Ankara, Turkey. aoruc@metu.edu.tr, htuydes@metu.edu.tr 1 Introduction Big university campuses may generate a travel demand like a
small city, where a strong commute behavior is inevitable. In
the case of Middle East Technical University (METU) campus in
Ankara, Turkey, we see a total population over 30000 people,
and 21000 of them are students: omitting the approximately
6000 students living in dormitories, 15000 students regularly
commute; while only 2000 of them hold stickers for private car
usage, the remaining mainly use public transit and paratransit
services in accessing to the campus. Out of 4300 people who
work as faculty and administrative personnel at METU, only
350 of them live in on-campus housing units; among the non-
campus dwellers, a significant portion of the administrative
personnel use commute buses provided by the university, and
most of the academics use private car. The research and
development park on campus, called Technopolis, has a
population of 3000, and is another region triggering commute
travel. Besides, the campus also has K-12 educational units METU campus originally developed outside the city limits at a
distance of approximately 13 km to the city center. Currently, it
is surrounded by the city and access is controlled at 3 main
gates (Gate A1, A4 and A7) as shown in Figure 1. The campus is
accessible by bus and minibus services operated by the
municipality or privately, departing from the city center. However, private car is an ever-increasing commute mode. In
order to monitor and control the campus road network usage,
Radio Frequency IDentification (RFID) system is installed at the
main entry gates; RFID stickers are granted to faculty and
administrative personnel directly, and to students in limited
number. Additionally, RFID gate is in use to control the traffic
from Technopolis to campus (see Figure 1). The determination of the travel behavior of METU campus
users requires traditional survey approaches, which would 171 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman riding with a friend or on a bus. Another study conducted by
Gilhooly and Low [5] investigated the primary school travel
behavior in Midlothian, Scotland, via survey of 1008 primary
school children and 776 parents. They stated that travel
behavior was significantly influenced by age and the distance
from school. 1 Introduction As an evaluation of parking management on
Beijing University of Aeronautics and Astronautics, China,
Huayan et al. [6] obtained inflow and outflow of vehicles during
the day and calculated the average parking stay time of vehicles
and drew conclusions about the travel behavior of university
travelers. need a big amount of resources. However, the integration of a
series of data from different campus data sources (RFID and
video recordings) provided a cheaper and an effective approach
to determine the basic characteristics of the campus commute
behavior, which is the main focus of this study. The layout of this paper is as follows: After a brief review of
literature on commute travel studies in university campuses in
Section 2, the RFID data analysis approach is summarized in
Section 3, followed by the major commute behavior findings
summarized in Section 4 and followed by the discussion and
conclusions in the last section. There has been no campus travel study that took advantage of
data from new technologies, such as RFID, mostly because, such
data does not include traditional travel demand data; but, it is
mainly being used to develop parking management policies for
university campuses. It enables identification of the vehicle
movements, records the vehicle data, analyzes the traffic
pattern different time of a day, manages staffing peak hour
traffic and relieves congestion [7]. Arizona State University, in
USA, installed RFID system to all parking lots to implement
parking management strategies, such as more parking charges
for students [8]. Wayne State University, in USA, installed RFID
system to the campus parking lot locations to implement
parking charges for different commute travelers [9]. University
of Wisconsin, in Madison, in USA, RFID system was installed to
the gate activation in parking ramps to investigate the
environmental impact the RFID gate project has on
starting/stopping at the gate entrance. The results showed a
significant savings in fuel due to reduction in start, stop and idle
time [10]. Furthermore, Portland State University, in USA, RFID
system was used to track their employees who sign up for a bike
commute incentives program [11]. 4 METU commute traveler characteristics To study the commute characteristics, a whole week RFID data
from Nov 21-25, 2011 was processed. To give an idea of the
scale, the statistics from Wednesday of the control week is
summarized in Table 2. The analysis result showed that 91% of
the vehicles tracked by RFID systems were private cars (the
remaining was the bus, taxi and minibuses serving the campus). It shows that the majority of the motorized vehicle demand in
the METU campus was due to the private car access. To validate
the results from RFID data, video recordings of the security
cameras at the entry gates were processed for another
Wednesday, which showed that there were almost 3000
additional vehicle entries, some of which can be due to daily
fluctuations but the majority is due to the vehicles visiting the
campus. In the video recordings, the difference between the
total entries (15280) and exits (14828) was very small,
suggesting that the majority of the vehicles did not stay
overnight. However, this difference in the RFID data was 5074
movements due to significantly lower number of recorded
exits. Further calculation of the entry-to-exit ratios for each
gate from RFID and video data showed that the majority of this
difference was caused by a reading error in the exit lanes of the
gate A1 (see Table 2). Exit behavior in this study is
underestimated; however, this systematic error happened
throughout the whole observation day and affects all the
cardholder types similarly. Thus, it does not create any bias on
the time of the day or the cardholder type analysis. In the current study, the existence of RFID control system for
private car users at all campus access gates made it possible to
capture the mobility of all the car-based commuters. As the
RIFD sticker includes the license plate number, sticker type,
and the entry and exit location (see Table 1), it was possible to
obtain campus entry and exit information for all the
movements of different commuter types (academic and
administrative personnel, students, Technopolis workers, and
parents of elementary-high school children). Tabulation of the
entry and exit movements hourly (or in 15-minute intervals, if
desired) easily provides the daily campus profiles. Further processing the RFID data for every unique license plate
enabled the detection of all the recorded movements of the
vehicles, leading to matching of entry-exit pattern that would
define a “trip” (see Table 1). 2 Literature review The analysis of the travel behavior of campus users has been
the focus of many studies so far. Zhou [1] studied the commute
behaviors of university students in Los Angeles. He stated that
improvement of multimodal transportation system and
discounts in public transit may greatly change the travel
behavior of students. Miralles-Guasch and Domene [2]
determined the travel pattern and transportation challenges of
university travelers in Barcelona through an online survey,
where the lack of adequate infrastructure, the marginal role of
walking and cycling and longer time involved in using public
transport were detected as the main barriers to shift from
private car to non-motorized modes. Akar et al. [3] also
examined the travel patterns of the campus community at Ohio
State University. The results demonstrated that students were
more likely to travel by alternative modes compared to faculty
members. Limanond et al. [4] studied the travel behavior of 130
students who live on campus in a rural university, and found
that males and females had similar travel pattern; students
owning a car preferred driving and non-car owners preferred Figure 1: The location and the layout of METU Campus. Figure 1: The location and the layout of METU Campus. 172 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman 3 Utilization of RFID data to evaluate commute
behavior endanger the study of basic characteristics of the campus
commute behaviors. 3 RFID data would have some reliability issues, as well. Due to
some reading errors, it is possible to miss an entry or an exit of
a vehicle, which would leave unmatched recording. However,
an unmatched trip can be due to an over-night or late stay in the
campus, or leaving the car in the campus and having a return
trip with another mode for some reason. Similarly, an exit with
a missing entry could indicate a car trip from a previous day. The RFID data can be further analyzed to reveal travel pattern
behavior, if supported with additional counts and/or data
processing. Nevertheless, the location of the RFID readers in a
region would inherently shape the capability and limits of such
evaluations; if a region has limited entry points which are fully
RFID controlled creating a closed network like METU campus,
it would provide a very rich data that could portray campus
access behaviors of the commuters, but it would not reveal
much about their destinations or route choice within the
campus. If not, RFID data would reveal information about the
behavior of users enrolled in the system only, which means it
would be a sample of the whole commuter; in such cases, it is
important to consider the enrollment conditions, to get an idea
about the randomness of the sampling. While evaluating the
benefits of RFID data usage, it should be kept in mind that
traditional commute behavior studies rely on sampling in their
surveys, which may include some sources of bias, themselves. But, RFID data-based evaluations would present “revealed”
behaviors as opposed to “stated” ones in the survey-based
approaches. Thus, it is impossible to capture everything about
commute trips via either survey-based or RFID-based
approaches, and it is important to understand the limitations
and sources of bias in the natures of the different approaches. 4 METU commute traveler characteristics Even though it was not needed in
the campus daily profile calculation, the minor gate controlling
the access to/from Technopolis is also considered as a gate in
the trip detections so that the trips destined to and originating
from Technopolis region could be identified separately. Moreover, calculation of a “stay time” for a trip, which is simply
the difference of the exit and entry times, sheds more light on
the commuter behavior of the campus user. As the trips and
their stay times can be time-stamped, it is possible to see the
change in the stay times in a day. 4.3
Stay times of private car commuters The stay time analysis results in Table 3 of the METU campus
users showed that in the overall evaluations, 42.8% of the trips
by the RFID cardholders were “short stay”, that is less than 15
minutes. A second major traveler group stayed between 1-5
hours (22.9% in a day), which is more like a half workday time. Only 16.1% had long stays of 5-10 hours suggesting that they
may be academic or administrative personnel. The low
percentage of the long stays in spite of the large number of
personnel may be due to the fact that some of the personnel had
multiple trips in and out of the campus. •
Administrative personnel showed a sharper morning
arrival (see Figure 3) and evening departure times
(see Figure 4), parallel to definitions of their work
hours between 08:30-17:30, which is expected as
their work schedules are more definite. •
Academic personnel had also a sharp morning arrival
peak. A major exit demand was observed during the
evening hours, which started from 15:00 and
continued until 21:00. The small peak in the exit
profile during 08:00-09:00, may very well be the
private car users of families of academic personnel
residing on campus creating the reverse commute. During the early morning hours (07:00 to 10:00), more than 40
% of the entering vehicles stayed for a short time, 20-30%
stayed almost the whole work day (5-10 hours), while another
major group stayed half a day (1-5hours). The further
investigation of the RFID cardholders among these drivers
revealed that the major short stays were performed by
Technopolis workers (46.0%). While academic and students
had almost same ratio (17.5%), the parents of the children at
the elementary and high school constituted 11.7%. •
The entry profile of student travelers showed that
travel to the campus started to increase after 08:00;
a delayed morning peak was seen around 09:00-
10:00 (see Figure 3). After, entries gradually
decrease during the day. The exits of students started
from 08:00 and gradually increased throughout the
day (see Figure 4). After that, they had again
scattered evening peak that start from as early as
15:00 and continue until 20:00. The short stay ratios were predominant in the evening hours
(between
17:00-20:00),
exceeding
60%. The
traveler
distributions in these short stays were: 35.7% for Technopolis
workers, 28.1% for academics, 24.0% for students and 8.2% for
administrative personnel. 4.1
Campus daily travel profile The RFID gate data can simply be used to derive the daily
demand profile of METU campus and to detect the peak hours. Daily analyses revealed very small variations between the
weekdays in METU campus [12], thus, the average entry and
exit profiles is used to illustrate the travel demand profile as
shown in Figure 2. Both entry and exit profiles support the
existence of the urban commute behavior among the METU
campus travelers, where majority lived in the city and arrived
METU as their workplace. Only a small reverse commute
pattern was observed due to the on-campus housing
population. The characteristics of the daily commute profile
were as follows: Normally, trips detected from an RFID data processing should
be regarded as “commute trips” directly; the purpose of the
trips must be checked. However, in the case of METU campus
RFID data study, it should be noted that METU grants RFID data
only to campus commuters, which dismisses any concern on
the matter. Secondly, although the majority of the commute
trips are “work” trips, which are expected to happen in the
morning and in the evening, it is not possible to generalize it for
every campus user, as some would be working the late evening
and night shifts in different units. Thirdly, it is not possible to
know the true origin or destination of these trips from RFID
data, yet, the lack of such information does not necessarily
A major entry demand was observed between 07:00-
09:00; during which hourly arrivals reach up to 3000. Then, the campus entry demand gradually decreased
until 11:00; after a small peak around 12:00, entry
demand was almost constant at a rate of 1000
vehicles/hour until 18:00, after which it diminished
significantly till midnight.
The exit profile of METU campus showed little activity
until 07:00, after which the number of exiting vehicles
increased
creating
the
first
peak
between
08:00-09:00 with 1500 exits. This may be due to i) 173 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman commuting from the family members of personnel
residing in the on-campus housing units, and ii) car
users doing quick drop-off for a campus user. The
second peak was seen at noon (12:00-13:00) with
1200 exits. The majority of the exit demand was
scattered over time, starting from 15:00 to 19:00,
which revealed the highest volume (over 2300)
during 17:00-18:00. 4.2
Commute behavior of different campus travelers Availability of the cardholder information in the RFID data
revealed more about the commute behaviors of the different
campus users. The extensive analysis of the commute behaviors
of the academic and administrative personnel and students was
provided in [12], which can be summarized as follows, for the
sake of continuity: 4.1
Campus daily travel profile After 19:00, the number of
exiting vehicles gradually decreased. •
Private car usage among Technopolis workers was a
major component of the campus car usage. Their
movements suggested a much clearer “work” trip
purpose with sharper arrival and departure time
windows. Their entries started as early as 06:00 and
continue until 09:00, after which it dropped
significantly (see Figure 3). The second peak during
lunch time definitely indicated a strong “lunch trip”
demand which showed a typical urban travel
demand profile. Lastly, parents of children were
active only at 08:00-09:00 and 15:00-16:00. •
Private car usage among Technopolis workers was a
major component of the campus car usage. Their
movements suggested a much clearer “work” trip
purpose with sharper arrival and departure time
windows. Their entries started as early as 06:00 and
continue until 09:00, after which it dropped
significantly (see Figure 3). The second peak during
lunch time definitely indicated a strong “lunch trip”
demand which showed a typical urban travel
demand profile. Lastly, parents of children were
active only at 08:00-09:00 and 15:00-16:00. 4.3
Stay times of private car commuters Only 4.2% of the total short trips
were performed by the parents of the children, which is
proportional to the number of stickers provided. p
p
p
Table 1: Vehicle movements as a result of RFID gate data processing. License Plate
Sticker Type
Time 1
Gate
Entry/Exit
Time 2
Gate
Entry/Exit
01HJ361
Academic
07:54
A1
Entry
12:00
A4
Exit
06AC651
Student
15:05
A4
Entry
19:49
A4
Exit
Table 2: METU campus vehicle activity statistics. RFID data
Nov 23, 2011 (Wed)
Video data
Oct 19, 2011 (Wed)
All Vehicles
Private Cars
All Vehicles
Private Cars
Total
Entry
12194
11471
15280
14363
Exit
7120
6694
14828
13938
Entry-Exit
5074
4777
452
425
All Vehicles
Gate
#
Ratio
#
Ratio
A1
Entry
5354
3.61
5746
0.94
Exit
1482
6066
A4
Entry
4116
1.16
5839
1.01
Exit
3562
5777
A7
Entry
2724
1.31
3695
1.24
Exit
2076
2985 Table 1: Vehicle movements as a result of RFID gate data processing. 174 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 3: Entry profiles of major traveler groups in a day. Figure 4: Exit profiles of major traveler groups in a day. Figure 3: Entry profiles of major traveler groups in a day. Figure 3: Entry profiles of major traveler groups in a day. Figure 4: Exit profiles of major traveler groups in a day. 175 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016
O. Altıntaşı, H. Tüydeş Yaman Table 3: Campus stay time of vehicles by entry time. 4.3
Stay times of private car commuters Entry Time
# of Trips
Stay Time (Nov 23, 2011) (% vehicles)
0-15 min
15-30 min
30 min-1h
1h-5h
5h-10h
10h >
7-8
177
44.1
0.6
5.6
14.7
21.5
13.6
8-9
1210
47.4
6.2
2.5
11.7
26.6
5.7
9-10
821
39.0
3.3
3.7
16.3
31.8
6.0
10-11
414
21.7
5.6
6.5
30.2
32.1
3.9
11-12
319
26.6
8.2
9.4
27.3
27.6
0.9
12-13
394
27.2
5.3
7.6
41.4
18.0
0.5
13-14
465
37.4
5.6
6.5
39.8
10.8
---
14-15
378
28.8
10.1
16.9
37.6
6.6
---
15-16
415
38.3
18.6
13.0
26.7
3.4
---
16-17
393
46.1
16.5
12.5
23.2
1.8
---
17-18
494
62.3
12.8
5.3
18.6
1.0
---
18-19
393
63.9
9.2
5.9
19.8
1.3
---
19-20
212
54.7
11.8
12.7
20.8
---
---
20-21
167
65.3
10.8
8.4
15.6
---
---
21-22
92
60.9
12.0
19.6
7.6
---
---
Total
6344
42.8
8.4
7.3
22.9
16.1
2.6
*: Out of 12194 entries, there were a total 6344 trips with matched entry and exit times. Table 3: Campus stay time of vehicles by entry time. a good thing in terms of smaller demand for on-campus
parking, if it is because of a pick-up/drop-off a campus user. But, smaller rates of longer stays (up to 4 or 8 hours) show that
the current congestion on campus parking lots is due to the
almost must private car usage to access to/within the campus,
which can be improved by addressing campus commute needs
of both students and personnel in a broader perspective. 5 Conclusions Despite the need for traditional survey studies in commute
behavior studies, even for campuses, data collected from other
systems can be beneficial to understand basics of mobility
within the study area, and even in a very cost-effective way. For
example, availability of RFID control for all the private car
commuters at all the campus entry gates in the METU campus
provided the daily travel profile of the campus. Furthermore,
detection of a relatively small reverse peak hour brought up the
issue of commuting of family members of academic personnel
living on campus. The license plate and time stamp in the RFID
data made it possible to detect over 6300 trips from
approximately 12200 RFID entry records in a day, which makes
almost a 50% sampling rate; this is higher than any sampling
ratio aimed in a traditional survey. However, the lack of
purpose for the trips identified from RFID data does not enable
the identification of all components of commute behaviors
clearly and creates some room for speculation. In the longer run, RFID data can be collected over a long period
of time, such as an academic semester, using which differences
across weekdays, or the effects of weather condition on
commute behavior can be evaluated which may be the focus of
future studies. Furthermore, the travel behavior of each
individual commute traveler can be followed over a long time
which provides to build more comprehensive campus
transportation model for different commute travelers. Finally,
installing the RFID system to all parking lots in METU campus
enables to analyze the time dependent parking lot capacity
analysis, to analyze campus travel time analysis and to develop
parking management policies for METU campus, which can be
also considered in future studies. Furthermore, RFID cardholder type information made it
possible to study commuter arrival and departure times of the
different campus users, which showed that administrative
personnel travel demand is more likely to be served with
morning and evening commuter buses, as they have more
definite work hours, whereas academic personnel needs more
flexible services, if any kind of shared-ride models would be
promoted for more sustainable campus transportation. Students on the other hand show a definite delayed arrival and
a much longer exit profile, which should be better supported
with municipal public transit services to discourage private car
usage in this group. 6 References [1] Zhou J. “Sustainable commute in a car-dominant city:
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Wisconsin. “Campus
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https://openalex.org/W4301011041 | http://deepblue.lib.umich.edu/bitstream/2027.42/110506/1/12967_2014_Article_374.pdf | English | null | Design of a multi-center immunophenotyping analysis of peripheral blood, sputum and bronchoalveolar lavage fluid in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) | Carolina Digital Repository (University of North Carolina at Chapel Hill) | 2,015 | cc-by | 11,364 | * Correspondence: jlcurtis@umich.edu
2Pulmonary & Critical Care Medicine Section, Medicine Service, VA Ann Arbor
Healthcare System, Ann Arbor, MI 48105, USA
3Pulmonary & Critical Care Medicine Division, Department of Internal
Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA
Full list of author information is available at the end of the article Freeman et al. Journal of Translational Medicine (2015) 13:19
DOI 10.1186/s12967-014-0374-z Design of a multi-center immunophenotyping
analysis of peripheral blood, sputum and
bronchoalveolar lavage fluid in the
Subpopulations and Intermediate Outcome
Measures in COPD Study (SPIROMICS) Design of a multi-center immunophenotyping
analysis of peripheral blood, sputum and
bronchoalveolar lavage fluid in the
Subpopulations and Intermediate Outcome
Measures in COPD Study (SPIROMICS) Christine M Freeman1,3, Sean Crudgington3, Valerie R Stolberg1, Jeanette P Brown3, Joanne Sonstein3,
Neil E Alexis4, Claire M Doerschuk5, Patricia V Basta6, Elizabeth E Carretta6, David J Couper6, Annette T Hastie7,
Robert J Kaner8, Wanda K O’Neal6, Robert Paine III9, Stephen I Rennard10, Daichi Shimbo11, Prescott G Woodruff12,
Michelle Zeidler13 and Jeffrey L Curtis2,3,14* RESEARCH Open Access Background four flow cytometry laboratories analyzed identical per-
ipheral blood specimens, identified the importance of
standardizing the model of flow cytometer, the antibody
reagents and fluorochromes, the procedure for sample
preparation and the procedure for sample analysis [7]. Many multicenter trials continue to stain the sample lo-
cally and use the flow cytometry instruments that are
available at each participating institution [8-10]. Other
studies have employed fixatives to stabilize receptor ex-
pression before staining, particularly in peripheral blood
samples, with subsequent centralized core staining and
flow cytometric analysis has also been explored; however
preservation of individual surface markers by this ap-
proach was variable [11,12]. Chronic obstructive pulmonary disease (COPD) is a
chronic disease that is defined by the presence of airflow
limitation that is not fully reversible. COPD is the third-
leading cause of death in the United States [1] and is
projected to become the fifth-leading cause of disease
burden worldwide by the year 2020 [2]. COPD is associ-
ated with a persistent inflammatory immune response in
the lungs in response to inhaled oxidants, including in-
door air pollution from biomass fuels and cigarette
smoke [3]. However, COPD is a complex disease involv-
ing more than just airflow obstruction. In many patients,
COPD is associated with systemic manifestations or co-
morbidities that can result in reduced quality of life and
increased mortality [4]. There is significant heterogeneity
between COPD patients with regard to symptoms, clin-
ical characteristics and co-morbidities, physiology, im-
aging, response to therapy, decline in lung function and
survival [5]. Identifying subtypes of patients may lead to
more targeted and personalized therapeutic treatment. The goal of this sub-study is to provide state-of-the-
art immunophenotyping of sputum, blood and BAL to
be correlated with the abundance of other clinical, radio-
graphic, physiological, genetic and biomarker data being
collected on this cohort. We took the approach of “just-in-
time” provision of reagents from a centralized Immunophe-
notyping Core, which prepares the 12-color antibody panels
and ships them to the institutions as needed. On the day
when samples are collected at each clinical site, they are
stained without pre-fixation, then fixed and shipped over-
night express on cold packs to the Immunophenotyping
Core for data acquisition and analysis on a single flow cyt-
ometer. The choice of leukocyte cell types and their recep-
tors was based on a series of pre-specified hypotheses plus
research interests of the coauthors. Background This interim report
demonstrates the feasibility of our approach, which may
be of value in the design of multicenter trials in COPD or
other disease states. The Subpopulations and Intermediate Outcomes in
COPD Study (SPIROMICS) is an ongoing multicenter
observational study funded by the National Heart, Lung
and Blood Institute, NIH, with a primary goal of identi-
fying homogenous subgroups of patients with COPD [6]. SPIROMICS is currently assembling a prospective co-
hort of 3200 participants for the collection and analysis
of extensive phenotypic, biomarker, genetic, genomic
and clinical data. In a subset of 300 subjects, peripheral
blood, sputum and bronchoalveolar lavage (BAL) is be-
ing collected to immunophenotype multiple cell popula-
tions using flow cytometry. Cell populations of interest,
including neutrophils, monocytes, macrophages, eosino-
phils, dendritic cells, T cells and B cells, as well as their
activation states, are being identified using a 12-color
antibody panel. (Continued from previous page) (Continued from previous page) Conclusions: Our study design, which relies on bi-directional communication between clinical centers and the Core
according to a pre-specified protocol, appears to reduce several sources of variability often seen in flow cytometric
studies involving multiple clinical sites. Because leukocytes contribute to lung pathology in COPD, these analyses will
help achieve SPIROMICS aims of identifying subgroups of patients with specific COPD phenotypes. Future analyses will
correlate cell-surface markers on a given cell type with smoking history, spirometry, airway measurements, and other
parameters. Trial registration: This study was registered with ClinicalTrials.gov as NCT01969344. Keywords: Human, COPD, Flow cytometry, Sputum, Bronchoalveolar lavage, Immunophenotyping Abstract Background: Subpopulations and Intermediate Outcomes in COPD Study (SPIROMICS) is a multi-center longitudinal,
observational study to identify novel phenotypes and biomarkers of chronic obstructive pulmonary disease (COPD). In
a subset of 300 subjects enrolled at six clinical centers, we are performing flow cytometric analyses of leukocytes from
induced sputum, bronchoalveolar lavage (BAL) and peripheral blood. To minimize several sources of variability, we use
a “just-in-time” design that permits immediate staining without pre-fixation of samples, followed by centralized analysis
on a single instrument. Methods: The Immunophenotyping Core prepares 12-color antibody panels, which are shipped to the six Clinical
Centers shortly before study visits. Sputum induction occurs at least two weeks before a bronchoscopy visit, at which
time peripheral blood and bronchoalveolar lavage are collected. Immunostaining is performed at each clinical site on
the day that the samples are collected. Samples are fixed and express shipped to the Immunophenotyping Core for
data acquisition on a single modified LSR II flow cytometer. Results are analyzed using FACS Diva and FloJo software
and cross-checked by Core scientists who are blinded to subject data. Results: Thus far, a total of 152 sputum samples and 117 samples of blood and BAL have been returned to the
Immunophenotyping Core. Initial quality checks indicate useable data from 126 sputum samples (83%), 106 blood
samples (91%) and 91 BAL samples (78%). In all three sample types, we are able to identify and characterize the
activation state or subset of multiple leukocyte cell populations (including CD4+ and CD8+ T cells, B cells, monocytes,
macrophages, neutrophils and eosinophils), thereby demonstrating the validity of the antibody panel. (Continued on next page) © 2015 Freeman et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain
Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,
unless otherwise stated. Page 2 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Materials and methods
Ethics statement All clinical investigations are conducted according to the
principles of the Declaration of Helsinki. The study
protocol was approved by the individual institutional
review boards (Columbia University; Weill Cornell Medical
College; University of California Los Angeles; University of
California San Francisco; University of Michigan, University
of Utah; Wake Forest University). All participants Immunofluorescence analysis by flow cytometry is the
gold-standard for defining leukocyte populations. How-
ever, due to the complexity and sensitivity of flow cy-
tometry, there are significant methodological hurdles
when applied to a multicenter trial. Early studies from
the Multicenter AIDS Cohort Study (MACS), in which Page 3 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 understand the purpose of the study and provide writ-
ten informed consent before they undergo any research
activities or procedures. about the subjects at the time of the flow cytometry ana-
lysis, as the only link between sample labels and subject
IDs is held by the GIC. Once antibodies are aliquoted, tubes are capped and
centrifuged at 300 × g for 5 minutes, the tubes are placed
in wire tacks, which are wrapped in aluminum foil to
shield them from light, and are stored at 4°C until ship-
ment. Tubes are affixed with a sample-specific label
(which can later be matched by the GIC to specific subject
information) and then are shipped from the Immunophe-
notyping Core to the Clinical Centers between 3–7 days
before the scheduled appointment. The Immunopheno-
typing Core notifies the Clinical Center by email that the
assay tubes have been shipped and provides the tracking
information. When assays are shipped, the Immunophe-
notyping Core records the assay ID number from the la-
bels, plus the date and Clinical Center to which that
particular assay was shipped. This information is trans-
mitted to the GIC. Study design and logistics A subgroup of 50 subjects from each of six clinical sites
(total n = 300) is being enrolled from the parent SPIRO-
MICS study. The enrollment strata for the bronchoscopy
sub-study are described in Table 1. Subjects participate
in this sub-study during two separate visits. At the first
visit, a sputum sample is collected by induction. In the
second visit, which takes place two to four weeks later,
peripheral blood and bronchoalveolar lavage samples are
collected. The SPIROMICS clinical sites are broadly distributed
geographically, being located in Ann Arbor (University
of Michigan); Los Angeles (University of California); New
York City (Columbia & Cornell Universities); Salt Lake
City (University of Utah); San Francisco (University of
California); and Winston-Salem (Wake Forest University). To assure efficient communication, we follow a stan-
dardized notification process. Study coordinators at the
Clinical Centers are required to notify both the Immu-
nophenotyping Core and their local collaborating la-
boratory as soon as the first bronchoscopy sub-study
visit is scheduled, so that antibody panels can be pre-
pared and shipped overnight to that site. Notification
occurs by email to multiple individuals at both the clinical
sites and the Immunophenotyping Core, to minimize the
chance that an absence of one individual will interfere
with the tight shipping schedule. The individuals primarily
responsible for this protocol at both the Clinical Centers
and the Immunophenotyping Core follow a strict pol-
icy of immediately “replying to all” at both sites, con-
firming receipt of each email and repeating back the
received information, to affirm that the message has
been received correctly. An identical process of email communication between
the Clinical Centers, the Immunophenotyping Core and
the GIC is followed once the sample has been collected,
stained and fixed. Thus, the GIC records the date on
which an assay was shipped; the Immunophenotyping
Core records the date on which it was received, facilitating
prompt location of any assays that become delayed or
lost in transit. To reduce the chance that assays will not
be properly chilled during transit, shipping in either dir-
ection is permitted only Monday through Thursdays. Additionally, care is taken to assure that the timing of
holidays (especially Federal, given that the Immunophe-
notyping Core is a VA facility) is considered before ship-
ments are released. Biospecimen collection
d Sputum induction was performed according to the
methods of Alexis et al. [13]. Personnel at the clinical
sites involved in sputum induction and sample process-
ing received onsite, in-person training from Dr. Alexis. Briefly, subjects undergo seven-minute exposures to in-
creasing concentrations of aerosolized hypertonic saline
by inhaling via a mouthpiece. To minimize oral contam-
ination of induced sputum specimens, subjects are asked
to rinse their mouths with water, to blow their noses
and to clear their throat at the end of each inhalation
period, then to “cough from their chest” and immediately Next, assay tubes, each containing all the antibodies
(or isotype controls) for a given cell type or groups of re-
lated cell types, are prepared by the Immunophenotyp-
ing Core. Each tube is identified using labels supplied by
the SPIROMICS Genomics and Informatics Core (GIC)
at the University of North Carolina. These labels are spe-
cific to sample type and subject, but do not include the
SPIROMICS-wide subject identifier. Thus, the Immuno-
phenotyping Core is blinded to any clinical information Table 1 Planned subject enrollment distribution by strata
Never-smokers
Smokers without
airflow obstruction
Smokers with mild to
moderate COPD
Smokers with severe COPD
Smoking status
<1 pack year
>20 pack years
>20 pack years
>20 pack years
Lung function
FEV1/FVC >0.7
FEV1/FVC >0.7
FEV1 > 50% predicted
50% > FEV1 > 30% predicted
Sample size
N = 60 (20%)
N = 60 (20%)
N = 140 (47%)
N = 40 (13%) Table 1 Planned subject enrollment distribution by strata Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 4 of 17 phycoerythrin Texas red (PE-TR), phycoerythrin-cyanine
7 (PE-Cy7), allophycocyanin (APC), allophycocyanin-
cyanine 7 (APC-Cy7), BD Horizon™V500 (V500), Pacific
Blue, Alexa Fluor 700 (AF 700), and QDot® 655. Vendors
from which antibodies were purchased include Biolegend
(San Diego, CA), eBioscience (San Diego, CA), BD
Biosciences (San Jose, CA), R&D Systems (Minneapolis,
MN), Miltenyi Biotec (Auburn CA), and Invitrogen
(Carlsbad, CA). Antibodies against CX3CR1, CD133,
and their respective isotypes, were purchased unconju-
gated, and we used Lightning-Link antibody labeling kit
(Novus Biologicals, Littleton, CO) to conjugate these anti-
bodies to APC-Cy7 and Atto 700, respectively. expectorate into a cup without holding the specimen in
their mouths. To assure subject safety, spirometry is per-
formed during the inhalation period and again at the end
of each seven minute exposure. Biospecimen collection
d The saline concentrations
used and frequency of spirometric testing vary according
to the subject’s baseline forced expiratory volume in 1 sec-
ond (FEV1). Subjects with baseline FEV1 ≥50% predicted
inhale 3%, 4% and 5% saline, and undergo spirometry two
minutes into each exposure and at the end of the expos-
ure. By contrast, subjects with baseline FEV1 < 50% pre-
dicted inhale 0.9% and 3% saline, and undergo spirometry
at 1, 2, 5 and 7 minutes of exposure. If at any point the
FEV1 decreases by >20% from baseline, the induction is
stopped; otherwise, subjects either continue the current
exposure period or proceed to the next saline concentra-
tion. Sputum samples were kept on ice throughout the in-
duction procedure and processed for immunophenotyping
immediately following collection. Antibodies are centrally prepared for each clinical site
at the Immunophenotyping Core at the VA Ann Arbor
Healthcare System. Antibodies are aliquoted into flow
tubes (BD #352008 and #35203; Becton Dickinson)
which are capped, placed in a rack (Fisher #14-793-14),
and covered with aluminum foil. Antibodies are shipped
overnight in a Styrofoam box with multiple cold packs,
frozen to −20°C, and typically arrive at the clinical site
1–3 days before the study visit. At the second visit, during which blood and BAL are
collected, post-bronchodilator FEV1 is measured before
any procedures. Only subjects with an FEV1 > 30% pre-
dicted that day are allowed to participate in the bron-
choscopy visit. At the time of IV placement, blood is
drawn into a 10 ml heparin plasma tube, and immedi-
ately to the laboratory for immunophenotyping staining. A complete blood count (CBC) is also collected, and
processed by the medical center clinical laboratory. Staining of samples At each clinical site, mucus plugs from the sputum sam-
ple are selected, weighed, and then incubated with 1×
Sputolysin® Reagent (EMD Millipore, Billerica, MA) in a
37°C water bath for 20 minutes. Samples are washed and
filtered before resuspending the cell pellet in Staining
Buffer with FBS (BD #340345; BD Biosciences). The spu-
tum assay antibody tubes from the Immunophenotyping
Core are briefly centrifuged and then the entire sputum
sample is divided among seven antibody tubes (100 μL
per tube). Tubes are covered with aluminum foil and
incubated at room temperature for 25 minutes with con-
tinuous shaking or rocking (depending on the equip-
ment available at the clinical site laboratory). After the
incubation, samples are washed with 2 mL Staining
Buffer, centrifuged, and resuspended for storage in 2%
freshly-prepared formaldehyde in PBS. Tubes are then
stored at 4°C in a rack wrapped in aluminum foil before
being shipped back to the Immunophenotyping Core. The BAL sample for Immunophenotyping is only one
portion of collection of multiple samples that comprise
the entire Bronchoscopy sub-study. BAL is performed in
the right middle lobe and lingula by instilling two aliquots
of 40 mL and one aliquot of 50 mL of sterile saline per
lobe (i.e., 130 mL per lobe, total volume = 260 mL per
subject), which is withdrawn by gentle manual suction. The BAL return is collected into specifically designated
specimen traps, kept on ice. The BAL from both lung
sites was pooled and used for immunophenotyping. Antibody panels
d
d We designed 12-color monoclonal antibody panels with
isotype controls to analyze multiple leukocyte popula-
tions. The antibody panel, with clones listed in paren-
theses, is shown in Table 2. The panels for BAL and
sputum differ from the panel for peripheral blood in that
they do not contain antibodies for basophils or endothelial
cells. Additionally, the sputum panel does not contain
antibodies for dendritic cells or B cells. These choices
were made based on pilot data from our laboratory indi-
cating that these cell types were present in such low fre-
quency as to be impractical to identify. Antibodies and
isotype-matched controls were directly conjugated to
either fluorescein isothiocyanate (FITC), eFluor 450,
phycoerythrin (PE), phycoerythrin-cyanine 5 (PE-Cy5),
peridinin chlorophyll protein-cyanin 5.5 (PerCP-Cy5.5), BAL samples are centrifuged and resuspended in Staining
Buffer, then 100 μL of the BAL sample is added to each
of the BAL assay antibody tubes. Staining then proceeds
as described above for sputum samples. Blood tubes are inverted eight times and then 100 μL
of the undiluted blood sample is added to each of the
blood assay antibody tubes. Similar to the staining pro-
cedure for sputum and BAL, samples are incubated with
the antibodies for 25 minutes. Next, to remove red blood
cells, 2 mL of 1× BD Pharm Lyse (BD Biosciences) are
added to each tube and incubated at room temperature
for another 25 minutes. *not included in BAL samples; #not included in sputum samples. Statistical analysis Statistical analysis
Analyses were performed using GraphPad Prism 6.0
(GraphPad Software, Inc., La Jolla, CA) on a Macintosh
Quad-Core Intel Xeon computer running OS 10.10
(Apple; Cupertino, CA). A two-tailed p value of < 0.05
was considered to indicate significance. Sample acquisition success rate p
q
As of September 17, 2014, a total of 152 sputum samples
and 117 blood/BAL samples had been returned to the
Immunophenotyping Core. Disparity between collection
of sputum samples and of blood plus BAL samples from
what was planned appears to have resulted primarily
from missed or yet to be completed return visits, and
not from any adverse events related to the study proce-
dures. For each specimen, we performed an initial ana-
lysis of the number of CD45+ cells in sputum, blood,
and BAL, stratified by clinical site. Samples averaged
7.7×104 ± 8.2×104 (mean ± SD), 8.9×104 ± 10.7×104, and
20.3×104 ± 36.6x104 CD45+ events (leukocytes) per tube
for sputum, BAL and blood, respectively. Samples con-
taining fewer than 1×104 leukocytes are deemed un-
usable and are not analyzed. Low cell yield was most
typically seen in the sputum and BAL samples. We have
deliberately not yet broken the codes linking samples to
subjects, so that initial analyses are not biased by know-
ledge of clinical data. Data are collected using FACSDiva software (BD
Biosciences) with automatic compensation. CS&T Research
beads (BD Biosciences) are used during instrument setup
to maintain baseline performance values, thereby ensuring
that the cytometer performed the same every time. Because cell yields varied, we collect all possible events to
maximize our ability to detect rare populations. Within 1–2 days after the sample has been run on the
flow cytometer, we perform an initial quality check. We
record the absolute number of CD45+ leukocytes in the
sample and also look at the percentage of low side scat-
ter cells, indicative of lymphocytes, and high side scatter
cells, such as macrophages, neutrophils, and monocytes. Our preliminary analyses indicate that a total of 126 of
152 sputum samples (83%), 106 of 117 blood samples
(91%) and 91 of 117 BAL samples (78%) provided usable
data (Table 3). It seems likely that there may have been a Antibody panels
d
d All analyses undergo a secondary
evaluation by a third individual (CMF) to help maintain
consistency in the gating and analysis between samples. Data, including analysis files, are immediately backed up
to DVD-R disks. Antibody panels
d
d Samples are centrifuged and Table 2 Standardized antibody panel Leukocyte population
Fluorochrome (directly conjugated to monoclonal antibody)
FITC
PE
PE-Cy5
PerCP-Cy5.5
PE-TR
PE-Cy7
APC
APC-Cy7
V500
Pacific blue
AF 700
QDot 655
Surface antigen detected with monoclonal antibody clone used (italicized)
Dendritic cells#
BDCA-2
AC144
BDCA-1
AD5-8E7
CD123 6H6
CCR2 TG5
CD45 HI30 CD103 B-Ly7
BDCA-3 AD5-
14H12
CX3CR1 2A9-1 HLA-DR
L243
CD11c 3.9
CD11b CBRM1/5 CD3 7D6 &
CD19 SJ25-C1
Mø &
monocytes
CD14 HCD14
CCR6 R6H1
CD16 3G8
CCR2 TG5
CD45 HI30 TLR2 T2.5
CD206 15-2
CX3CR1 2A9-1
HLA-DR
L243
CD11c 3.9
CD11b CBRM1/5
Mø &
monocytes
CD14 HCD14
Axl 108737
CD16 3G8
DC-Sign
9E9A8
CD45 HI30 TLR4 HTA125
Mertk 125518
HLA-DR
L243
CD11c 3.9
CD11b CBRM1/5
Basophils*#
CD33 HIM3-4 CD9C3-3A2
CD13 TuK1
CD203c
NP4D6
CD45 HI30 CD63 H5C6
CD22 HIB22
CD34 581
HLA-DR
L243
CD69 FN50
CD11b CBRM1/5 CD19 SJ25-C1
Eosinophils
CD49d 9 F10
CDw125 A14
CD16 3G8
CD69 FN50
CD45 HI30
CCR3 5E8
CD34 581
CD11b CBRM1/5
Neutrophils
CD177
MEM-166
CD16b
CLB-gran 11.5
CXCR1 8 F1
CD66b G10F5
CD45 HI30 TLR4 HTA125
CXCR2 5E8
CD10 HI10a
TLR2 T2.5
CD11b CBRM1/5
Endothelial
cells*#
CD33 HIM3-4 CD146
SHM-57
VCAM-1
STA
VEGFR2
HKDR-1
CD45 HI30 PECAM
WM59
CD144 16B1
CD34 581
ICAM-1
HCD54
CD133 293C3
CD37D6 &
CD19 SJ25-C1
B cells#
IgD IA6-2
CD80 2D10.4
CD86 B7-2
CD27 O323
CD45 HI30 CXCR4 12G5
CD23 EBVCS-5
CD20 2H7
CD38 HIT2
CD19 SJ25-C1
T cells
γδ -TCR B1.1
CTLA-4 14D3
CD28
CD28.2
CD27 O323
CD45 HI30 ICOS ISA-3
CD56 CMSSB
CD62L
DREG-56
CD3 UCHT1
CD8 OKT-8
CD4 OKT-4
T cells
CCR7 150503
CCR5 T21/8
CXCR3 1C6
CD27 O323
CD45 HI30
CD56 CMSSB
CD62L
DREG-56
CD3 UCHT1
CD8 OKT-8
CD4 OKT-4
# Page 6 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 washed with Staining Buffer before being stored in 2%
formaldehyde in a refrigerator wrapped in aluminum foil. on Macintosh Quad-Core Intel Xeon computers running
OS X 10.10.1 (Apple; Cupertino, CA). We use pre-printed
sample report forms and a flow analysis worksheet to
standardize the process. All analyses undergo a secondary
evaluation by a third individual (CMF) to help maintain
consistency in the gating and analysis between samples. Data, including analysis files, are immediately backed up
to DVD-R disks. on Macintosh Quad-Core Intel Xeon computers running
OS X 10.10.1 (Apple; Cupertino, CA). We use pre-printed
sample report forms and a flow analysis worksheet to
standardize the process. Flow cytometry instrument setup and data acquisition Flow cytometry instrument setup and data acquisition
Samples are wrapped in aluminum foil and are shipped
overnight in a Styrofoam box with cold packs to the
Immunophenotyping Core. Upon arrival, samples are
physically inspected and any issues (e.g. cracked tubes,
inconsistent volumes, missing tubes) are recorded along
with the sample ID. Samples are transferred to a 96-well
U-bottom plate and data are acquired on an LSR II flow
cytometer (BD Bioscience, San Jose, CA) with a High
Throughput Sampler, equipped with the following four
lasers, listed with their associated fluorochromes and fil-
ter sets: 488 nm blue laser (APC-Cy7: 735 nm long-pass
(LP), 780/60 nm short band-pass (SBP); AF700: 690 nm
LP, 730/45 nm SBP; APC: 660/20 nm SBP); 405 nm vio-
let laser (Qdot655: 630 nm LP, 660/20 nm SBP; Horizon
V500: 505 LP, 530/30 SBP; Pacific Blue: 450/50 SBP);
633 nm red HeNe laser (PerCP-Cy5.5: 685 nm LP, 695/
40 SBP; FITC: 505 LP, 530/30 SBP); and a 561 nm
yellow-green laser (PE-Cy7: 735 nm LP, 780/60 nm SBP;
PE-Cy5: 635 nm LP, 670/30 nm SBP; PE-TR: 600 nm LP,
610/20 nm SBP; PE: 582/15 nm SBP). Flow cytometry data analysis Data are analyzed by two trained individuals (SC, VRS)
using FlowJo software v.9.6.2 (Tree Star, Ashland, OR) Table 3 Number and percentage of usable specimens by clinical site
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
Total
Sputum visits, n:
16
26
38
30
23
19
152
Usable specimens, n
13
21
34
27
17
14
126
Usable specimens,%
81%
81%
89%
90%
74%
74%
83%
Blood & BAL visits, n:
7
26
28
19
19
18
117
Usable blood specimens, n
6
22
25
19
17
17
106
Usable blood specimens, %
86%
85%
89%
100%
89%
94%
91%
Usable BAL specimens, n
6
21
22
12
15
15
91
Usable BAL specimens, %
86%
81%
76%
63%
79%
83%
78% Table 3 Number and percentage of usable specimens by clinical site Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 7 of 17 the vast majority of antigens were unaffected by duration
of storage in PFA. learning curve in obtaining or processing the samples,
particularly sputum. The percentage of usable sputum
data has increased from 69% in 2012, to 88% in 2013,
and 92% in 2014. BAL samples also showed a modest in-
crease: 71% usable samples in 2012, 78% in 2013 and
80% in 2014 (data not shown). Identification of T cell populations in blood, sputum and BAL
Lung T cells have been linked to progression of COPD,
especially of emphysema, in multiple studies [14-19]. We used a combination of anti-CD45 (leukocyte common
antigen), forward and side light scatter properties, and dif-
ferential expression of lineage-specific surface markers to
identify leukocyte populations, as has been previously
shown to be effective for sputum leukocytes [13,20]. To
identify CD4+ and CD8+ T cells, we first gated on CD45+
CD3+ cells with a low side scatter. Representative staining
demonstrates the ability of this strategy plus comparison
to isotype controls to distinguish CD4+ and CD8+ T cells
in blood, BAL and sputum (Figure 2). The numbers in
each quadrant indicate the percentage of that subset
among all CD45+ cells. These numbers are consistent
with what other studies have found in sputum [21], blood
and BAL [22]. Processing errors may also account for some of the
unusable data. Identification of macrophage populations in sputum and
BAL Alveolar macrophage (AMø) numbers are increased and
their function is altered in COPD [23]. There is consider-
able interest in whether polarization of their gene prod-
ucts drives inflammation in COPD [24,25]. To identify
AMø, we gated on CD45+, auto-fluorescent cells and then
selected HLA-DR+ CD11c + cells (Figure 3). This ap-
proach was chosen after a preliminary analysis of a var-
iety of alternative gating approaches, including use of
Mertk (a putative pan-Mø marker in mice) [26], as the
one giving the most unambiguous distinction of mature
AMø. Although CD11b is included in the panel for ana-
lysis, we did not use it to gate on macrophages, as AMø
have been shown to be negative for CD11b, unless acti-
vated, therefore their expression is not uniformly positive
[27]. As expected, BAL samples contained the largest
percentage of macrophages. As the numbers of subjects
increase, this dataset will be analyzed further for correl-
ation of macrophage surface receptor expression with
spirometrically-defined disease severity and other clin-
ical data. Flow cytometry data analysis The most commonly detected processing
error was resuspension of the samples in an incorrect
fixative volume, such that the concentration of parafor-
maldehyde, which must be held constant to stabilize the
light scatter and antibody labeling, was likely much
lower than the 2% specified in the protocol. Other less
common errors result from shipping delays, which re-
sulted in samples no longer protected by the ice packs;
cracked tubes with low or missing sample; and improp-
erly capped tubes, resulting in loss of entire samples. Al-
though there was variation between clinical sites in the
percentage of usable samples of different types, no site
was routinely underperforming compared to the other
sites (Table 3), supporting our impression that random
errors, rather that systematic problems, were responsible
for lost data. Duration between fixation and data acquisition has only
minor effect on fluorescence intensity One variable in this study is the duration between fixa-
tive addition and data acquisition on the flow cytometer. This duration typically varies between two and seven
days, because sites that have study visits on Thursday or
Friday are unable to ship specimens until the following
Monday. To determine whether time of storage in PFA
affected fluorescent intensity, in locally-performed pilot
experiments, we analyzed blood and BAL samples at
days 2, 5, and 7 post-PFA. Results indicated no differ-
ence in forward scatter, side scatter or CD45+ staining
(not shown). Among 68 surface molecules, fluorescence
intensity for 61 was either unaffected by storage in PFA,
as shown for CD16 (Figure 1A), or had modest increases
in specific staining and in the corresponding isotype
control, such that there was no difference in overall
positive staining. In blood specimens, antibodies against
TLR4 (PE-Cy7), gamma-delta T cell receptor (FITC),
and CCR7 (FITC) had increased specific fluorescence
(relative to isotype control) from day 2 to day 5, but no
further increase at day 7 (data not shown). In BAL
specimens, antibodies against BDCA-1 (PE), CX3CR1
(APC-Cy7), and TLR2 (eFluor 450) also showed mod-
est increases in specific fluorescence at days 5 and 7
(Figure 1B). Only CD103 (PE-Cy7) in the BAL samples
exhibited decreased fluorescent intensity, which was
seen at both days 5 and 7 (Figure 2C). Although small
in absolute terms, these changes will need to be accounted
for in future analyses. Importantly, however, staining for Identification of monocyte populations in blood, sputum
and BAL Monocytes constitute 5 to 10% of peripheral blood leu-
kocytes where they circulate for several days before mi-
grating into tissues. The degree to which recruitment of
blood monocytes contributes to the expansion of the
mononuclear phagocyte population in COPD is con-
tested. Monocytes were originally divided into “classical”
CD14++ CD16- cells and “nonclassical” CD14+ CD16+
cells. The classical monocytes were considered to be Page 8 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 1 Storage in PFA affects fluorescent intensity of specific surface receptor-monoclonal antibody combinations. After addition of
PFA, BAL samples were divided into three samples and data was acquired after storage at 4°C for either 2, 5, or 7 days. A) CD16 (and the majority
of the surface antigens) showed no change in fluorescent intensity between days 2, 5, and 7. B) TLR2 showed an increase in fluorescent intensity
at day 5 and at day 7. C) CD103 was the only receptor to show a decrease in fluorescent intensity at days 5 and 7. Figure 1 Storage in PFA affects fluorescent intensity of specific surface receptor-monoclonal antibody combinations. After addition of
PFA, BAL samples were divided into three samples and data was acquired after storage at 4°C for either 2, 5, or 7 days. A) CD16 (and the majority
of the surface antigens) showed no change in fluorescent intensity between days 2, 5, and 7. B) TLR2 showed an increase in fluorescent intensity
at day 5 and at day 7. C) CD103 was the only receptor to show a decrease in fluorescent intensity at days 5 and 7. after gating on CD45+, non-autofluorescent cells with a
medium side-scatter that were HLA-DR+, relative to iso-
type controls (Figure 4A-4C). We chose to define mono-
cytes by HLA-DR+ staining, rather than expression of
CD11b (typically positive on monocytes in peripheral
blood) or CD11c (negative on blood monocytes, but po-
tentially upregulated in GM-CSF-rich environments such
as the lungs), so that we could independently analyze ex-
pression of the latter two markers in samples other than
blood. As shown in the representative staining (Figure 4D),
we can easily see distinct populations for the classical,
non-classical, and intermediate monocytes in peripheral
blood. better at secreting proinflammatory cytokines and con-
stitute the majority of all monocytes in healthy persons,
whereas the nonclassical monocytes more closely resem-
ble resident tissue macrophages [28-30]. Identification of monocyte populations in blood, sputum
and BAL A third subset
of peripheral blood monocytes, termed “intermediate”
monocytes are CD14++ CD16+ [31]. It is not clear
whether these intermediate monocytes have a biologic-
ally meaningful role or are an intermediate step in the
differentiation of monocytes but they have been shown
to be increased in certain conditions including rheuma-
toid arthritis and severe asthma [32]. In our study, monocytes were readily identified in all
three compartments using CD14 and CD16 antibodies, Page 9 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 2 Representative staining of CD4+ and CD8+ T lymphocytes in blood, BAL, and sputum. Samples of peripheral blood (A, D), BAL
(B, E) and sputum (C, F) were gated on cells that were CD45+, CD3+, and had a low side-scatter. Next, using the isotype control (A-C), quadrants
denoting specific staining for CD4 (horizontal axis) and CD8 (vertical axis) were determined (D-F). Numbers in the CD4+ and CD8+ quadrants
represent the percent of each subset among all CD45+ cells. Figure 2 Representative staining of CD4+ and CD8+ T lymphocytes in blood, BAL, and sputum. Samples of peripheral blood (A, D), BAL
(B, E) and sputum (C, F) were gated on cells that were CD45+, CD3+, and had a low side-scatter. Next, using the isotype control (A-C), quadrants
denoting specific staining for CD4 (horizontal axis) and CD8 (vertical axis) were determined (D-F). Numbers in the CD4+ and CD8+ quadrants
represent the percent of each subset among all CD45+ cells. In the BAL and sputum, monocytes were distinct from
alveolar macrophages due to their reduced size and
granularity, evident by forward scatter and side scatter
(data not shown). Monocytes were again divided into
the three populations: classical, intermediate, and non-
classical (Figure 4E, 4F). The populations appear to be
more limited to the classical and intermediate pheno-
types, reminiscent of a gating strategy developed by
Brittan et al. [33] which uses the terms “inducible” and
“resident”, respectively, due to the observation that LPS
inhalation resulted in an increase in the CD14++ CD16-
population, in comparison to a saline-treated group, but
the CD14++ CD16+ population was unchanged between
groups [33]. We also found that the monocytes from
BAL and sputum were predominantly CD14++ CD16+,
the so-called “resident” monocytes (Figures 4E, 4F). Identification of monocyte populations in blood, sputum
and BAL Numbers
represent the percent of AMø among all CD45+ cells. were identified as being double positive for HLA-DR and
BDCA-3 (CD141). To identify pDC, we selected cells that
were CD123+ and BDCA-2 (CD303) +. although it is now recognized that this acute phase react-
ant has important actions independent of elastase inhib-
ition [36]. Hence, clarifying the exact role of neutrophils
in COPD phenotypes is an important goal. We identified
neutrophils by gating on CD45+, high side scatter
cells and then, based on appropriate isotype control
(Figures 6A-6C), selected cells that were positive for
two neutrophil-specific surface markers [37], CD16b
and CD66b (Figure 6D-6 F). From the representative
staining we saw that neutrophils were most abundant in
blood and sputum samples, as expected, and were very
infrequent in BAL. Using this method we were able to identify mDC1
subsets in blood and BAL (Figure 5). Similar results were
found for mDC2 and pDCs (data not shown). CD11c,
CD11b, and CD103, which are also routinely used to
identify DCs, were also included in the panel for DCs. Future analyses could utilize these markers to perform
more in-depth analysis of DC subsets and to compare al-
ternative methods of DC identification. Identification of monocyte populations in blood, sputum
and BAL Identification of myeloid dendritic cell (mDC) populations
in blood, sputum and BAL
In the present study, we examined markers of three
human pulmonary DC subsets: myeloid DC type 1
(mDC1), myeloid DC type 2 (mDC2), and plasmacytoid
DCs (pDCs). DCs were only analyzed in BAL and blood
due to concerns that they would be too small of a popu-
lation to identify in sputum. To identify the DC subsets,
we used blood dendritic cell antigen (BDCA) markers,
which we and others have previously shown accurately
identifies these cell types in lung parenchyma [34,35]. First, CD45+ cells were selected followed by exclusion of
cells that were positive for either CD3 or CD19+ cells, and
of cells with a high forward scatter or high side-scatter. Next, mDC1 cells were identified as being double-positive
for HLA-DR and BDCA-1 (CD1c), whereas mDC2 cells Identification of myeloid dendritic cell (mDC) populations
in blood, sputum and BAL
In the present study, we examined markers of three
human pulmonary DC subsets: myeloid DC type 1
(mDC1), myeloid DC type 2 (mDC2), and plasmacytoid
DCs (pDCs). DCs were only analyzed in BAL and blood
due to concerns that they would be too small of a popu-
lation to identify in sputum. To identify the DC subsets,
we used blood dendritic cell antigen (BDCA) markers,
which we and others have previously shown accurately
identifies these cell types in lung parenchyma [34,35]. First, CD45+ cells were selected followed by exclusion of
cells that were positive for either CD3 or CD19+ cells, and
of cells with a high forward scatter or high side-scatter. Next, mDC1 cells were identified as being double-positive
for HLA-DR and BDCA-1 (CD1c), whereas mDC2 cells Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 10 of 17 Figure 3 Representative staining of macrophages in BAL and sputum. To identify macrophages in samples of BAL (A, C) and sputum (B, D),
we gated on CD45+ auto-fluorescent cells and used isotype controls (A,B) to gate on cells specifically staining for HLA-DR+ CD11c + (C, D). Numbers
represent the percent of AMø among all CD45+ cells. Figure 3 Representative staining of macrophages in BAL and sputum. To identify macrophages in samples of BAL (A, C) and sputum (B, D),
we gated on CD45+ auto-fluorescent cells and used isotype controls (A,B) to gate on cells specifically staining for HLA-DR+ CD11c + (C, D). Identification of neutrophil populations in blood, sputum
and BAL In peripheral blood samples, we also observed a
CD66b + CD16b- population (R1 in Figure 6D), which
was not present in the BAL or sputum samples. In design-
ing this study, we had hypothesized that in COPD subjects
we might see a population of circulating neutrophils The concept that neutrophils contribute centrally to
emphysema stems primarily from genetic deficiency of
alpha-1 antiprotease, which inhibits neutrophil elastase, Page 11 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 4 CD14 and CD16 identify populations of monocytes in blood, BAL, and sputum. To identify monocyte in samples of peripheral
blood (A, D), BAL (B, E) and sputum (C, F), we first gated on non-autofluorescent, CD45+ cells with a medium side-scatter, then using isotype
controls (A-C), chose HLA-DR+ cells (D-E). In all analyses, we then separated the monocytes into “classical” CD14++ CD16- cells (R1), “intermediate”
CD14++ CD16+ (R2), and “nonclassical” CD14+ CD16+ (R3) cells. Numbers represent the percent of each monocyte subset among all CD45+ cells. Figure 4 CD14 and CD16 identify populations of monocytes in blood, BAL, and sputum. To identify monocyte in samples of peripheral
blood (A, D), BAL (B, E) and sputum (C, F), we first gated on non-autofluorescent, CD45+ cells with a medium side-scatter, then using isotype
controls (A-C), chose HLA-DR+ cells (D-E). In all analyses, we then separated the monocytes into “classical” CD14++ CD16- cells (R1), “intermediate”
CD14++ CD16+ (R2), and “nonclassical” CD14+ CD16+ (R3) cells. Numbers represent the percent of each monocyte subset among all CD45+ cells. recently released from the bone marrow, identifiable as
CD16b- (low) and CD10- cells [38]. We gated on both
CD16b low and high populations and analyzed expres-
sion of CD10 (Figure 6B). The CD66b + CD16b- cells
had reduced expression of CD10, especially in com-
parison to the CD66b + CD16b + cells, suggesting that
we are able to identify a population of circulating im-
mature neutrophils. to be positive for CD16. Eosinophils do contain intra-
cellular CD16 and it has been shown that blood eosino-
phils express surface CD16 when stimulated in vitro with
platelet-activating factor or IFN-γ [43]. Hence, these pre-
liminary data are compatible with activation of eosinophils
in the airways of some subjects with COPD. In future
studies once we have data on all subjects, we will look for
correlations between eosinophil CD16 expression and
clinical characteristics. Discussion This interim analysis, describing the design and early
data collection of a clinical trial involving six clinical
centers throughout the United States, demonstrates
the feasibility of our approach of “just-in-time” provision
of antibodies, distributed staining and fixation, and cen-
tralized analysis to perform 12-color immunophenotyping
of samples from three different tissue origins. We have
demonstrated successful identification of multiple leukocyte
cell populations, including CD4+ and CD8+ T cells, Eosinophilic lung inflammation appears to identify a sub-
set of COPD patients who are more responsive to cortico-
steroids or leukotriene inhibition [39-41]. We identified
eosinophils in blood and BAL by first gating on CD45+
high side scatter cells and then identifying cells that,
compared to isotype controls (Figure 7A-7C) were
CCR3+ and CD16- [42] (Figure 7D-7F). In sputum
samples, we also identified a cell population that was
CCR3+ but based on the isotype control, they appeared Page 12 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 5 BDCA-1 and HLA-DR identify mDC1 cells in blood and BAL. To identify dendritic cells in samples of peripheral blood (A, C) and
BAL (B, D), we first gated on CD45+ cells, then excluded CD3+, CD19+, and cells with a high forward and side-scatter, and finally using isotype
controls (A,B), chose HLA-DR and BDCA-1 double-positive cells (C,D). Numbers represent the percent of mDC1 cells among all CD45+ cells. Figure 5 BDCA-1 and HLA-DR identify mDC1 cells in blood and BAL. To identify dendritic cells in samples of peripheral blood (A, C) and
BAL (B, D), we first gated on CD45+ cells, then excluded CD3+, CD19+, and cells with a high forward and side-scatter, and finally using isotype
controls (A,B), chose HLA-DR and BDCA-1 double-positive cells (C,D). Numbers represent the percent of mDC1 cells among all CD45+ cells. allows us to standardize three out of those four variables. In our study, all samples are run on the same instrument,
a modified LSR II flow cytometer containing a high-
throughput sampler to improve efficiency of analysis and
a yellow-green laser that permits use of multiple PE-
conjugated fluorochromes. Data are collected and ana-
lyzed by a small team of highly trained scientists with
adherence to a standardized gating strategy and fre-
quent evaluation of the raw data and instrument con-
trols. Discussion We have even minimized variability in the
antibody reagents and fluorochromes by preparing the
antibodies at the centralized core before shipping them
to the Clinical Centers. In comparison, other multicen-
ter trials have opted to combine local sample staining
with the flow cytometry instruments that are available
at each participating institution, although often the monocytes, macrophages, neutrophils, and eosinophils,
in blood, BAL and sputum, thereby demonstrating the
validity of our antibody panel and the fixation method. We have also shown that the vast majority of samples
provide usable data, supporting the feasibility of this
logistic approach. This design should be considered for
immunophenotyping in comparable clinical studies in
other disease states. Our approach differs from that of several other multicen-
ter trials. The Multicenter AIDS Cohort Study (MACS)
used four flow cytometry laboratories to analyze identical
peripheral blood specimens. MACS identified the import-
ance of standardizing the following variables: (1) the
model of flow cytometer; (2) the antibody reagents and
fluorochromes; (3) the procedure for sample preparation;
and (4) the procedure for sample analysis [7]. Our approach Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 13 of 17 Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D),
BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical
axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all
CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). G) Histograms depicting expression of
CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D),
BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical
axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all
CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). Discussion G) Histograms depicting expression of
CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D),
BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical
axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all
CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). G) Histograms depicting expression of
CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). instruments vary in type of instrument and number of
lasers [8-10]. Della Porta et al. attempted to control for
this variability by including daily instrument quality
controls, including fluorescence standardization, to en-
sure consistent operation. However, the analysis was
not centrally reviewed and was performed using multiple
platforms [10]. In the study by Benevolo et al., laboratories
had either a 3- or 4-color instruments, which resulted in
the use of different antibody panels between centers. To minimize that variable, all data in that study were
reviewed by a single person [9]. instruments vary in type of instrument and number of
lasers [8-10]. Della Porta et al. attempted to control for
this variability by including daily instrument quality
controls, including fluorescence standardization, to en-
sure consistent operation. However, the analysis was
not centrally reviewed and was performed using multiple
platforms [10]. In the study by Benevolo et al., laboratories
had either a 3- or 4-color instruments, which resulted in
the use of different antibody panels between centers. To Although in our study there is a single procedure for
sample preparation, given that six different sites are re-
sponsible for staining the samples, there is likely some
variability being introduced at this stage. We considered
the idea of cryopreserving or stabilizing samples and
then shipping them to a centralized flow cytometry core
for staining and analysis, but ultimately decided against Page 14 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 7 Eosinophils in blood, BAL, and sputum express CCR3 but have variable expression of CD16. Discussion To identify eosinophils in samples
of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on cells that were CD45+ with a high side scatter that were also CCR3+
(vertical axis), relative to isotype controls (A-C). In blood (panel D) and BAL samples (panel E), eosinophils were also CD16- (horizontal axis). In
sputum samples (panel F), eosinophils were positive for CD16. Numbers represent the percent of each subset among all CD45+ cells. Figure 7 Eosinophils in blood, BAL, and sputum express CCR3 but have variable expression of CD16. To identify eosinophils in samples
of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on cells that were CD45+ with a high side scatter that were also CCR3+
(vertical axis), relative to isotype controls (A-C). In blood (panel D) and BAL samples (panel E), eosinophils were also CD16- (horizontal axis). In
sputum samples (panel F), eosinophils were positive for CD16. Numbers represent the percent of each subset among all CD45+ cells. this approach, as the preservation of individual surface
antigens is quite variable [11,12] (and our own unpub-
lished data from pilot experiments). For the most part,
our preliminary analyses have not demonstrated system-
atic differences between clinical centers for staining
efficiency. been shown to result in a slight decrease in fluorescent in-
tensity [44] and a decrease in forward scatter and side
scatter [45]. Our analysis of changes in fluorescence inten-
sity for 68 leukocyte surface receptors for up to seven days
generally agrees with a previous analysis showing that
staining generally remained consistent and highly repro-
ducible at days 1, 3 and 5 post-staining [44]. However, we
found better preservation of staining intensity at day 7
than in that previous study, although two of the four re-
ceptors they studied were also stable at 7 days, suggesting
that these changes are receptor-specific. Furthermore, we
did not observe a change in forward scatter and side scat-
ter. Of the molecules that were affected by storage in PFA
in our study, only CD103 had decreased fluorescent inten-
sity. The other markers that were affected, TLR4, gamma-
delta T cell receptor, CCR7, BDCA-1, CX3CR1 and TLR2
actually had a slight increase in fluorescent intensity. Discussion In
more detailed analyses, we will need to take this change in Another variable that we are unable to control entirely
using this approach is the amount of time that the sam-
ples remain in PFA before data collection on the flow
cytometer. Although we stipulate that sites send samples
back as soon as possible, samples that are collected on a
Thursday or Friday are not shipped until the next Monday. Excluding those days from sample collection was not
compatible with the overall logistics of the Bronchoscopy
sub-study. An essential feature of our study design was
sample fixation using 2% paraformaldehyde post-staining
to permit delayed analysis. However, paraformaldehyde it-
self affects flow cytometry readings. Staining with PFA has Page 15 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 fluorescence into account for samples that were unable to
be analyzed within 2 days. Acknowledgments We are grateful to SPIROMICS participants for their willingness to participate
in this study and to the Study Coordinators and staff who though their hard
work make this study possible. SPIROMICS is funded by the National Heart,
Lung, and Blood Institute NHLBI (NHLBI-HR-08-08) with support from a
variety of industry partners whose representatives serve on the SPIROMICS
External Scientific Board. Specifically, SPIROMICS is funded by contract from
the NHLBI: HHSN268200900013C, HHSN268200900014C,
HHSN268200900015C, HHSN268200900016C, HHSN268200900017C,
HHSN268200900018C, HHSN2682009000019C, HHSN268200900020C. Private
sector contributions to SPIROMICS are facilitated by the Foundation for the
National Institutes of Health (www.fnih.org). CMF and JLC are supported in
part by funding from the Clinical Research & Development Service,
Department of Veterans Affairs. We are grateful to SPIROMICS participants for their willingness to participate
in this study and to the Study Coordinators and staff who though their hard
work make this study possible. SPIROMICS is funded by the National Heart,
Lung, and Blood Institute NHLBI (NHLBI-HR-08-08) with support from a
variety of industry partners whose representatives serve on the SPIROMICS
External Scientific Board. Specifically, SPIROMICS is funded by contract from
the NHLBI: HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C,
HHSN268200900018C, HHSN2682009000019C, HHSN268200900020C. Private
sector contributions to SPIROMICS are facilitated by the Foundation for the
National Institutes of Health (www.fnih.org). CMF and JLC are supported in
part by funding from the Clinical Research & Development Service,
Department of Veterans Affairs. Conclusion
l In conclusion, we have demonstrated the feasibility of
providing state-of-the-art immunophenotyping of spu-
tum, peripheral blood and BAL in a multicenter obser-
vational study of COPD biomarkers. Key features of our
approach that minimize potential sources of experimen-
tal variation include “just-in-time” provision of reagents
from a centralized Immunophenotyping Core, local im-
munostaining and fixation, and return of samples for
analysis on a single flow cytometer. The choice of
leukocyte cell types and their receptors was based on a
series of pre-specified hypotheses plus research interests
of the coauthors. This interim report demonstrates the
success of our approach, which may be of value in the
design of multicenter trials in other disease states. Enroll-
ment to this sub-study is anticipated to be completed in
the summer of 2015, so results should be analyzed and
published over the next two years. Competing interests Competing interests
SC, VRS, JPB, JS, NEA, CMD, PVB, EEC, DJC, ATH, WKO, RJK, RP, DS, MZ:
These authors declare that they have no competing interests. CMF and JLC have grant support from MedImmune, Ltd. to analyze lung NK
cells in human lungs resected for clinical indications. SIR has received money for service on advisory boards of the following
companies: A2B Bio, Almirall, CSL Behring, Dailchi Sanyko, Novartis, Nycomed
and Pfizer; and as a consultant to: Almirall, APT Pharma/Brtinall, AstraZeneca,
Boehringer Ingelheim, Chiesi, Decision Resource, Dunn Group, Easton Associates,
Gerson, GlaxoSmithKline, MedImmune, Novartis, Pearl, Roche, Takeda, Theravance. PGW has a research grant from Pfizer and is a consultant for Genentech,
Roche, BI, J&J, NeoStem, Novartis, Astra Zeneca and Merck. He is co-inventor
on a patent for asthma biomarkers. g
Roche, BI, J&J, NeoStem, Novartis, Astra Zeneca and Merck. He is co-inventor
on a patent for asthma biomarkers. Authors’ contributions
CMF
d
i
d h CMF co-designed the antibody panel and the experimental design, wrote
the original manuscript draft and oversaw all aspects of flow cytometric data
analysis. SC, VRS, JPB and JS participated in assay preparation, coordination
with clinical sites, data acquisition, and data analysis. NEA, CMD, SIR and
PGW participated in study design. PVB, EEC, DJC, and WKO provided data
coordinating support. ATH, JRH, RJK, RP, DS, PGW and MZ oversaw sample
collection and preparation at the clinical sites. JLC conceived of the study,
participated in its design and helped prepare the manuscript. All authors
read and approved the final manuscript. Part of our future analysis strategy will be to correlate
the relative proportions of a given cell type in BAL ver-
sus sputum versus blood in the same subject. Other ana-
lyses will correlate cell-surface markers on a given cell
type with smoking history, spirometry, airway measure-
ments, and other parameters. As part of the parent
SPIROMICS project, individuals will also be character-
ized via physiological, imaging, biochemical, and genetic
parameters. These data will also be available for correlat-
ing with immunophenotyping analyses. Abbreviations
BAL B
h
l Abbreviations
BAL: Bronchoalveolar lavage; COPD: Chronic obstructive pulmonary disease;
MACS: Multicenter AIDS Cohort Study; PFA: Paraformaldehyde;
SPIROMICS: Subpopulations and Intermediate Outcomes in COPD Study. BAL: Bronchoalveolar lavage; COPD: Chronic obstructive pulmonary disease;
MACS: Multicenter AIDS Cohort Study; PFA: Paraformaldehyde; SPIROMICS: Subpopulations and Intermediate Outcomes in COPD Study. Consent Written informed consent was obtained from each
participant for the publication of this report and any
accompanying images. An additional limitation of this study is the lack of a
live/dead exclusion gate. FSC and SSC gating was used
to eliminate cell debris, but cannot guarantee that all
dead cells were excluded. A final limitation is that the
protocol of the current SPIROMICS Immunophenotyp-
ing project does not include staining of intracellular
antigens, isolation of specific cell types or in vitro stimu-
lation to induce production of gene products such as cy-
tokines or inflammatory mediators. We considered those
undertakings premature until we had both demonstrated
the ability of this multi-center experimental design to
produce usable surface staining data, and had advanced
the characterization of specific cell types in our popula-
tion. However, given the technical success illustrated by
these results, we believe that such extension are entirely
feasible and should be an important goal of future stud-
ies in this cohort. For example, it would be of particular
interest to extend previous observations supporting a
role for granzyme B in the pathogenesis of emphysema
[46,47] by defining which cell types harvested by BAL
from area of radiographically-confirmed emphysema ex-
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et al. Smoking-dependent reprogramming of alveolar macrophage
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Stat Rep. 2010;59:1–72. 2. Murray CJ, Lopez AD. Alternative projections of mortality and disability by
cause 1990–2020: global burden of disease study. Lancet. 1997;349:1498–504. 26. Gautier EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, et al. Gene-
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1R
h S 1Research Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, 48105, USA. 2Pulmonary & Critical Care Medicine Section, Medicine Service, VA Ann Arbor
Healthcare System, Ann Arbor, MI 48105, USA. 3Pulmonary & Critical Care
Medicine Division, Department of Internal Medicine, University of Michigan
Health System, Ann Arbor, MI 48109, USA. 4Center for Environmental Medicine,
Asthma, and Lung Biology, Chapel Hill, NC 27599, USA. 5Center for Airways
Disease, Department of Medicine, University of North Carolina at Chapel Hill,
Chapel Hill, NC 27599, USA. 6Marsico Lung Institute/University of North Carolina
Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
27599, USA. 7Center for Genomics and Personalized Medicine, Wake Forest
University, Winston-Salem, NC 27157, USA. 8Division of Pulmonary and Critical
Care Medicine, Departments of Medicine and Genetic Medicine, Weill Cornell
Medical College, New York, NY 10021, USA. 9Division of Pulmonary, Department
of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City,
UT 84112, USA. 10Pulmonary, Critical Care, Sleep and Allergy Division,
Department of Internal Medicine, University of Nebraska Medical Center,
Omaha, NE 68198, USA. 11Department of Medicine, Columbia University
Medical Center, New York, NY 10032, USA. 12Division of Pulmonary, Critical Care,
Sleep and Allergy, Department of Medicine, University of California at San Page 16 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 16 of 17 Francisco, San Francisco, CA 94143, USA. 13Division of Pulmonary, Critical Care,
and Sleep Medicine, David Geffen School of Medicine, University of California at
Los Angeles, Los Angeles, CA 90095, USA. 14Pulmonary and Critical Care
Medicine Section (506/111G), Department of Veterans Affairs Healthsystem,
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Kim WD, Chi HS, Choe KH, Oh YM, Lee SD, Kim KR, et al. A possible role for
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inflammation and immune response elements in the bronchial airways. Inhal Toxicol. 2011;23:392–406. Page 17 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Submit your next manuscript to BioMed Central
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https://openalex.org/W2600083737 | https://www.nature.com/articles/s41598-017-00382-7.pdf | English | null | The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma | Scientific reports | 2,017 | cc-by | 5,538 | The long non-coding RNA
LINC01013 enhances invasion
of human anaplastic large-cell
lymphoma Received: 31 May 2016
Accepted: 22 February 2017
Published: xx xx xxxx I-Hsiao Chung1, Pei-Hsuan Lu1,2, Yang-Hsiang Lin1, Ming-Ming Tsai3,4, Yun-Wen Lin1, Chau-
Ting Yeh5 & Kwang-Huei Lin1,5,6 Anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma
(NHL). Currently, only studies on the chimeric oncogene NPM-ALK have reported a link to ALCL
progression. However, the specific molecular mechanisms underlying the invasion of ALCL are still
unclear. Here, we sought to investigate differentially expressed, long non-coding RNAs (lncRNAs)
in ALCL and their potential biological function. Our microarray analyses revealed that LINC01013, a
novel non-coding RNA gene, was highly expressed in clinical specimens of ALCL and was significantly
upregulated in invasive ALCL cell lines. Knockdown of LINC01013 suppressed tumor cell invasion;
conversely, its overexpression enhanced tumor cell invasion. LINC01013-induced invasion was
mediated by activation of the epithelial-to-mesenchymal transition (EMT)-associated proteins,
snail and fibronectin. Specifically, LINC01013 induced snail, resulting in activation of fibronectin and
enhanced ALCL cell invasion. Collectively, these findings support a potential role for LINC01013 in
cancer cell invasion through the snail-fibronectin activation cascade and suggest that LINC01013 could
potentially be utilized as a metastasis marker in ALCL. ALCL is a distinct subset of non-Hodgkin T-cell lymphoma associated with the presence of large pleomor-
phic and aberrant cells that express CD30 and T-cell markers1. The well known t(2;5)(p23;q35) translocation
is the most frequent genetic background in ALCL. This translocation was identified from the resulting fusion
of the receptor tyrosine kinase (RTK), anaplastic lymphoma kinase (ALK), with nucleophosmin (NPM)2. This
NPM-ALK fusion protein, which is highly tyrosine phosphorylated and recruits more than 40 proteins, has been
reported to promote ALCL progression by triggering activation of transduction pathways primarily involved in
proliferative and antiapoptotic responses3, 4. Nevertheless, neither ALK nor other recurrent translocations are
expressed in approximately 15–40% of ALCL cases5. Although the current World Health Organization classifi-
cation of lymphomas places ALK(+) and ALK(−) ALCL in the same category, more recent studies suggest that
these two types of lymphomas, as well as cutaneous ALCL, might correspond to different entities.h y
y
gf
The majority of ALK(+) ALCL cases are diagnosed at advanced stages (III and IV) that display systemic dis-
ease with generalized lymphadenopathy and extranodal metastasis, especially in the skin and in soft tissues, such
as the liver, lung, and spleen6. Similar observations were made in NPM-ALK transgenic mice, confirming that
ALK(+) malignancies are very invasive7. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 Results
E
i Expression of lncRNA in ALCL. To identify aberrantly expressed lncRNAs, we characterized lncRNA
expression patterns in ALCL specimens using oligonucleotide arrays. Overall, 51 altered lncRNAs were identi-
fied in ALCL; 20 were up-regulated and 31 were down-regulated (Fig. 1a). We investigated these overexpressed
lncRNAs for their potential function in ALCL progression, focusing on the top five non-coding genes (fold
change > 3.5), BMS1P20, LINC01013, MIR503HG, RNF144A-AS1 and CACNA1G-AS1 (Table 1). We validated
the increased expression of these genes in clinical specimens of ALCL, showing that expression levels were
increased ~10-fold for BMS1P20, ~17-fold for LINC01013, ~19-fold for MIR503HG, ~5-fold for CACNA1G-AS1
and ~15-fold for RNF144A-AS1 (Fig. 1b). Collectively, these results confirm that these five lncRNAs are highly
expressed in ALCL. LINC01013 is associated with ALCL cell invasion. To verify the specific functions of lncRNAs in
ALCL, we selected three ALK(+) ALCL cell lines: SR-786 (low-invasive), KARPAS-299 (moderately invasive)
and Matrigel-selected KARPAS-invasive cells (high-invasive) (Fig. 2a). The expression levels of the lncRNAs,
BMS1P20, LINC01013, MIR503HG, CACNA1G-AS1 and RNF144A-AS1 were determined in these cell lines
(Fig. 2b). Notably, LINC01013 was highly expressed in the more invasive KARPAS-invasive cell line (Fig. 2b, left
panel), suggesting that LINC01013 may be played a pivotal role in ALCL cell invasion. LINC01013 depletion suppresses ALCL cell invasion. To determine the effects of LINC01013 on
cell invasion, we established LINC01013-knockdown KASPAS-299 and KASPAS-invasive cell lines. Notably,
KASPAS-299 and KASPAS-invasive cell lines depleted of LINC01013 displayed significantly decreased invasion
(~2-fold) compared with control cells (Fig. 3a). The epithelial-to-mesenchymal transition (EMT)-associated
markers, snail and fibronectin, were also significantly decreased in LINC01013-depleted cells compared with con-
trol cells (Fig. 3b,c). Snail, a transcription factor associated with cancer metastasis, regulates fibronectin to pro-
mote lymphoma cell invasion. Similarly, depletion of snail in KASPAS-299 and KASPAS-invasive cells decreased
invasion ability compared with control cells (Fig. 4a), and markedly down-regulated fibronectin (Fig. 4b,c). The
expression levels of other Snail targets or EMT regulators have no effect between control and snail-depleted cells
(Fig. S1) or control and LINC01013-depleted cells (Fig. S2). Taken together, these data confirm the requirement
of LINC01013 to accelerate tumor cell invasion and implicate the snail-fibronectin cascade in this process. LINC01013 promotes ALCL cell invasion by activating the snail pathway. To further confirm
the involvement of snail activation in LINC01013-induced phenotypic changes, we performed invasion assays
using LINC01013-overexpressing cells. Results
E
i Notably, LINC01013-overexpressing SR-786 cells (SR-786-LINC01013)
displayed significantly increased invasion (~2–3-fold) compared with parental SR-786 cell controls (Fig. 5a,b, left
panel), and this phenotype was attenuated by snail depletion (Fig. 5a, right panel). SR-786-LINC01013 cells also
exhibited marked upregulation of snail and fibronectin, an increase that was specifically blocked by depletion of
snail (Fig. 5b, right panel, and c). Collectively, these results support a potential role of LINC01013 in promoting
cancer cell invasion through activation of the snail-fibronectin cascade in ALCL (Fig. 5d). The long non-coding RNA
LINC01013 enhances invasion
of human anaplastic large-cell
lymphoma However, the specific regulatory mechanisms underlying the invasion
of ALK(+) ALCL are still unclear. Recent reports have demonstrated the important role of non-protein–coding RNA (ncRNA) components of
the human genome, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), in cancer forma-
tion or development8, 9. Many types of ncRNA play pivotal roles in cancer biology10, 11. LncRNAs are aberrantly 1Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.). 2Department
of Dermatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.). 3Department of Nursing, Chang
Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.). 4Department of General Surgery, Chang Gung
Memorial Hospital, Chiayi, Taiwan (R.O.C.). 5Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan,
Taiwan (R.O.C.). 6Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University
of Science and Technology, Taoyuan, Taiwan (R.O.C.). I-Hsiao Chung and Pei-Hsuan Lu contributed equally to this
work. Correspondence and requests for materials should be addressed to K.-H.L. (email: khlin@mail.cgu.edu.tw) Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 1 www.nature.com/scientificreports/ expressed in various kinds of cancer, and the expression levels of certain lncRNAs are associated with disease pro-
gression or diagnosis, or might serve as potential therapeutic targets12–14. Further, the clinical significance of the
contribution of lncRNAs to ALCL development and the key roles of lncRNA functional networks are currently
unknown. In this study, we investigated the invasion activity involving ALK and the molecular mechanisms underlying
the pathogenesis of ALK(+) ALCL. We found that several lncRNA genes were highly expressed in ALCL clin-
ical specimens and hypothesized that their functions were associated with cancer progression. Specifically, our
microarray analysis revealed that LINC01013 (long intergenic non-protein–coding RNA 1013), a novel lncRNA
that has not been linked to human cancer in the literature, is overexpressed in clinical specimens of ALCL and
is significantly up-regulated in invasive ALK(+) ALCL cell lines. We further investigated and characterized this
aberrantly expressed lncRNA in ALCL to determine whether it can be used as a novel biomarker and/or thera-
peutic target for ALCL. Discussion No recent studies have reported an association between lncRNAs and ALCL progression or, by extension, the
involvement of an lncRNA-mediated mechanism in the invasion of ALCL. To identify specific pathways under-
lying ALCL carcinogenesis, we used an oligonucleotide microarray analysis of ncRNA genes to identify lncRNAs
that were differentially expressed in ALCL. We further evaluated clinical specimens for aberrantly expressed lncR-
NAs to identify potential biomarkers of ALCL invasion. Notably, we found that the novel lncRNA, LINC01013,
is highly expressed in ALCL specimens and showed that its expression is positively correlated with the invasiv-
ity of ALK(+) cells. Gain- and loss-of-function experimental strategies clearly demonstrated that LINC01013
enhanced ALK(+) ALCL cell invasion. Thus, LINC01013 may be a novel oncogene that could serve as an invasion
marker for ALK(+) ALCL metastases. LncRNAs are important regulators of gene expression and are thought to have a wide range of functions in
cellular and developmental processes16–18. The functions of a few lncRNAs have been experimentally defined19,
20. These studies have demonstrated the involvement of lncRNAs in fundamental processes of gene regulation,
including chromatin modification, direct transcriptional regulation, RNA processing, post-translational regu-
lation of protein activity or localization, and miRNA modulation. In the current study, we demonstrated that
LINC01013 promotes an increase in mRNA and protein expression levels of snail and fibronectin, indicating the
involvement of lncRNA in the transcriptional regulation of downstream genes. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 2 www.nature.com/scientificreports/ Figure 1. Analysis and validation of lncRNAs in ALCL specimens. (a) Schematic diagram showing application
of gene expression microarrays (~7419 lncRNAs) to the analysis of lncRNAs. These lncRNAs were selected
based on the cut-off value. The 20 up-regulated (fold change > 2.0) and 31 down-regulated (fold change < 0.5)
lncRNA were filtered and narrowed down form data base. (b) Expression levels of LncRNAs in ALCL specimens
(3 paired specimens of patients) were measured by q-RT-PCR. Differences were analyzed using a Kruskal-Wallis
test (*P < 0.05). Figure 1. Analysis and validation of lncRNAs in ALCL
of gene expression microarrays ( 7419 lncRNAs) to th Figure 1. Analysis and validation of lncRNAs in ALCL specimens. (a) Schematic diagram showing application
of gene expression microarrays (~7419 lncRNAs) to the analysis of lncRNAs. These lncRNAs were selected
based on the cut-off value. The 20 up-regulated (fold change > 2.0) and 31 down-regulated (fold change < 0.5)
lncRNA were filtered and narrowed down form data base. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Gene Symbol
Fold change
BMS1P20
6.707
LINC01013
5.025
MIR503HG
4.419
CACNA1G-AS1
3.712
RNF144A-AS1
3.631
LOC100506027
3.300
MIAT
3.119
FLJ42709
2.767
LOC100506013
2.734
SNORD113-2
2.605
FLJ42709
2.503
MIAT
2.444
LOC339240
2.255
KIAA0125
2.226
MIAT
2.215
MIAT
2.209
MIAT
2.150
SNORD114-11
2.006
SNORD111B
2.004
MIAT
2.001
Table 1. Up-regulated lncRNAs of anaplastic large T cell lymphoma (ALK+). T/N > 2.0. Table 1. Up-regulated lncRNAs of anaplastic large T cell lymphoma (ALK+). T/N > 2.0. activator of transcription) pathways24, 25. Activation of STAT3 is associated with a specific signature that includes
several transcription factors (e.g., CEBP/β), cell cycle (e.g., cyclin D, c-myc) and survival/apoptosis molecules
(e.g., Bcl-A2, Bcl-XL, survivin, MCL-1), and cell-adhesion proteins26. These studies have demonstrated the regu-
lation of coding genes and their cross-talk in ALCL tumor formation. Several reports have shown that miRNAs,
a type of short non-coding RNA, regulate ALCL malignancies. For example, miR-29a expression was found to
modulate apoptosis through inhibition of MCL-1 expression in ALCL27; ectopic expression of miR-150 inhib-
its proliferation and blocks S-phase entry of ALK(+) cells28; and downregulation of miR-16 induces vascular
endothelial growth factor (VEGF) expression in ALK(+) ALCL29. However, the detailed role of long non-coding
genes in the pathogenesis of ALCL is still unclear and may represent an important avenue for future research.i g
p
g
y
p
p
In conclusion, this study is the first to demonstrate the involvement of an lncRNA in ALCL tumor progres-
sion. The results provide new insights into the mechanism by which the lncRNA, LINC01013, contributes to the
promotion of ALCL cell invasion, showing that it acts through activation of the snail-fibronectin cascade. Our
findings collectively support a potential role of LINC01013 in ALCL progression and suggest that LINC01013
expression could be effectively utilized as a metastatic marker in ALCL. Discussion (b) Expression levels of LncRNAs in ALCL specimens
(3 paired specimens of patients) were measured by q-RT-PCR. Differences were analyzed using a Kruskal-Wallis
test (*P < 0.05). The mesenchymal marker snail is a core transcription factor in the EMT process that stimulates expression of
the downstream target gene encoding fibronectin to enhance cancer invasion21. To date, few studies have linked
the regulation of lncRNA and snail/fibronectin in lymphoma. LINC01013 enhances invasion abilities in ALK(+)
ALCL cell lines and may stimulate metastasis through activation of snail-fibronectin components. Our findings
are consistent with the conclusion that activation of these mesenchymal markers leads to ALCL cell metastasis. Previous studies of ALCL progression have focused on NPM1-ALK translocation and its relative contribu-
tion to pathogenesis22. Fusions of ALK have oncogenic potential because their aberrant tyrosine kinase activ-
ity enhances cell proliferation and survival and promotes cytoskeletal earrangement23. NPM1-ALK–interacting
molecules ultimately lead to the activation of key pathways, including RAS/ERK (extracellular signal-regulated
kinase), phospholipase C (PLC-γ), phosphoinositide 3-kinase (PI3K), and JAK/STAT (signal transducer and The mesenchymal marker snail is a core transcription factor in the EMT process that stimulates expression of
the downstream target gene encoding fibronectin to enhance cancer invasion21. To date, few studies have linked
the regulation of lncRNA and snail/fibronectin in lymphoma. LINC01013 enhances invasion abilities in ALK(+)
ALCL cell lines and may stimulate metastasis through activation of snail-fibronectin components. Our findings
are consistent with the conclusion that activation of these mesenchymal markers leads to ALCL cell metastasis. y
Previous studies of ALCL progression have focused on NPM1-ALK translocation and its relative contribu-
tion to pathogenesis22. Fusions of ALK have oncogenic potential because their aberrant tyrosine kinase activ-
ity enhances cell proliferation and survival and promotes cytoskeletal earrangement23. NPM1-ALK–interacting
molecules ultimately lead to the activation of key pathways, including RAS/ERK (extracellular signal-regulated
kinase), phospholipase C (PLC-γ), phosphoinositide 3-kinase (PI3K), and JAK/STAT (signal transducer and Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 3 Materials and Methods Ethics statement. All the experiments were performed in accordance with the approved guidelines of the
Chang Gung Memorial Hospital Institutions Review Board (IRB: 103-3205B). Informed consent was obtained
from all patients involved in this study. Tissue specimens. A total of ALCL tumor tissue and adjacent noncancerous mucosa were obtained from
Department of Dermatology, Chang Gung Memorial Hospital. RNA extraction and gene expression microarrays. Total RNA from paired ALCL tumor tissue and
adjacent noncancerous mucosa samples (N = 3) were extracted using the TRIzol reagent (Life Technologies,
Rockville, MD, USA), as described previously15. Total RNA (20 μg) was used for labeling and hybridization with
the SurePrint G3 Human Gene Expression array (Agilent, Welgene Biotech, Taiwan) containing 7419 lncRNAs
and 27958 human genes. Slides were scanned and intensities were acquired using GenePix Pro 4.1 software (Axon
Instruments Inc. Foster City, CA, USA). Cell culture. SR-786, KARPAS-299, and Matrigel-selected KARPAS-invasive human ALK(+) ALCL cell lines
were routinely cultured at 37 °C in a humidified atmosphere of 95% air and 5% CO2 in Dulbecco’s modified
Eagle’s medium (DMEM) supplemented with 10% or 15% fetal bovine serum (FBS). The references for SR-786
and KARPAS-299 cell lines are Human Cell Culture Vol. III, 355–370 (J.R.W. Masters and B.O. Palsson). These are
human ALK(+) large T cell lymphoma cell lines. KASPAS-invasive cells were harvested form three rounds of
Matrigel-selected (invasion assay) KASPAS-299. Cloning of LINC01013. cDNA was synthesized from total RNA (1 μg) using Superscript II reverse tran-
scriptase (Invitrogen, Carlsbad, CA, USA) and random hexamer primers (Invitrogen). LINC01013 was amplified
by polymerase chain reaction (PCR) using the primer pair 5′-CAG GAA GCC AGC ATT TTT AAT-3′ (forward)
and 5′-CAA ATA ATA TCT TGC TTT TAT-3′ (reverse), and the following thermocycling conditions: 30 cycles Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 4 www.nature.com/scientificreports/ ntificreports/
Figure 2. LINC01013 is associated with tumor-invasive functions. (a) Left panel: Invasion ability was analyzed
in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was
determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters
were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013,
MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT-
PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 2. LINC01013 is associated with tumor-invasive functions. Materials and Methods (a) Left panel: Invasion ability was analyzed
in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was
determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters
were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013,
MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT-
PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 2. LINC01013 is associated with tumor-invasive functions. (a) Left panel: Invasion ability was analyzed
in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was
determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters
were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013,
MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT-
PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). at 95 °C for 1 min, 58 °C for 1 min, and 72 °C for 2 min. The LINC01013 open reading frame was ligated into the
pcDNA 3.0 expression vector, and the resulting construct was sequenced to confirm the presence of the gene. t 95 °C for 1 min, 58 °C for 1 min, and 72 °C for 2 min. The LINC01013 open reading frame was ligated into the
cDNA 3.0 expression vector, and the resulting construct was sequenced to confirm the presence of the gene. Immunoblot analysis. Total cell lysates and conditioned media were prepared, and protein concentrations
were determined using a Bradford assay kit (Pierce Biotechnology, Rockford, IL, USA). Equivalent amounts
of protein were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on
a 10% gel. Separated proteins were transferred to a nitrocellulose membrane (pH 7.9; Amersham Biosciences
Inc., Piscataway, NJ, USA), blocked with 5% non-fat powdered milk, and incubated with specific anti-snail (Cell
Signaling Technology, Cell Signaling, Danvers, USA; #6615) and anti-fibronectin (Santa Cruz Biotechnology,
Santa Cruz, CA, USA; sc-9068) primary antibodies at 4 °C overnight. After washing, membranes were incubated
with horseradish peroxidase (HRP)-conjugated anti-mouse, anti-rabbit or anti-goat IgG secondary antibody, as
appropriate, for 1 h at room temperature. Immune complexes were visualized using an enhanced chemilumines-
cence (ECL) detection kit (Amersham) and Fuji X-ray film. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 5 entificreports/
Figure 3. LINC01013 depletion suppresses ALCL cell invasion. Materials and Methods (a) Left panel: The invasion ability of
KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under LINC01013-depleted
(LINC01013 KD) and control (Luc.) conditions. Right panel: Quantification of invasive ability and LINC01013
expression levels. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR
(c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 3. LINC01013 depletion suppresses ALCL cell invasion. (a) Left panel: The invasion ability of
KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under LINC01013-depleted
(LINC01013 KD) and control (Luc.) conditions. Right panel: Quantification of invasive ability and LINC01013
expression levels. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR
(c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Establishing SR-786 cell lines stably overexpressing LINC01013. The SR-786 cell line, grown in
10-cm cell culture dishes, was transfected with the LINC01013 expression plasmid using the Lipofectamine rea-
gent (Invitrogen). After 24 h, transformants were selected from transfected cells by growing in medium con-
taining the antibiotic neomycin G418 (400–800 μg/ml) for 2–3 weeks. Survival clones were pooled and used to
western blot or functional assay. Expression levels of LINC01013 RNA in the selected clones were determined
using quantitative reverse transcription-PCR (q-RT-PCR). shRNA-mediated LINC01013 knockdown. Short hairpin RNA (shRNA) sequences targeting
LINC01013 were purchased from the National RNAi Core Facility (Institute of Molecular Biology, Academia
Sinica, Taiwan). The KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with shRNA tar-
geting the endogenous LINC01013 gene using the TurboFect reagent (Invitrogen). LINC01013 repression was
confirmed by q-RT-PCR. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 6 www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 5. LINC01013 acts through the snail-fibronectin cascade to enhance cell invasion. (a) The invasion
ability of SR-786 and SR-786-LINC01013 cells was analyzed using Transwell assays under snail-depleted (Snail
KD) and control (Luc.) conditions. (b) Left panel: Quantification of invasive ability and LINC01013 expression
levels. Right panel: Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR
(c) and Western blot analysis. (d) Schematic depiction of LINC01013 promotion of ALCL invasion through
activation of the snail-fibronectin cascade. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 5. LINC01013 acts through the snail-fibronectin cascade to enhance cell invasion. (a) The invasion
ability of SR-786 and SR-786-LINC01013 cells was analyzed using Transwell assays under snail-depleted (Snail
KD) and control (Luc.) conditions. (b) Left panel: Quantification of invasive ability and LINC01013 expression
levels. Right panel: Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR
(c) and Western blot analysis. (d) Schematic depiction of LINC01013 promotion of ALCL invasion through
activation of the snail-fibronectin cascade. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Matrigel (Becton-Dickinson). For both assays, the pore size of the upper chamber was 8 mm. The medium in the
upper chamber was serum-free DMEM, and the lower chamber contained DMEM supplemented with 20% FBS,
included as a chemoattractant. After incubation for 24 h at 37 °C, cells traversing the filter from the upper to lower
chamber were stained with crystal violet and counted. Experiments were repeated at least three times. Matrigel (Becton-Dickinson). For both assays, the pore size of the upper chamber was 8 mm. The medium in the
upper chamber was serum-free DMEM, and the lower chamber contained DMEM supplemented with 20% FBS,
included as a chemoattractant. After incubation for 24 h at 37 °C, cells traversing the filter from the upper to lower
chamber were stained with crystal violet and counted. Experiments were repeated at least three times. Statistical analysis. Data are expressed as mean values ± SEM of at least three experiments. Statistical anal-
yses were performed using Student’s t test and one-way analysis of variance (ANOVA). Where appropriate, the
Mann–Whitney U test or Fisher’s exact test was used to compare two groups; a Kruskal–Wallis test or Pearson’s χ2
test was used if more than two groups were compared. The relationship between the results of two different exam-
inations was analyzed with Spearman’s correlation test. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 4. Snail depletion suppresses ALCL cell invasion. (a) Left panel: Invasion ability of KARPAS-299 and
KARPAS-invasive cell lines was analyzed using Transwell assays under snail-depleted (Snail KD) and control
(Luc.) conditions. Right panel: Quantification of invasion assay results. (b) Snail and fibronectin expression
levels in these cell lines were determined by q-RT-PC (c) and Western blot analysis. Differences were analyzed
using a Kruskal-Wallis test (*P < 0.05). Figure 4. Snail depletion suppresses ALCL cell invasion. (a) Left panel: Invasion ability of KARPAS-299 and
KARPAS-invasive cell lines was analyzed using Transwell assays under snail-depleted (Snail KD) and control
(Luc.) conditions. Right panel: Quantification of invasion assay results. (b) Snail and fibronectin expression
levels in these cell lines were determined by q-RT-PC (c) and Western blot analysis. Differences were analyzed
using a Kruskal-Wallis test (*P < 0.05). shRNA-mediated snail knockdown. Short hairpin RNA (shRNA) sequences targeting snail were pur-
chased from the National RNAi Core Facility (Institute of Molecular Biology, Academia Sinica, Taiwan). The
SR-786, SR-786-LINC01013, KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with
shRNA targeting endogenous snail mRNA using the TurboFect reagent (Invitrogen). Snail repression was con-
firmed by Western blot analysis. shRNA-mediated snail knockdown. Short hairpin RNA (shRNA) sequences targeting snail were pur-
chased from the National RNAi Core Facility (Institute of Molecular Biology, Academia Sinica, Taiwan). The
SR-786, SR-786-LINC01013, KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with
shRNA targeting endogenous snail mRNA using the TurboFect reagent (Invitrogen). Snail repression was con-
firmed by Western blot analysis. Invasion assays. The influence of LINC01013 on invasion ability in vitro was determined by Transwell assay
(Falcon BD, Franklin Lakes, NJ) using LINC01013-depleted KARPAS-299 or LINC01013-overexpressed SR-786
cells, as described previously15. Briefly, cell density was adjusted to 105 cells/ml, and 100 μl of the suspension
was seeded into upper chambers of the Transwell plate, either coated (invasion) or not coated (migration) with Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 7 Acknowledgementsh g
This work is supported by grants from the Chang Gung Memorial Hospital (CMRPG3D1841 to P.H.L. and
MRP130, CMRPD1D0381, 0382, 0383 to K.H.L.). g
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W1995655532.txt | https://zenodo.org/records/1530390/files/article.pdf | de | Klinische und histopathologische Beobachtungen an einem intra vitam diagnostizierten Fall von bronchialem Adenocarcinom mit Hautmetastasen | Journal of cancer research and clinical oncology | 1,910 | public-domain | 9,257 | I.
( A u s d e m I n s t i t u t ffir spez. P a t h o l . i n n e r e r K r a n k h e i t e n d e r K g l .
U n i v e r s i t ~ t P a v i a [Prof. M:. A s c o l i ] . - - A u s d e m L a b o r a t o r i u m
ffir a l l g e m . P a t h o l o g i e u n d H i s t o l o g i e [Prof. C. G o l g i ] . )
Klinische und histopathologische Beobachtungen
an einem intra vitam diagnostizierten Fall yon
bronchialem •denocarcinom mit Itautmetastasen.
~ron
Laigi Stropeni.
(Hierzu Tafel I.)
Wenn auch die F'~lle yon Carcinom der Bronchien heutzutage nicht
mehr jene grosse Seltenheit bilden, wie sie L a n g e r h a n s mit. Rticksicht
auf seine Zeit wohl mit Recht hinstellte, so halte ich es doch fiir angezeigt,
nachstehenden Fall aazuffihren, nicht nut, weii demselben eine vollst~indige
kliniscbe Beobachtung zuteil geworden - - die einschl'~gige K.~uistik wurde
ja gr6sstenteils yon Fachm~nnern der pathologischon Anatomie zusammengestellt - - soadern vor allem deshalb, well er mir ein gewisses Interesse
darzubieten schien und schIiesslich auch wegea der Eigentfimlichkei~
mancher klinischea bzw. pathologisch-anatomischen Erscheinungen sowie
der intra vitam mit Sicherheit und Genauigkeit gestellten Diagnose.
Z u s a m m e n f a s s u n g der K r a n k e n g e s c h i c h t e .
M. V[, 35 Jahre alt, Haush~ilterin, verheiratet, aus Zinasco (Provinz Pavia)
tritt am 10. Dezember 1908 in die Klinik ein.
Anamnese: Keine Erinnerung beztiglich der Voreltern. Der Vater starb
75 Jahre alt; an wolcher Krankheit ist unbekannt, die Mutter in ihrem 42. Jahre
infolge einer Zwillingsgeburt. Von 5 Kindern ist Pat. das j/ingste, eine Schwester
ist an Lunge~schwindsucht gestorben, 3 Brfider sind noch am Leben und gesund.
In ihrer Kindheit erkraukte Pat. an Masern, im ftinften Lebensjahre an Diphtheritis; mit I2 Jahren stellten sich die ersten Menses ein. Mit 20 Jahren heiratete
sie einen gesunden Mann: sechsmaligo Konzeption, jedoch nut viormal ausgetragene
Schwangerschaft; die geborenen Kinder sind noch am Leben und gesund. Mit
Zeitschriff fiir ,Krebsforschung.
9. Bd.
i. Heft.
1
L. S t r o p e n i~ Fall yon bronchialem Adenoearcinom.
25 Jahron wurde sie yon einem Schlundabszess befallen; derselbe 5ffnete sieh
spontan und heilte in etwa vierzehn Tagen. In ihrem 31. Jahre litt sio im Laufo
einor Stillung an Mastitis. Im Oktober 1907 stelite sich links heftiges, bei tiefem
Inspirium sich steigerndes, mit Fieber und troekenem Husten einhergehendes
Seitenstechen ein; die als Pleuritis diagnostizierte Erkrankung hatte einen akuten
Verlauf und heilte in etwa vierzehn Tagen dureh Pinselungen mit Jodtinktur.
Veto Monat November 1907 bis zum Monat M~irz 1908 vollkommenes Wohlbefinden. Von dieser Zeit an begann Pat. h~iufig leiehte, nut selten heftige
stechende Schmerzen am Thorax zu verspfiren, dieselben traten in der Regel links
auf und mit vieltiigigen Zwisehenpausen; ihr Sitz war ein variabler: bald wurden
sic auf die Seite, bald auf die Sehulter, bald w~eder auf den R@ken verlegt; sic
wurden beim Atmen stErker, 5fret stellte sich gleiehzeitig und naehher Husten
ein, mitunter trocken 7 zuweilen hingegen mit zEhem, klebrigem, nur ausnahmsweise Blutstreifen enthaltendemAuswurf. Gleichzeitig Unlust zur Arbeit, Appetitlosigkeit, m~ssiges Fieber, Kopfschmerzen, so dass w~hrend der seltenen schwereren
Anfiille sich Patientin zu Bert legen musste. Durch eine nicht n~iher zu bestimmende Behandlung per os und dureh wiederholtes Finseln mit Jodtinktur versehwanden die krankhaften Erseheinungen 7 um aber nach einer bzw. zwei Woohen
wieder aufzutreten.
In den Intervallen ffihlte sieh Patientin vollkommen wohl. Unter diesem Abweohseln yon Wohl- und Unwohlsein verlief das Frfihjahr und der Sommer;
anfangs Oktober aber gestaltete sich das Krankheitsbild zu einem bedenklicheren:
links am Thorax stellte sieh heftiges, intermittierendes~ h/iufig auftretendes Seitenstechen ein, ferner Mattigkeit, Kopfweh, leiehtes Fieber, leiehte Atemnot, jedoch
ohno Husten oder Auswurf. Naeh ein paar Woehen trat eine geringe Besserung
ein und Pat. verliess das Bett. Aber recht bald musste si~ dasselbe wegen eines
ganz gleiehen: yon hohem Fieber, sp~irliehem schleimigen Auswurf, Kopfschmerzen,
Atemnot begleiteten rechts aufgetretenen Schmerzes wieder aufsuehen. Derselbe
war liings der zehnten gippe Iokalisiert, stellte sieh anfallsweise ein - - wobei jeder
Anfall ungef~hr zohn Minuten anhielt - - ; hierauf wurde er allm~hlieh schw~icher
aber kontinuierlieh, mit Exazerbationen boim Tiefatmen und Nachlassen beim
Liegen auf tier schmerzhaften Seite.
Da Pat. keine Besserung zu erzielen vermoehte, suchte sie am 10. Dezember
die Klinik auf.
S t a t u s p r a e s e n s : Die Kranke klagt fiber allgemeine Sohw~iche, Appetitlosigkeit, Atemnot~ Sehmerz hinten reehts an der Thoraxbasis, l~ings der zehnten
Rippe lokalisiert, kontinuierlich~ zu gewissen Tagesstunden sich steigernd.
Pat. ist bei vollem Bewasstsein. Gesichtsausdruck leidend; obligate aktive
Riiekenlage. Skelett kr~iftig, Muskelmassen entwickelt~ Fettpolster erhalten~ Haut
braunfarbig~ feucht, elastiseh; keine 0edeme wahrnehmbar, keine Lymphganglien
palpierbar. Temperatur 38, Atmung 44, Puls 98.
An Hals und Kopf nichts Bemerkenswertes.
T h o r a x : Stark asymmetrisch wegen st~irkerer huswSlbung der rechten
H~ilf~e; die in tote retrahiert erscheinende linke H~ilfte weist - - jedoch nur vorn
zwei erheblichere Einsenkungen auf, deren eine die zwei ersten ttippen, die
anderr die fiinfte und sechste betrifft. Supra- und lnh'aklavikulargruben beider-
-
L. S t r o p e n i , Fall yon bronchialem Adenocaroinom.
3
seits eingesunken~ Interkostalriiume fiach, epigastrischer Winkel stumpf. Hinten
Abfiachung der linken Thoraxh~ilfte an der Basis~ die rechte dagegen hervorragend.
Vorwiegend kostal% wegen mangelhafter Ausdehnung der ~usserst schwach bewegliohen linken H~lfte asymmetrische Atmung; ebenso ist hinten an der Basis
die Ausdehnung der reehten eine geringe. Kechter Thorax elastisch~ weniger links.
Die rechtsseitige zehnte Rippe yon der Angularis scapulae bis zur mittleren
Axiltaris druckempfindlich.
Ffihlharer Stimmfremitus links-vorn-unten abgeschw~icht~ hinted Yon der Schulterblattgr~ite naeh unten aufgehoben; rechts
erhalten.
Die rechte Lungenspitze ragt um etwa 4 cm fiber das Schlfisselbein hinauf;
die unteren K~nder haben normale Lage. Die linke Lungenspitze ist retrahiert und
fiberragt nur um 2 cm das Schliisselbein.
Die aktive Bewegliehkeit ist links nahezu aufgehoben; reehts auf der mittleren hxillaris betr~igt dieselbe 1 em. Perkussionssohall hell rechts vorn~ etwas
ged~impft hinten an der Basis. Links hinten oben his zur Spina scapulae allmiihlich deutlicher werdende Hypophonese; yon dieser Stell~ ab vollst~ndige Diimpfung
mit starkem Widerstand. Vorn oben hoher tympanitischer Sehall; derselbe zeigt
weder Wintriehschen noch Gerhardtschen Schallwechsel; unten ged~mpfter
Schall; die D~mpfungsgrenze vorl~uft veto unteren Rand der sechsten Rippe
zwischen der Hemiklavikularis und der vorderen Axillaris~ auf dieser letzteren zum
fiinften Interkostalraum~ erreieht auf der mittleren Axillaris die fiinfte Rippe und
geht in die hintere D~mpfung fiber. Das Groeeosche paravertebrale Dreieck ist
hinten reehts unten nicht vorhanden.
Reehts vesikul~res Atmen~ hinted gross-~ mittel- und ldeinblasiges nieht
klingendes Rasseln. Links iiberall abgeschw~chtes Atmen~ gross- und mittelblasige
sehwach konsonierendo Rasselgeriiusche auf der Spitze und in der Axillargegend~
in welcher amphorisehes Atmen bestoht; vorn zerstreutes feinblasiges und subkrepierendes Rasseln; hinten ~iusserst schwache Atmung bis zur Schultcrblattgr~t%
Stille an der Basis.
Dutch die Probepunktion am unteren Winkel des linken Schulterblattes
wcrden 2 ccm einer trfiben zitronengelben~ spoutan gerinnenden Fliissigkeit
herausbefSrdert; Rivaltasche Reaktion negativ; Sediment aus vorwiegend einkernigen Leukozyten bcstehend; Agarausstriche steril. Frobepunktion ira achten
Interkostalraum rechts negativ. Die Herzgegend nicht hervorgewSlbt; Spitzenstoss
nicht sichtbar~ im fiinften Interkostalraum links, 1/2 cm innerhalb der Papillarlinie schwaeh fiihlbar. Die relative D~impfung ist durch eine yon der dritten Rippe
auf der Parasternalis abgehendo, schr~ig naeh unten und aussen verlaufende~
schliesslich mit der Spitze zusammenfallende Linie begrenzt; die rechtsseitige
Grenze reicht bis .9 ern welt rechts veto Sternalrand im vierten Interl~ostalraum.
Die HerztSne siad schwach, dumpf, tier vernehmbar. Puls leicht arhythmisch.
Nichts Nennenswertes beider Palpation und Perkussion der A b d o m i n a l organe.
G e w i c h t : 44~500 kg.
H a m : Strohgelb, sauer~ Durchschnittsmenge 500 ecru. Spez. Gew. 1021,
Eiweiss~ Zucker, Blut fehlend; im Sediment wenige Epithelzellen der Harnblasr
und unteren tlarnweg% sp~irliche Leukozyten..
1"
L. S t r o p e n i , Fall yon bronchialem Adenocarcinom.
F ~ize s: breiartig~ gelbbraun ; niehts Bemerkenswertes bei der mikroskopischen
Untersuchung.
B l u t : Rote BlutkSrperehen 4000000; weisse 7000. Die mikroskopische
Untersuchung (F~rbung nach R o m a n o w ski) ergibt keinen pathologischen Befund,
ausser leichter Polyohromatophilie.
S p u t u m : Schleimig-eitrig, nummul~r~ sp~rlioh~ Untersuehung auf K o c h sche
Bazillen negativ~ ebenso jene auf elastische Fasern, sowie auf neoplastisch verd~ehtige Elemente; biologische Probe darch Einffihrung des Auswurfs in die PeritonealhShle zweier Meerschweinohen negativ.
W~ihrend ihres Aufenthaltes in der l(linik zeigt Patientin eine langsame aber
doeh fortschreitende Verschlimmerung~ ohne jedoch hierbei ein kachektisches Aussehen zu gewinnen. KSrpertemperatur morgens normal bzw. subfebril mit Steigerungen bis 38750--39 0 am Abend ; profuse Na~htsehweisse. Mitunter Schfittelfrost~
wobei das Fieber 2--3 Tage unausgesetzt anh~lt, um sodann seinen gewShnlichen
Verlauf wieder zu nehmen. Appetit stets gering~ die Funktionen des Verdauungsapparats trage, die fast t~iglich vorgenommene Untersuehung des Harns hat niemals
etwas Bemerkenswertes ergeben ; B en ee- J o n e s scher E[weisskSrper nicht vorhanden. Das SputurTl wird zu einem ziemlieh reichliehen ohne oder mit nur
~iusserst wenigen Blatstreifen~ yon. sehleimig-eitriger Beschaffenheit~ ohne bemerkenswerte mikroskopisohe Merkmale. Die Konfiguration des Thorax bleibt
w~hrend des ganzen Aufenthaltes in der Klinik nahezu unver~,ndert, ebenso die
Perkussions- und Auskultationsbefunde; nur in tier zweiten H~.lfte des November
treten Anzeichen eines m~issigen perikardialen Ergusses auf, der dann in etwa
zehn Tagen raseh wieder zur Resorption kam. Gegen Ende Januar beginnt der
Stimmfremitus auoh auf der linken hinteren D~mpfungszone - - wenn auch etwas
abgesehw~eht - - ffihlbar zu werden; eine ausgepr~gte Hyp(~phonese breitet sich
allm~ihlich fiber den ganzen vorderen Lungenbezirk aus~ die subklavikul~re Grube
ausgenommen, we der Perkussionssehall 7 stets hoch tympanitisch bleibt, die bestandig sehwache Atmung aber einen amphoriscben Charakter angenommen hat
und die HerztSne mit einem ausgesprochen metallischen Klang fortgeleitet werden.
Es werden zu versehiedenen Zeiten am ]inken Thorax ffinf Probepunktionen vorgenommen mit negativem Erfolge oder nur wenige Tr0pfen hellroter~ blutiger
Flfissigkeit entleert; zweimal bekommt man mit Miihe ein pear Kubikzentimeter
einer zitronengelben durehsiehtigen Flfissigkeit heraus, bei welcher die R i v a l t a sche Probe positiv ausfiillt und die mikroskopische Untersuehung sp~irliehe Leukozyten und wenige rote BlutkSrperehen zeigt; Kulturen bleiben steril. Die Kutanreaktion mit 25 proz. Tuberknlin ergibt wiederholt und stets negativen Erfolg.
Die Kranke klagt h/~ufig fiber Sohmerzen neuralgischen Charakters, bald am
linken Thorax~ bald am rechten, bald an den Extremit~ten, we dieselben insbesondere gegen Mitre Januar heftiger auftreten, um niemals mehr g~nzlir zu
verschwinden.
Bei einer allgemeinen Untersuchung, der die Kranke am 31. J a n u a r unterzogen- wird~ bemerkt man am unteren Drittel des linken Armes~ dicht unter der
Epitrochlea eine kleine Geschwulst. Dieselbe ist haselnussgross~ hart~ fibrSs~ auf
dan darunter- und umliegenden Geweben verschieblich, innig abet auf eine nur
sehr kurze Strecke mit der vollkommen intakten Haut zusammenhangend~ an und
L. S t r o p e n i , Fall yon bronchialem Adenocarcinom.
f~ir sich schmerzlos und nieht druokempfindlich. Es wird keineLymphdrfise palpiert~
weder in der Axillar-~ noch in der Supra- bzw. Infraklavikular-~ noch in der
Zervikalgegend.
Mit Zustimmung der Krankeo wird der soeben besehriebene kleine Tumor am
1. Februar abgetragen.
Am 2. Februar 7 w~hrend Patien~in nach dem Weehsel der W~isehe wieder in
ihr Bert gelegt wird~ klagt sie fiber einen am linken Oberschenkel p15tzlieh aufgetretenen Sehmerz; bei der Untersuehung zeigt sich ein 0bersehenkelbruch an
der Vereinigungsstelle des oberen mit dem mittleren Drittel. An den Leisten sind
keine Ganglien zu fiihlen. Mit Rficksieht auf dieses unerwartete Vorkommnis
werden nun regelm~ssig und mit grSsserer Frequenz Blutuntersuchungen angestellt
(Deckglastrockenpr~iparat% F~rbung nach R o m a n o w s k i oder J e n n e r ) .
Einzig
wichtiger Befund hierbei: das Vorhandensein yon Myelozyten in sehr sp~irlieher
Menge (1 pCt. der weissen BlutkSrperehen).
Die mit der Tralaionsmethode behandelte Fraktur heilte niemals wieder: an
der verletzten Stelle war zuletzt eine harte fihrSse Masse durehfiihlbar; dieselbe
war mit dem Knoehen verwachsen und nur bei Druek oder bei aktiven bzw.passiven
Bewegungsversuchen schmerzhaft.
Am 26. Februar maeht sieh entspreehend dem unteren Rande des grossen
Pektoralis, etwas unterhalb der M o h r e n h e i m s e h e n Grube ein zweiter kleiner
Tumor bemerkbar, mit denselben Merkmalen wio der am hrme abgetragene; eine
wallnussgrosse Gesehwulst wir~t aueh an der Nabelnarbe angetroffen, ganz gleieh
beschaffen wie die beiden oben besehriebenen. Nirgends sind ver~'Ssserte Lymph. drfisen zu palpieren.
Klein% harte, verschiebliehe Ganglien beginnen anfangs M~irz in der reehten
und linken Axillargegend und an den Leiston fiihlbar zu werden; keines jedoeh
am Halse oder in der Sapraklavikulargrube.
Allm~ihlicher Kr~ifteverfall; am 15. M~rz 8 Uhr frfih Exitus.
I. P a t h o l o g i s c h - a n a t o m i s c h e r Teil.
Die mikroskopische Untersuchung der wiihrend des Lebens am Arme
abgetragenen kleinen Geschwulst ergab~ d a s s e s sich um eine aus tells
kubischen, tells zylindrischen Epithelzellen bestehende Neubildung handelte.
Diese Zellen begrenzten mehrere den Alveolen einer Driise sehr Ahnlich
sehende HohlrS.ume yon verschiedener Gestalt und GrSsse und waren reich
an Protoplasma; letzteres war hell und schien an mancher Stelle des
Sehnittes einen sich intensiver f~rbenden, dem Driisenlumen zugekehrten
schmalen Saum zu besitzen, ohne dass selbst feinere F i i r b u n g s m e t h o d e n wie z. B. die yon S a u e r fiir den Bfirstenbesatz e m p f o h l e n e - es gestattet
h~ttten, eine Differenzierung in F~iden und Wimpern wahrzunehmen. Der
dem Basalteile der Zelle niiher gelegene Kern war gross, eif0rmig gestaltet~
nahezu bl~ischenartig mit sp~rlichem Chromatinnetz, zuweilen in Karyokinese
begriffen.
Hie und da war der Zellenbelag unterbrochen; die Zellkgirper waren
L. Stropeni, Fall yon bronchialem Adenocarcinom.
zerfallen, ja zerstSrt, und ihre Triimmer waren in den Lumina der Alveolen
bemerkbar. Diese Epithelien lagen nicht auf einer elastischen Membran,
vielmehr befand sich zwische,~ den ZellstrRngen ein aus sehr feinen, selten
zu st~rkeren auff~lligeren Biindeln vereinigten Bindegewebsfasern bestehendes Stroma.
An vielen Stellen war die sonst so gleichm~issige Struktur der Geschwulst durch ein wirres, stfirmisches Durcheinander yon Strangen atypischer, poly~drischer oder kubischer Zellen ver~indert, die ordnungslos und
ohne eine bestimmte Richtung und hie und da eine mehr oder weniger weite
H6hle begrenzend in die Tiefe des umliegenden Bindegewebes drangen.
Diese Hohlrliume sowie die derjenigen Pattie des Tumors, die man als
die typisch adenomat0se bezeichnen k6nnte, hatten tells das Aussehen vou
AIveolen, tells yon R6hrchen und waren mit einer bald homogenen, bald
granulSsen, im allgemeinen jedoch fibrilliiren Substanz angefiillt, worin Zelldetritus und Kerntrfimmer zu sehen waren.
Der Tumor sass im Unterhautgewebe ohne irgend welchen Zusammenhang mit den Hautepithelien, doch waren die Sch'weissdrfisen so welt 'r
gerfickt, dass ihre Kn~uel mit den Grenzen der Neubildung in Berfihrung
getreten waren; an einigen Stellen bekam man den Eindruck, als ob diese
Hautgebilde in Kontinuit~tsbeziehtulgen zu ddr Geschwulst stiinden. Es
wird daher wohl kaum befremden, wenn mit Rficksicht auf die Aehnlichkeit dieser Befunde mit den von P e t e r s e n , Unna, C a m p a n i n i u. a. mitgeteilten ich anfangs der Ansicht war, man h~,tte es mit einem Adenocarcinom der Schweissdrfisen zu tun. Allein derartige Ne(lbildungen kommeu
so selten vor~ dass es gerechtfertigt erscheinen musst% wenn fiber die Herkunft des untersuchten Tumors Zweifel aufstiegen und ich reich daher be-.
m[ihte, yon der im ersten Augenblick gestellten Diagnose reich besser ztl
fiberzeugen. Icb. suchte daher die Beschaffenheit des Inhaltes der Drfisenriiume zu bestimmen: mit Hilfe d e r - wegea des dabei sich rot fiirbenden
Kolloids so vorzfiglich spezifischen - - Trainaschen Methode bekam ich
eine lila-blaue F~i.rbung, wobei das Thionin eine metachromatische Rotfiirbung lieferte und das Meyersehe Muzikarmin durch elektive Farbung
dieser Substanz gleichfalls den Beweis lieferte, dass es sich um Schleim
handelte. Es zeigte sich somit deutlich, dass hier nicht eine primate Geschwulst vorliegen musste, sondern eine Metastas% fiir welche Annahme
das u
der anderen Hautgeschwfilstchen sowie die bereits oben
erw~.hnte spontane Fraktur sprach. Diese Metastase musste notwendigerweise yon einem Adenocarcinom herstammeu, das in einem Schleimdriisen
enthaltenden Gewebe zustaude gekommen.
Auf Grund der welter unten angeffihrten Eriirterung fiber die Symptomatologie und mit Rficksicht auf das oben erwlihnte Ergebnis der mikro-
L. Stropeni, Fall yon bronchialem Adenocarcinom.
skopischen Untersuchung wurde nachstehende Diagnose gestellt und dem
Obduzenten fibergeben :
C a r c i n o m des l i n k e n H a u p t b r o n c h u s , i i b e r g r e i f e n d auf die
g a u z e d a z u g e h S r i g e Lunge; E r w e i c h u n g , K a v e r n e n b i l d u n g und
r e a k t i v e P l e u r i t i s ; M e t a s t a s e n an der H a u t , an den L y m p h driisen, am K n o c h e n m a r k mit k o n s e k u t i v e r F r a k t u r des l i n k e n
Femurs.
Bei der yon Prof. T r a i n a ausgeffihrten Obduktion land sich die
klinische Diagnose in allen Punkten besti~tigt, wobei noch andere unauffMlig verlaufene Metastasen zutage kamen. Ich iibergehe hier alles im
Sektionsprotokoll nicht streng Interessierende und beschriinke reich lediglich
auf die Mitteilung der bemerkenswertesten bei der Leichemmtersuchung erhobenen Befnnde.
Bei ErSffnung des Thorax stellen sich rechts alte Verwachsungen heraus; ebensolche auch links, sehr z~ihe und ganz besonders in tier diaphragmatischen Pleura dick. Verwachsungen bestehen auch zwischen der Thoraxwand und dem Perikardium, welches letztere Entziindungsvorg~inge mit serofibrinOsem h'~imorrhagischem Exsudat erkennen liisst. Entsprechend der linken
V o r k a m m e r hiingt das Perikardium durch eine die oberste Partie des
Mediastinum, den Lungenhilus, die peribronchialen Lymphganglien, den
Bogen der Aorta und den absteigenden Anteil derselben zu einem einzigen
Klumpen involvierende grauliche Masse mit der Pleura innig zusammen.
Die ]inke Lunge ist kleiner, an der Spitze retrahiert, nicht erschlafft,
hart, stellenweise mit weisslichen, verschieden grossen Kn6tchen von fibriiser
Konsistenz besetzt. Die rechte Lunge zeigt neben Emphysemherden auch
noch spiirliche neoplastische Knoten.
Dureh einen in der Richtung des Hilus gefiihrten Schnitt wird die
linke Lunge ihrer Liingsachse nacb und dabei auch die darunter liegende
Milz geteilt. Auf der Schnittfli~che wird, entsprechend der Bifurkation der
grossen Bronchien eine harte, graue, druckwiderstehende, yon erhabenen
Strangen durchzogene Masse angetroffen, welche in die beiden Lappen des
Organs in ihrer dem Hilus zugekehrten Seite eindringt und hierbei die
Bronchien und die als schwarze Knoten auf der schmutzig-weissen Neoplasie hervortretenden peribronchialen Lymphdrfisen einhiillt. Durch diese
Masse ziehen die Bronchien hindurch; infolgedessen sieht dieselbe wie ein
BadesChwamm durchlOchert aus; das Bronchiallumen ist hierbei durch
Granulationen und Unebenheiten der Schleimhaut - - die mitunter auch vollst~ndigen Versehluss bedingen kiinnen - - etwas verengert.
Solche Unebenheiten der Bronchialschleimhaut nehmen im Hauptbronchus ihren Anfang, ungefahr 4 cm entfernt yon der Luftr(ihrenbifurkation und in Form yon knotenartigen Erhabenheiten und harten, derben
L. Stropeni, Fall yon bronchialem Adenocarcinom.
Streifen~ die das Bronchiallumen bis auf ein Drittel reduzieren und sich
dann in die Bronchien des oberen bzw. unteren Lappens welter fortsetzen.
Es finden sich keine Spuren eines in diese neoplastische Zentralmasse eingehiillten Parenchyms; yon der soeben genannten Masse gehen jedoch vereinzelte weisslich gefiirbte Strange ab, welche in die beiden Lappen
eindringen, ohne aber jene eigentiimliche Tendenz, den Verzweigungen
der Bronchien zu folgen, die Wolf als so charakteristisch ffir Bronchialcarcinome bezeichnet hat, dasses auch schon makroskopisch eine sichere
Diagnose in diesem Sinne gestatte.
Hie und da in der Lunge weissliche Knoten, anseheinend yon der
Hauptmasse getrennt; ebenso unter der Pleura.
Das schw[irzlich gefarbte, an mehreren Stellen atelektatisehe, hepatisierte Lungenparenehym weist -au.~serst kieine Ka~,ernen und Bronehiektasien
auf, aus denen bei Druck Sehleimeiterkltimpehen mit Gewebsfetzen heraustreten. Die Spitze wird yon einer dieht unter der Pleura befindliehen
taubeneigrossen, glatte, harte Wiinde besitzenden leeren Kaverne eingenommen; andere haselnussgrosse, im allgemeinen an der Peripherie unter
der Pleura gelegene Kavernen nehmen den unteren Lappen ein; einige
haben glatte, polierte, andere rauhe, zerfressene Wiinde, wo das Gewebe
mit der grSssten Leiehtigkeit in Form yon sehwarzbraunen, zerreissliehen,
reichlieh Detritus und eitrigen Sehleim enthaltenden Massen sieh abl6st;
der Tumor dringt hliufig in diese Wlinde ein, wobei er denselben eine
grSssere Harte und Festigkeit verleiht.
Rechts Lungenstauung mit emphysematisehen Horden und nnter der
Pleura vereinzelte neoplastische Knoten.
Das I-terz zeigt sieh - - yon den bereits beschriebeneu das Perikardium
betreffenden Erseheinungen abgesehen - - schlaff; die Vorkammern mit
Fibringerinnseln erfiillt; die linke yore Tumor direkt e r g r i f f e n - wobei
letzterer nieht bis zam Endokardium vorgerfiekt ist --- an der Spitze ein
auf das Myokardium und Epikardium sieh besehrfi.nkender haselnussgrosser
metastatischer Knoten. Oas Myokard fettig entartet.
Kein Hineitiwuehern des Tumors in die grossen MediastinalgeNsse,
deren Wandungen slimtlieh yon der neoplastisehen Masse dnrchsetzt und
eingehiillt sind; !etztere hatte jedoeh keine VergrSsserung des Mediastinums
veranlasst.
L e b e r mit zahlreiehen versehieden grossen, teilweise benabelten
Metastasen.
L i n k e Niere: Zahlreiche Metastasen; in d'er r e c h t e n nur spiirliehe.
Milz: Ausgedehnte Verwachsungen mit dem Zwerehfell; zaMreiche
Metastasen; ein grosser Infarkt am oberen Pol.
K n o c h e n : Im oberen Drittel des reehten Femur Fraktur mit einer
mannsfaustgrossen, aueh das Knochenmark einnehmenden neoplastischen
L. Stropeni, Fall yon bronchialem Adenocaroinom.
Wucherung; aeoplastische Erweichungsherde in den KSrpern zweier Brustund eines Lendenwirbels.
Sch~tdel: Drei Metastasen im Schi~deldach von der GrSsse eiaes Fiinfcentimesstiickes, auf die Dura iibergreifend.
Gross- und K l e i n h i r n : Interstitielles Oedem~ keine Metastase.
t I i s t o l o g i s c h e U n t e r s u c h u n g des T u m o r s . - Auf Schnitten, die
parallel zur Langsachse des linken Hauptbronchus hergestellt wurden~ ist
der Uebergang yore gesunden Gewebe ins neoplastische deutlich wahrnehmbar. Im vom Carcinom erfassten Teile zeigt sich der Bronchus yon
einem schweren~ mit Riicksicht auf die Natur und die Dauer der Lungenerkrankung wohl begreifiichen Entztindungsprozess ergriffen; das submukSse
Gewebe ist stark infiltriert~ das zylindrische Flimmerepithel stellenweise
abgelSst oder zerstSrt~ doch zeigen die in den tieferen Schichten sitzenden
Drfisenacini keine VerRnderungen und die anatomische Strukmr der
Bronchialwand ist nicht deformiert. In dem Masse aber~ als die kleinzellige Infiltration dem neoplastischen Herde naher kommt, wird dieselbe
auch ansehnlicher; die Tubuli der Schleimdrfisen zeigen sich erweitert~
das Epithel ist grSsstenteils abgeschuppt und seine Reste liegen im Lumen
des Kanals angehiiuft; keine Wacherung~ weder typisch noch atypisch und
keine Karyokinese. Weniger tief und zwar dicht unter dem Bronchialepithel liegen grosse Zellen mit den iiblichen protoplasmatischen Farbstoffen intensiv tingierbar~ zu isoliert im Bindegewebe stehenden Haufen
vereinigt; nliher der Stelle der starksten careinomatiisen Wucherung verwandeln sich diese kleinen Schollen in dickere Striinge7 die sich his zum
Knorpel herabsenken~ anscheinend ohne irgend welchen Zusammenhang mit
d e n Schleimdriisen oder mit der Hauptmasse des Tumors.
Der Kern dieser Zellen ist gross, bl~schenfSrmig, selten in Karyokinese
begriffen, das Protoplasma reichlich, gut tingierbar~ mitunter einen dicken
Muzinklumpen enthaltend; hier liegen die Zellen fast tiberall um ungleichmiissige, den Drfisenalveolen Rhnlich sehende Hohlr~tume angeordnet, und
zeigen dann einen~ der Hohlfl~che des Alveolus zugekehrten, mit den das
Muzin farbenden Stoffen intensiv tingierbaren schmaleu Saum. In diesem
letzteren Anteil sind die in den frtiheren wahrnehmbar gewesenen DriisenkSrper nicht mehr sichtbar. Obe~J zeigt das Flimmerepithel keine Veranderungen, die yon den bereits beschriebenen abweichen.
Weiterhin aber schmelzen alle diese krebsigen Anh~tufungen zu einer
einzigen mit atypischen Zellen wirr durchsetzten Masse zusammen~ welche
die ganze Wand des Bronchus ersetzt, in das Lumen desselben in ungleichm!issiger Weise hineinwuchert und letzteres verengert; nur in den zwischen
den Erhabenheiten des Tumors liegenden Furchen sieht man zuweilen Reihen
yon Flimmerepithelien auf der diese von der darunter liegenden Neubildung
scheidenden Basalmembran gelagert. Die neoplastische Masse besteht nahezu
10
L. Stropeni, Fall yon bronchialem Adenocarcinom.
ganz aus Zellen mit sehr spiirlichen Trabekeln und aus mit filamentiisem
Schleim gefiillten ovalen Hohlraumen; Schleimklumpen finden sich auch
im Protoplasma maneher im Inneren yon massiven earcinomatSsen Strangen
gedr~ngt sitzenden Zellen. Der Charakter dieser Zellen ist in allem der
bereits angegebene.
In dem dem Bronchiallumen anliegenden Tell zeigt der Tumor deutliche Erosion and Nekrose sowie starke leukozytare Infiltration; in der Tiefe
reicht er his an die Knorpelringe heran, ohne jedoch dieselben anzugreifen:
er umgeht dieselbert und dringt dureh zwei benachbarte Ringe hindurch in
das darunter liegende Bindegewebe ein.
Hier tritt der Tumor nicht mehr als eine dicht gedrangte Masse
und ansehnliche Wucherung auf, sondern in der Form yon spiirlichen
Zapfen, welche mit Schleim angefiillte Alveolen begrenzen und durch weite
Bindegewebsbfindel mit wenigen darin eingelagerten Kernen voneinander
getrennt sind; lctztere zeigen welt um sich greifende Vorg/i.nge yon hyaliner
Entartung und Nekrose, yon denen haufig auch die neoplastischen Epithelialelemente betroffen sind. Oefters nimmt dieses Bindegewebe die typische
Muzinfarbung schwach an, als ob es selber die schleimige Entartung erfahren h~,tte oder mit Schleim durchtrankt ware.
Die gleichen pathologisch-anatomischen Veranderungen sind in den
anderen Nebenbronchien anzutreffen. Auf Querschnitten der sekundaren
und tertiaren Abzweigungen, dio eine Untersuchung des ganzen Bronchus
gestatten, sieht man, dass deE" Tumor nicht die ganze Bronchialwand ergriffen 7 sondern sich auf einen Teil derselben beschrankt hat und hierbei
etwas ins Lumen hineingewuchert ist, welch' letzteres dadurch verengert,
aber doch immer noch durchgangig geblieben ist; dagegen ist er in d i e
Tiefe gewachsen, fiber die Knorpel hinaus, ohne jedoch in dieselben einzudringen.
Makroskopisch untersucht~ hatte sich die Lunge als eine an vielen
Stellen atelektatische, zahlreiche HShlen enthaltende erwiesen; bei Untersuchung des in deE" Nahe dieser H6111en getegenen L u n g e n g e w e b e s mochten nun die Schnitte was immer fiir einer Partie der Lunge entnommen sein - - zeigte sich das Lungenparenchym stets in unkenntlicher
Weise verandert, so dass die Vermutung gerechtfertigt erschien, es sei
funk.tionsunfahig geworden. Ueberall bestand eine auffallige kleinzellige
Infiltration, fibrSse Bindegewebsstr[~nge, sehr zahlreiche Anhaufungen von
Plasmazellen, insbesondere um die Gefasse herum, difl[use Blutungen und
Verdickung des viszeralen Pleurablattes, welches nicht mehr mit Epithel
bekleidet, sondern in eine yon Krebsstrangen dnrchsetzte, mit neoplastischen
Schollen und Haufen yon Plasmazellen besate fibrSse Schwarte umgewandelt
war. Bei einer so reiehlichen Bindegewebswucherung waren die elastischen
Fasern in sparlicher Anzahl und nur um die 6efasse herum vorhanden;
L. Stropeni, Fall yon bronchialem Adenocarcinom.
11
viele dieser letzteren~ namentlich die grSsseren, waren dutch deutlich erkennbare in Organisation begriffene Thromben verschlossen, in denen es
mir aber niemals gelungen ist~ Krebszellen ausfindig zu machen. In der
Wand einer an der Lungenspitze befindlichen Kaverne habe ich zahlreiehe
Riesenzellen angetroffen yon dem gleichen Typus wie die L a n g e r h a n s schen der Tuberkeln; dieselben lagen neben einander gereiht am Rande
des Hohlraums 7 einige davon teilweise schon losgelSst~ als ob sie nahe
daran w'~ren ill letzteren hineinzufallen; es fehlten jedoch Epitheloidzellen
und Kaseifikationsvorg~nge.
In dem eine andere H~ihle umgebenden Gewebe liessen sich zwei Partien
deutiich yon einander unterscheiden: die eine der Pleura entsprechend aus
Bindegewebsbalken zusammengesetzt, yon Strii.ngen und Schli~uchen durchzogen~ die den bereits beschriebenen ganz Rhnlich waren; die andere war
dem Lumen der HShle zugekehrt und bestand aus mehrkernigen Massen,
Plasmazellen, zahllosen nekrotischen und nekrobiotischen Zellen mit nicht
tingierbarem Kern, aus kurzen Abschnitten yon Stiitzbindegeweb% ferner
aus einer diffusen Infiltration yon ahgeplatteten grossen Zellen mit scharf
begrenztem, polymorphem Protoplasma und blaschenf~hnlichem~ h~ufig in
Karyokinese begriffenem Kern; 5fter fanden sieh zwei oder mehrere Kerne
in der gleichen Zelle.
Offenbar handelt es sich um Krebszellen~ allein ihre Gestalt und vor
allem infiltratartige Verteilung war grundverschieden yon jener der fibrigen
Lungenpartien; bei fieissigem Nachsuchen war es jedoch mSglich, eine
deutlich ausgepragte Kontinuit~t und einen Uebergang yon einer Form in
die andere wahrzunehmen.
In den M e t a s t a s e n zeigte die Struktur der Neoplasie eine welt adenomatSsere Beschaffenheit als in der Lunge und entsprach im a|lgemeinen
den ersten Anffaben fiber die wiihrend des Lebens abgetragene kleine Gesehwulst. Ebenso in den fibrigen Hautknoten des Thorax und des Abdomens 7 in der Niere und in der Milz, wo aber auch zahlreieh% wohl auf
Embolie durch vom Blutkreislauf mitgerissene Tumormassen zurfickzufiihrende
Infarkte vorhanden waren.
lm H e r z e n war der Knoten an der Spitze gut umschrieben und
offenbar ein metastatischer; an der linken Kammer gingen die Zellhaufen
in jene des Lungenhilus fiber. Die Fasern des Myokards erschienen infolge
dieses Eindringens yon heterogenen Zel[en in Begleitung yon reichlichem
Bindegewebe auseinander-bzw, zusammengedr~ngt oder zerstSrt; das Endokardium war intakt~ das Epikardium hingegen gleiehfalls befallen und
stark verdickt, in gleicher Weise wie dies bezfiglich der Pleura beobaehtet worden.
In den Knochen~ namentlich am Femur~ befanden sich die Krebszapfen mitten in einem nekrotischen Gewebe mit ordnungs- und richtungslos
12
L. Stropeni, Fall yon bronchialem Adenocarcinom.
zerstreut liegenden Trabekeln an einem fibrtisen, zum grossen Teil in
schleimiger Entartung begriffenen Gewebe. Im Femur, an der Frakturstelle, war keine Spur yon Knoehenmark mehr erkennbar, aber die gleiche
heterogene, tumultuarische Struktur war sowohl an tier Peripherie als auch
in der Mitte der den Fraktnrherd verdeckenden fibrSsen Masse anzutreffen.
Das Mark der vom Tumor nicht ergriffenen Pattie zeigte den Typus des
gelben Marks, aber sonst nichts Bemerkenswertes.
Will man nun eine Diagnose stellen~ so glaube ich, man sei zur Annahme berechtigt, dass hier ein von den Schleimdrfisen der Bronchialwand
ausgegangenes A d e n o c a r c i n o m vorlag. Diese an und ffir sich sehr
seltene Art yon Tumoren wird yon einigen Autoren eifrig erSrtert und angezweifelt, namentlich yon Pass] er~ der nicht nut bei zwei seiner von ihm
mitgeteilten FaIle - - der histologischen Beschreibung nach, dem meinen
ahnlich - - einen glandularen Ursprung in Abrede stetlt~ sondern auch alle
frfiheren yon L a n g h a n s , T i l l m a n n , Beck, S t i l l i n g , H o y l e u. a. geschilderten entschieden in Frage stellt, obwohl die zwei ersten der genannten Autoren innige, unmittelbare Beziehungen der Schleimdriisen zu
den Krebsstrangen beschrieben hatten. Allerdings liefern viele der selbst
nach Erseheinen yon P a s s l e r s Arbeit als Carcinome der Schleiaidriisen
beschriebenen Falle so sparliche Anhaltspunkte ftir eine Diagnose, dass
einige Autoren, wie L. B. Meunier und L6vy redlich erkl'~rt haben, dass
,,cette origine admise par Chiari', Z i e g l e r , B i r s c h - H i r s c h f e l d , ne
peut 6tre aftirm6e d'une far
formelle."
Auch kann die Neigung der Epithelzellen zur Bildung schleimhaltiger
Acini wohl kaum dazu geniigen - - wenn auch Davis und Le C o u n t
noch gelegentlich eines neueren Falles dies angenommen - - uns yon dem
glandularen Ursprung des Tumors zu iiberzeugen. Denn, wie P $ s s l e r
scharfsinnig bemerkt und F r i e d l a n d e r experimentell nachgewiesen hat,
ist es einer Wucherung des Deckepithels der Bronchien wohl m6gli~h, eine
adenomatSse Struktur anzunehmen; andererseits ist es aber allgemein bekannt, dass auch im normalen Bronchialepithel kelchfSrmige Zellen zu
finden sind, we]che Schleim erzeugen.
Uebrigens ist das Bronchialepithel nicht gerade das einzige, welches
derartige adenomatSse Wucherungen darzubieten vermag, vielmehr kommt
diese Fahigkeit auch noch anderen Deekepithelien zu, wie z. B. jenem der
Gehirnventrikel und Plexus choroidei ( K a u f m a n n ) . Auch hier zeigen
sich Neoplasmen, die man mit Rficksieht auf ih,'e Struktur (Alveolen und
Infuudibuli mit darin enthaltenem Schleim, s o dass man - - wie im Falle
K a u f m a n n s - - an einen Darmpolyp erinnert wird) als Adenocarcinome
bezeichnet hat. In diesen Fallen ruft die Wucherung des Bindegewebsstromas die Anordnu~g ill Papillen und Alveolen hervor; dieselben k0nne,l
L. Stropeni~ Fall yon bronchialem Adenocaroinom.
13
dann infolge der schleimigen Degeneration des Bindegewebes selbst das
Aussehen yon Schleim enthaltenden R0hren und Schl'~uchen gewinnen, und
dies in einem Epithel 7 das~ normalerweise weder Driisen enth~lt, noch
iiberhaupt eine Schleimabsonderung aufweist.
Es kiinnte daher die Diagnose Adenocarcinom leichtfertig erscheinen.
Im vortiegenden Fall aber hat die genaue Untersuchung der Neubildung
und ihrer Metastasen jeden Zweifel an der Entstehung des Tumors aus den
Schleimdrfisen beseitigt. Denn nicht nur in den neugebildeten Schlliuchen,
sondern auch in durchaus atypischen Zellen sowohl in der Lung% als auch
in den Knoten anderweitiger Organe - - ist Schleim enth'dten~ ein Befund~
der dem yon T r a i n a neuerdings beschriebenen (Kolloidtropfen in atypischen
Zellen eines Carcinoms der Schilddriise) vollkommen entspricht. Hier kann
somit ffir die Gegenwart yon Schleim nicht eine Entartung des Stiitzbindegewebes~ sondern nur die T~tigkeit der Zellen selbst verantwortlich gemacht werden.
Es kiinnte jedoeh die Vermutung aufsteigen, dass diese Zellen yon
den kelchfSrmigen des •ronchialepithels herstammten~ welche letzteren~
wie im Falle H e l l y s , sich gleichfalls in den neugebildeten Strangen finden
kSnnen. Allein in den oben beschriebenen adenomatSsen Alveolen findet
sich Schleim in allen den Sehlauch umlagernden Elementen~ sowie in jenem
Tell derselben, der dem Lumen des Kanals zugekehrt ist, was darauf hindeutet, dass die schleimbildende Tiitigkeit nieht einzig nnd allein auf
einige Zellen der Neoplasie beschriinkt~ sondern eine samtlichen Zellen
zukommende ist.
In Anbetracht nun dieser Befunde, in Anbetracht des Umstandes, dass
hier Flimmerzellen~ wie solche doch in F~tllen yon Neubildung des bronchialert Deckepithels beschrieben wurden, fehlten~ in Anbetracht vor allem des
fast in jeder Gegend so ausgesprochen glandulliren Baues de," Geschwulst~
trage ich kein Bedenken~ obige Diagnose auf: Adenocarcinom~ yon
den Driisen der B r o n c h i a l w a n d h e r s t a m m e n d , ffir die einzig zul~ssige zu halten.
An einigen Stellen hat dieses Adenocarcinom, ein bei Drfisenkrebsen
nicht seltenes Vorkommnis~ seine adenomat6se Struktur eingebfisst und
dessert Bestandteile zeigen sich dann, wie ich bereits angegeben~ in Form
einer diffnsen Krebsinfiltration mit polymorphen haufig mosaikartg angeo,'dneten Zelle% g-~nziich verschieden yon jenen~ die Strange bzw. Alveolen bilden.
So erkliirt sich de,m auch~ wie eine Neoplasie bronchialen Ursprungs,
wenn sie den obeu angegebenen Typus aufweist~ noch mehr aber~ wenn
sich die Zellen i,1 den Lungenalveolen anhiiufen~ oder auch nur eif6rmige
Klumpen in der veriinderten Lunge bilden, als eine yon den Epithelien der
Lungenalveolen herstammende angesprochen werden kaun, falls es nicht
14
L. S t r o p o n i, Fall yon bronohialom Adenocarr
gelingt -- wie i m Falle H e l l y s und in dem aIlerj.'fingsten yon R a v e n n a
die sonst so wenig nachweisbaren urspriinglichen Verttnderungen der
Bronchien zu Gesicht zu bekommen.
Denn, ist auch Wolfs Angabe, - - es sei die Diagnose auf Bronchialcarcinom an makroskopisehen Schnitten leieht zu stellen, wegen der daran
sichtbaren entlang der Bronchienverzweigungen fortschreitenden Neoplasie
eine zutreffende, so ist sie es doch nieht in absoluter Weise und
wtirde die praktisehe An.wendung der yon D a l L a g o zitierten Angabe
L a r d i l l o n s - - es sei bei der Differentialdiagnose zwischen Bronchialund Langencarcinom das erste und grSssere Gewicht auf die makroskopischen Befunde zu legen - - unfehlbar za lrrttimern fiihren. Nur eine
genaue mikroskopische Uatersuchung vermag den Ursprung dieser Neubildungen zu ermitteln und hli.uiig ist auch auf diese Weise nur eine Wahrscheinlichkeitsdiagnose mSglich, oder es l~sst sich eine Diagnose tiberhaupt
nieht formulieren, wie im Falle P e p e r e s , wo die anscheinend in Hepatisierung begriffene Lunge in Wirkliehkeit in eine Zylinderzellen enthaltende
Krebsmasse umgewandelt war, sowie in dem yon L 5 h l e i n mitgeteilten,
einen cysto-papillaren Lungentumor betreffend.
Die grosse N e i g u n g zu Metastasen und die Ausbreitung dersr
in
die verschiedenartigsten Organe, sogar bis in das Gehirn~ ist, wie dies auch
neuerdings B u d a y und K a r r e n s t e i n dargetan haben~ ein Priirogativ des
Bronchialcarcinoms; vielleicht ist dieselbe~ wie W o l f annimmt~ bedingt
durch die rasche Invasion der peribronchialen Driisen, sowie durctl das
leicht mOgliche Eindringen in die Blutgefiisse.
Gleiehfalls sehr hi~ufig ist auch noch die schleimige Entartung des
Stfitzbindegewebes des Tumors und der Metastasen von Carcinomen anderweitiger Schleimhi~ute, namentlich des, Magens ( L a d e n ) . Es bewahrt sich
hier nur einfach das Gesetz~ dass den Krebsmetastasen die Fi~higkeit zukommt~ das ursprfingliche Gewebe nicht ntir in bezug auf Struktur~ sondern
aueh in bezug auf die Faaktion der einzelnen Zellen zu reprocluzieren;
ebenso sehr haufig ist auch das Vorkommen yon Kolloid in den metastatischen Zellen von Schilddrfisenkrebsen ( F l a t a u und K o e l i c h e n ,
T r a i n a n. a.).
Es kann somit in manchen Fallen ziemlich leicht gelingen~ mit Riicksicht auf die Untersnchung einer Metastase zur Diagnose der prim~ren Gcschwulst zu gelangen, wenn auch nicht genau bezfiglich der Stelle ihres
Sitzes -- wie dies eben in] vorliegenden Falle mSglich gewesen - - doch
wenigstens beziiglich des Organs~ wo sic ihren Ul~prung gehabt hat.
Recht selten mfissen aber jene Fii.lle sein - - und mir ist es aucl~ tats~chlich bisher nicht gegliickt~ einen derselben kennen zu lernen - - , in
denen~ wie im vorliegenden 7 es gehmgen w,tre, auf Grund der histologisehen
Untersuchung einer Hautmetastase den Ausgangspunkt der Geschwulst genau
-
-
L. Stropeni, Fall yon bronchialem Adenocarcinom.
15
festzustellen; bei unserer Kranken ist niimlich die Provenienz der Neoplasie
yon der Bronchialwand eben im Hinblick auf die Ergebnisse der mikroskopischen Untersuchung der Metastase diagnostiziert worden 7 Ergebnisse,
die auf eine Entstehung aus einem Schleimdrfisen enthaltenden Organ hinwiesen.
Die Sache ware an und ffir sich kein gar so seltenes Vorkommnis,
wenn nicht - - wie Daus und P e t r i dargetan haben - - die Hautmetastasen
yon Carcinomen der Innenorgane eine ausserordentlich grosse Seltenheit
waren. Speziell bei Lungencarcinomen aber hat sich besagtes Vorkommnis
als ein h6chst seltenes erwiesen, und auch in den neusten Zusammenstellungen yon selbst zahlreichen F~illen (Watsuji 6 F~ll% B u d a y 11,
K a r r e n s t e i n 32) findet sich davon kein einziger.
II. Klinischer Teil.
S'~mtliche Autoren 7 die sich mit der Symptomatologie des Bronchialund des Lungencarcinoms befasst haben~ haben sich fibereinstimmend dahin
ausgesprochen, dass die Zeichen dieser Erkrankung i~usserst unbestimmt
und bei einer ganzen Reihe anderer Krankheiten anzutreffen sind und dass
kein Syndptom ein pathognomonisches ist - - ausgenommen vielleicht die
Gegenwart yon Tumorfetzen im Sputum --, was jedoch auch bei einem Car~inom des Mediastinums vorkommen kiinnte, wenn dasselbe nach Perforation
des Bronchus Ausli~ufer in diesen letzteren hineintreibt.
So ~tussert sich
in diesem Sinne schon E b s t e i n in seinem grundlegenden diesbezfiglichen
Aufsatz, und dieser Ansicht huldigen noeh andere neuere, nicht minder
hervorragende Autoren ( A u f r e c h t , H o f f m a n n , B e n d a , Q u e i r o l o ) .
Wenn nun also Verlauf uud Anamnese kein Licht in die Sache bringen, so
kann begreiflicherweise eine Diagnose iiberhaupt nicht oder nur mit grosser
Unsicherheit gestellt werden.
In diesem meinen Falle eben sind weder die anamnestischen Angaben,
noch - - eine lange Zeit hindurch - der Verlauf dazu geeignet gewesen,
eine genaue Diagnose zu erm6gtieheo.
Denn der Beginn der Krankheit, die friiher bestandene Pleuritis, das
Vorkommen eines Falles yon Tuberkulose bei Kollateralverwandten, die
Lokalisierung der Erkrankung links, w:,'~hrend, wie dies auch durch die
neusten Statistiken ( H a b e r f e l d ) erwiesen ist, das Carcinom viel haufiger
rechts zustande kommt als links, die Retraktion der Spitze, dos Vorhandensein yon Zerst6rungsherden, das Fehlen yon Drfisenanschweltungen an der
Achsel u n d d e r Supraklavikulargrube, das eitrig-schleimige, sp-~rliche Blutstreifen enthaltende Sputum, vor allem aber dos verhRltnism~tssig jugendliche Alter der Kranken, sowie das Verhalten des Fiebers, alles dies bildete einen symptomatischen Komplex, der die Diagnose auf Tuberkulose
lenkte.
16
L. Str op e ni 7 Fall yon bronchialem Adenocarcinom.
Freilieh erschien die M6glichkeit eines Carcinoms durch diese Gesamtheit yon Symptomen keineswegs in formeller~ absoIuter Weise ausgeschlossen~
denn die Kasuistik dieser Form weist woh] Typen auf, bei denen derartige
Erscheinungen in grSsserer oder geringerer Zahl nebeneinander vorkommen
kSnnen, so dass die F~lle yon Lungenneoplasie grSsstenteils mit der
Diagnose: Tuberkulose oder mit der mehr allgemeinen yon Lungenschwindsucht zur Obduktion gelangten. Was das Alter. angeht~ so findet sich je
ein Fall yon Lungenearcinose bei einem 7jlihrigen M~t~tchen ( N u s c h e l e r )
und einem 51/2 Jahre alten Knaben (Mac Aldowie) verzeichnet. Mit
Rficksicht auf die unendlich gr~ssere Frequenz der Tuberkulose im Vergleich zu den Lungenneoplasien und auf dte ziemlich genaue Uebereinstimmung der Befunde hatte die Tuberkulose die grSssere Wahrscheinlichkeit fiir sich.
Allein eine Reihe anderweitiger Momente stand mit diesem Urteil in
Widerspruch, so der negative Ausfall der Tuberkulinreaktion~ die Abwesenheit yon Bazil]en und elastischen Fasern im Sputum: die negativ
ausgefaliene Probe bei dem mit dem Auswurf inokulierten Meerschweinchen.
Beziiglich der Kutanreaktion gibt es bekanntlich Fiille yon fortgeschrittener Tuberkulose, wo diese Reaktion ausbleibt; aber das "trotz der
wiederholt angestellten mikroskopischen Untersuchung konstante Fehlen
yon Tuberkelbazillen hatte gegen das Bestehen eines tuberkulSsen Prozesses kein geringes Gewicht, um so mehr aber als das Sputum einer oftmaligen Prfifung unterzogen worden war, unter anderem auch in der Hoffnang~ Tumorfragmente darin zu finden, ja, gelegentlich habe ich sogar die
dichteren Klumpen des Auswurfs in Paraffin eingebettet; das Sputum wurde
zuerst in eine Eprouvette gebracht~ darin absetzen gelassen, hierauf der
Boden der Eprouvette eingeschlagen; die dabei heraustretenden Klumpen
wurden mit der Schere durchschnitten und in die Fixierflfissigkeit (Alkohol
oder Sublimat) fallen gelassen. Auf diese Weise bekam ich Massen, die
hinreichend derb waren~ um weitere Manipulationen zu vertragen; die
Schnitte wurden nach W e i g e r t s Verfahren ffir elastische Fasern behandelt und nach G r a m , L S f f l e r und Koch ffir die Mikroorganismen
neugefarbt.
Neben diesen Argumeaten gese]lte sich zur Unsicherheit noch ein
drittes~ welches innerhalb gewisser Grenzen den Gedanken an eine Lungenneoplasie reehtfertigen machte: ich meine namlich die Thoraxd~tmpfung
bei normal grossem Weilschen Raume, die Retraktion des Thorax und die
normale Lage des Mediastinums.
Allein alle diese Erscheinungen sind auch teilweise bei Brustfellentzfindungen in dem Adh~isionen und Retraktionen aufweisenden Stadium
anzutreffen. Al[erdings brachte eine so schwere und insbesondere so ungleichmiissige Retraktion des Thorax~ wie sie sich eben in unserem Falle
L. Stroponi, Fall yon bronchialem Aclenocarcinom.
17
darstellte, jenes Symptom der Krebsinflltration in Erinnerung, das yon
W a l s h e beschrieben, yon Z a g a r i bekltmpft und in seiner theoretischen
Grundlage erschiittert, yon Q u e i r o l o wieder best'9.tigt und unter dem
3~amen ,,Walshesches Symptom" zu neuer Geltung gebracht und schliesslich in einer Reihe von Fallen yon Neoplasie der Pleura bzw. der Lunge
(Dean, D. Lewis~ B e z z o l a , C a l a b r e s e u. a.) nachgewiesen worden ist.
Dabei daft jedoch nicht vergessen werden, dass in den meisten dieser FMle
gleichzeitig mit der Retraktion auch noch ein 5fter reichliches hamorrhagisches Exsudat bestand, w~hrend in uaserem Falle es nur mit Mfihe gelungen war, 2--3 ccm einer meistens vollstlindig serSsen Fliissigkeit herauszubekommen. Es fehlte somit in diesem Falle jener scharfe, sofort auffallende, ffir die Carcinomdiagnose einen vortrefflichen Anhaltspunkt
bietende Gegensatz zwischen der Retraktion des Thorax und dem Vorhandensein eines Ergusses. Wenn fiberhaupt, hiitte hier also ein ,,Cancer
en cuirasse" angenommen werden mfissen.
Etwas aufgehellt wurden diese ziemlich dunklen Verh'~ltnisse dutch
zwei neu hinzugetretene wichtige Vorkommnisse: das Auftreten des Hautkn6tchens und die Fraktur des Femurs. Freilich hatte man, bevor das
Ergebnis der mikroskopisehen Untersuchung des Hautknotens bekannt geworden~ die Fraktur dutch die - - wenn auch etwas kfinstliehe - - Annahme
einer direkten traumatischen Einwirkung erkIi~ren kSnnen, letztere etwa
bedingt durch eine pliitzlich ausgefiihrte Bewegung, die schon an und fiir
sich hingereicht hii.tte~ bei einem bereits seit lange bettliigerigen, wenig
genlihrten, durch zahlreiche Sehwangersehaften geschwiichten Frauenzimmer
einen Knochenbruch zu veranlassen. Und dies umsomehr, als al|e Versuche
dureh tief eindringende Probepanktionen an der Frakturstelle eineu Krebsherd festzustellen, fehlsehlugen und andere Zeichen einer Markneoplasie,
wie Albumosurie, speziel] aber die eharakteristisehen Blutmerkmale vermisst wurden, und ein so geringer als eine Folge der Frakmr leichter zu
deutender Prozentsatz an Myelozyten doch nieht zu diagnostisehen Schltissen
berechtigen konnte.
Bekanntlich sind in einem Teile der F'~lle von Knoehenmarkca,'einose
die Verli.nderungen des Blutbildes derart ausgesprochen und h~ufig so imponierend, dass sie sogar - - wie im Falle R o t k y s -- die Erseheimmgen
der perniziSsen Ani~mie darbieten kSnnen.
Die mit hi~matologischem Befunde ausgestatteten F~ille yon Krebsmetastase des Kn0chenmarks sind allerdings selten, doch kSnnen gewisse
eigentfimliche Verlinderungen der Blutkrasis auch schon an und ffir sich
eine Diagnose gestatte n.
Entscheidender war das Ergebnis der Untersuchung der kleinen Hautgeschwulst, so dass es nunmehr nieht sehwer gelang, auch die fibrigen
Symptome zn einem harmonischen, eine sichere Diagnose gewlthrleistendea
Zeitschrift f f r Krebsforsehung.
9. Bd.
1. Heir.
.o
18
L. Stroponi, Fall yon bronchialem Adenocarcinom.
Ganzen zu vere!nigen. Selbst jene Vorkommnisse, die den Zweifel am
Vorhandensein einer Neoplasie zu rechtfertigen s c h i e n e n - wie der Fieberverlauf und das ganzliche Fehlen yon Krebmassen im Sputum - - erschienen
nun aufgekl~rt.
Es stimmte n~mlich der Fieberverlauf mit der Zerst6,'ung der Lunge
und der Sekretstauung in den Bronehiektasien und Kavernen mit konsekutiver, durch die dabei eingetretenen autolytisehen Vorg'~nge (F. MUller)
und die T~tigkeit der Bakterien bedingter Resorption pyrogener Produkte.
Das Fehlen yon Krebszellen im Sputum kann mit Rficksicht auf die
geringe Zahl der F'~lle, ill denen sic angetroffen wurden wohl kaum befremden. Denn, wahrend manche Autoren, wie E o k e r s d o r f f , behaupten,
dass, wenn man nach denselben mit der gleiehen Beharrlichkeit suchen
wfird% wie dies bezf@ich der Kochsehen Bazillen zu geschehen pflegt,
sic gewiss sehr h~ufig anzutreffen waren, behaupten ander% wie Wolf,
sogar, dass ,,der nach oftmaliger Untersuchung des Sputums erlangte negative Befund gerade ffir Carcinom pathognomonisch ist." Wie Wolf ausfahrt, wird die Permeabilitfit der Bronchien durch die Druckwirkung cter
vergr6sserten Lymphdr~isen sehon fraher beeintr'~ehtigt als das Carcinom
an und far sich so welt gewaehsen ist, dass es die Durchgangigkeit der
Bronehien in Frage stellt. Es tritt infolgedessen eine zylindrische Erweiterung der feineren Bronchien mit Sekretstauung ein; im Sekret sammeln
sieh hierauf die Entziindungskeime an, wodurch pu~ride Bronchitis und
bronchiektatische Kavernen zur Entstehung kommen, indem sich nun dieselben in einen Bronchus ~ffnen, erzeugen sic ausgedehnte ZerstSrungen des
Lungengewebes und aueh des neoplastischen Gewebes selbst. Daher kommt
es, dass man zwar zuweilen Tumorfetzen im Sputum vorfindet; h'~ufiger
aber dieselben so tiefgreifende Veranderungcn erfahren haben, dass es nicht
mehr gelingt~ sic zu identifizieren. So halle in dem Falle E c k e r s d o r f f s
wo sich im Schleimsekret des Hauptbronchus einer Leiche, Krebsnetze~
Zapfen und grosse polymorphe Zellen vorfanden - - der Tumor keinerlei
Ver~.nderungen im Lumen der Bronchien hervorgerufen, so dass die unmittelbar vorher abgel~sten Tumorpartikel mit dem Auswurf herausbefSrdert
werden konnten; in den F~llen H e r r m a n n s handelte es sich entweder
um weiehe, medull~re Tumoren, die, am Hilus in die Bronchien eingedrungen, ausserst leicht zerfallen konnten (Fall I und IV), oder um
Oarcinome der peripheren Teile (tier Spitze, Fail I): in den FMlen,
wo die Konsistenz eine harte und der Tumor am Hilus lokalisiert war
(Fall II und III und in einem Fall yon W e i n b e r g e r ) , so dass er zur
Bronchostenose und Sekretstauung Anlass gab, wurde im Sputum nicht
vorgefanden.
Was das Fehlen yon ausgepr~igten, dureh die Knoeheametastasen bedingten h~matologisehen Merkmalen angeht, so glaube ich wohl kaum, es
-
-
L. Stropeni~ Fall yon bronchialem Adenocarcinom.
19
lasse sich hier die fiir den so oft zitierten Fall yon N o t h n a g e l gegebene
Erkl~rung heranziehen - - dass nitmlich das Knochengewebe veto neoplastischen ggnzlich eingenommen und dutch dasselbe ersetzt worden; im
vorliegenden Falle waren die Knoehenmetastasen auf das Femur und auf
eine geringe AnzahI Wirbel beschr~tnkt, und die mikroskopische Untersuchung des Marks verschiedener Knochen sowie der in der N~he des
Tumors gelegenen Teile hat es erm6glicht, festzustellen, dass die Neubildung nicht jene Ausbreitung erlangt hatte, die man im Hinblick auf das
Fehlen yon charakteristischen Kundgebungen im Blute h'~tte erwarten
k6mmn. Zu]~ssiger erscheiut bier wohl eher die Annahme einer schwachen
Reaktion seiteus des Knochenmarks, gesteigert unter anderem auch dutch
die im Laufe befindliche Krankheit.
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Fall yon bronchialem Adenocarcinom.
21
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Figur I. Durchschnitt oines Bronchus. Uebergangspunkt vender hypertrophische
Driisen enthaltenden Schleimhaut ins neoplastische Gewehe. Das Bronchialepithel ist wohl yon der unterstehenden Tumormasse abgrenzbar.
SchleimfErbung mit Meyers Muzikarmin. Obj. 35 mm apochr. Zeiss, Ok. 3.
Figur 2. Metastatischer Knoten der Leher: Atypische Alveolen yon Schleim erfiillt; neoplastische Zellen Schleimklumpen einschliessend. Obj. 4 mm
Zeiss, Ok. 4 kemp.
FJgur 3. Lungenschnitt mit neopIastischen Elementen infiltriert. Obj. 4 mm Zeiss,
Ok. 4 kemp.
| |
https://openalex.org/W4384038901 | https://revistas.ufpi.br/index.php/entrerios/article/download/14250/8608 | Portuguese | null | Interlocuções esportivas: uma dobradinha entre Brasil e Argentina | Revista EntreRios | 2,023 | cc-by | 9,031 | Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Mariane da Silva Pisani
Doutora em Antropologia - Universidade Federal do Piauí. Monica da Silva Araujo
Doutora em Antropologia - Universidade Federal do Piauí. Mariane Pisani: Primeiramente agradecemos a disponibilidade de vocês em nos
conceder essa entrevista. Em segundo lugar, gostaríamos de pedir que vocês falem
sobre as suas trajetórias acadêmicas, abordando um pouco dos principais trabalhos
escritos, conceitos desenvolvidos e utilizados. Estamos pensando, de maneira mais
específica, em uma aproximação das Ciências Sociais com as práticas esportivas e de
lazer. Verônica Moreira: Bom, no meu caso eu gostaria de destacar o primeiro trabalho
desenvolvido a partir da minha tese de Licenciatura em Antropologia, pela Faculdade
de Filosofia e Letras da Universidade de Buenos Aires que eu defendi no ano de 2001. A minha pesquisa foi sobre e com os torcedores do Clube Atlético Independente. Eu
comecei essa pesquisa em 1998/99, e como estava realizando o meu primeiro trabalho
de campo, me custou bastante começar e saber o que eu queria fazer. Finalmente fiz
esse trabalho com as pessoas que integram o que, popularmente, se conhece como
"Barra Brava", o grupo de torcidas vinculadas principalmente à expressão da violência. Na Argentina, o movimento dos Barra Brava é considerado um problema gravíssimo sem
que se consiga chegar a uma solução. Revista Entrerios, Vol. 5, n. 2, p. 99-116 (2023) 99 Então, naquele momento, a pesquisa em campo foi me levando a esse grupo em
particular e eu fui me interessando muito em saber como se organizavam. Eles tinham
uma estrutura muito complexa, uma estrutura hierárquica e também territorial dividida
por bairros, e eu procurava entender como se organizavam, como as lideranças eram
construídas e como legitimavam essa posição de autoridade. Logicamente também
apareceu uma categoria que é típica na Argentina denominada “aguanter”, que é uma
categoria por meio da qual os torcedores constroem sua identidade e que possui
múltiplos significados associados à "barra" de futebol. O seu significado se refere às
práticas de combate, de pôr o corpo nos enfrentamentos físicos. Também era muito
típico nesse momento a prática do roubo de certos objetos entre as torcidas, sendo o
mais significativo o roubo das bandeiras. Então, para recuperarem a bandeira deviam
mostrar que tinham “aguanter”. Não era só recuperar a bandeira, mas também roubar
a bandeira alheia. Eu interpretei tudo isso utilizando a teoria da honra e da vergonha,
também muito discutível e típica da antropologia mediterrânea. Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Ou seja, eu estava
pensando em como esses "jogos de recuperação dos bens" tinham a ver com a ideia de
construir uma honra e também a vergonha, ou deixar em estado de humilhação o grupo
rival. Então, essas práticas levavam as torcidas, de maneira constante, a um círculo de
violência. As políticas públicas ao serem feitas e para que sejam efetivas precisam
compreender essas lógicas dos “aguanters”. Essa foi a minha primeira investigação e
depois continuei com uma pesquisa independente, pensando mais na questão de como
era a política no interior da instituição. Os clubes na Argentina são associações civis
sem fins lucrativos e isso faz com que a cada dois, três ou quatro anos, realizem eleições
no clube para eleger autoridades. E aí se armam campanhas políticas, os sócios e as
sócias se organizam para apresentar um candidato para liderar alguma lista em
particular. Então, me interessava pensar na política no ponto de vista dos sócios e das
sócias, e também, no que destaca a literatura do Brasil, pensando no tempo da política,
em como se armava o tempo de campanha eleitoral no clube, o momento em que
acontecia a política, das conversações entre os torcedores, os sócios e as sócias, além
dos dirigentes. O interesse por esse tema também foi esculpido no momento de defesa
da minha tese, quando um antropólogo que trabalhava com a temática, Fernando Alvim,
me questionou sobre o rigor em que se construíam os momentos políticos nas “barras”. Ele me perguntou se parecia um recorte de tempo onde a política aparecia ou se haviam
movimentações políticas de maneira cotidiana. Ou seja, como se houvesse uma
construção momentânea ou se a política estava sempre presente. Depois, na tese de
doutorado trabalhei pontualmente com os dirigentes de futebol pensando, por exemplo, 100 Pisani; Araujo na relevância que tinha o conceito de território para a construção do perfil dos dirigentes. O Club Atlético Independiente3 esteve sempre em uma cidade muito ao sul de Buenos
Aires e a relação entre o clube e o território é muito forte. Os dirigentes historicamente
eram pessoas conhecidas na cidade. Pessoas, por exemplo, que atuavam em profissões
liberais: advogado, médico ou comerciantes. E no momento em que eu fiz esse trabalho
de campo, aproximadamente entre 2007 e 2008, isso já estava se modificando. 3 Clube de futebol da Argentina, fundado em 1905 que tem sua sede social e seu estádio na cidade de
Avellaneda, Província de Buenos Aires. Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Haviam
pessoas com esse perfil tradicional, por exemplo, Julian Brandon que foi presidente do
ALFA durante 33 anos e também dirigente do Independiente. Era uma pessoa
empresária ou comerciante que entrou como dirigente e depois se converteu em
presidente da ALFA. No momento em que eu comecei a fazer o trabalho de campo isso
começou a se modificar, e o que eu compreendi era que estávamos em um ponto em
que havia dirigentes com o perfil mais tradicional e outras pessoas que poderiam ser
classificadas como “outsiders”. Há um capítulo na tese em que discorro sobre como nas
“barras” algumas pessoas estabeleciam relações de clientela com os dirigentes, ou seja,
que essas relações de clientela não eram unicamente um “toma lá, dá cá" de dinheiro
por apoio político, mas como estavam também atravessadas pelos afetos e pelas
realidades destes torcedores. Luiz Rojo: Diferente da Verônica, o início da minha trajetória na Antropologia não passa
pela Antropologia dos Esportes, do estudo dos esportes. Eu fiz a minha dissertação de
mestrado, e depois a tese de doutorado, discutindo fundamentalmente a questão das
amizades, esse era o meu tema central de pesquisa. No mestrado eu estudei as relações
de amizade entre estudantes de Medicina, e ali eu desenvolvi um conceito de “amizade
grupal”, porque até então a teoria sobre relações de amizade privilegiava os estudos,
praticamente todos, lidando com sociedades ocidentais, com muito pouca discussão de
amizade fora desse registro, e acabava se desenvolvendo uma noção de amizade a partir
de uma relação pessoa-pessoa. Então, não se pensava a ideia da amizade para além
dessas escolhas individuais, mesmo quando isso envolvia um leque de outras relações. E o que eu percebi dentro dessa pesquisa é que a ideia do grupo de amigos, a amizade
que se desenvolvia dentro do grupo, era muito mais relevante para aquelas pessoas do
que as relações de amizade um-a-um. Muitas vezes, fora daqueles espaços grupais
praticamente não havia interação individual, dois-a-dois. Em todos os momentos, não
só na universidade, - até para pensar nos caminhos e escolhas comuns - mas também
nos aniversários, nos eventos sociais da vida do centro acadêmico, as relações eram 101 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina sempre do grupo como um todo. Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Chegando ao ponto em que para alguém chegar ao
grupo não bastava ser apresentado por uma das pessoas do grupo, mas tinha que ser
incorporada ao grupo como um todo. Essas ações tornavam esse grupo com fronteiras
muito bem definidas. Quando eu terminei o mestrado, tendo desenvolvido um pouco
esse conceito, a minha ideia era buscar continuar esse estudo sobre amizade, mas agora
em um lugar em que a ideia de grupo tivesse mais consolidada, tivesse mais afirmada. Acabei conhecendo por acaso em uma revista uma comunidade naturista no Rio Grande
do Sul e que apontava muito para essa ideia dos naturistas como um grupo muito coeso,
muito fechado. Fiz minha tese de doutorado lá, trabalhando novamente o conceito de
amizade, mas também acabei me dando conta de que por ser uma comunidade naturista
eu tinha que trabalhar com o conceito de comunidade e corporalidade. Foi a partir
desses dois momentos que conheci e me aproximei da professora Simone Guedes4. Isso
aconteceu no finalzinho do meu doutorado, por acaso em uma Reunião de Antropologia
do Mercosul, na cidade de Florianópolis. Começamos a conversar sobre essa questão do
esporte e ela me convidou para fazer parte de uma rede mais ampla de pesquisas. Assim, logo que terminei meu doutorado, em 2005, eu participei da minha primeira
Reunião Brasileira de Antropologia, na cidade de Olinda. Ali fui trazendo, pouco a pouco,
as discussões que tinha realizado sobre amizade no mestrado e no doutorado. Para além
da questão das relações sociais, trabalhei com a ideia da amizade como emoção. Eu
trabalho com um referencial teórico para pensar como que as narrações, os comentários,
as colunas jornalísticas, em época dos jogos olímpicos, construiu o discurso sobre a
identidade nacional, sobre gênero, sobre questões étnico-raciais… Então, é o meu
primeiro trabalho discutindo a questão do esporte pensando, principalmente, a partir da
Catherine Lutz e da Lila Abu-Lughod, duas teóricas na Antropologia das Emoções e que
pensam a emoção como sendo construída no contexto em que ela está sendo
vivenciada, não como uma coisa meramente interna, quase que biológica . Então, eu
utilizei essa literatura para pensar o contexto dos eventos esportivos. 4 Simoni Lahud Guedes (1950 - 2019), antropóloga brasileira, professora da Universidade Federal
Fluminense e pesquisadora da área de Antropologia do Esporte. Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina A partir daí a
relação com a Simone se aprofunda, ela vai me supervisionar no pós-doutorado e,
seguindo esta minha preocupação, minha busca por esses esportes olímpicos, por não
pesquisar futebol, eu acabo fazendo um projeto comparativo entre o Rio de Janeiro e
Montevidéu para estudar a questão do gênero no hipismo. Principalmente motivado pelo
fato de que o hipismo é o único esporte olímpico, talvez o único esporte de todos, do
qual não há nenhum tipo de separação de categorias entre homens e mulheres. Todas Pisani; Araujo
4 Simoni Lahud Guedes (1950 - 2019), antropóloga brasileira, professora da Universidade Federal
Fluminense e pesquisadora da área de Antropologia do Esporte. 102 102 Pisani; Araujo as provas são necessariamente mistas. Então eu fui estudar essa relação do gênero
dentro do hipismo, isso acabou me motivando depois para a pesquisa posterior na vela,
na qual eu vou aprofundando a questão dos debates entre sexo e gênero, a partir da
noção de performance da Judith Butler, mas com uma leitura do conceito que eu sei
que é muito particular. Então, eu vou pensar o quanto que essas performances, quando
repetidas em determinados contextos,- dialogando com a “Catherine Lutz” e com a
“Abu-Lughod” - acabam por produzir gênero. E isso eu já tinha discutido na pesquisa do
hipismo quando transformo categorias nativas, como as modalidades de salto e
adestramento, em categorias analíticas de gênero. Eu discuto que o salto e o
adestramento seriam dois gêneros dentro do hipismo porque eles produziriam
performances próprias e, naquele contexto específico, independeria se era o caso de
um cavaleiro ou uma amazona. Ou seja, cavaleiros e amazonas performariam uma
identidade de gênero específica quando no momento do convívio ali, não apenas da
prova em si, mas em todo o convívio dentro do ambiente. Na pesquisa da vela que está
para ser publicada agora como livro, e que eu espero que saia já no início de 2023, eu
vou trabalhar a partir do conceito que é bastante utilizado de sociabilidade,
homossociabilidade e heterossociabilidade, mas eu vou transpor isso para um conceito
de sociabilidade “homo gênero” e sociabilidade “hétero gênero”, ou seja, pensando e
discutindo como que esses conceitos de homossociabilidade acabava reifincando o sexo:
homem e mulher. Um grupo de homens juntos seria uma homossociabilidade? E eu
coloco: “mas se essas pessoas forem de gêneros diferentes?”. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Ou seja, já havia trabalhado com aficionados, sócios, dirigentes, então acreditei
que era o momento de trabalhar com atletas. E em um esporte que para mim era muito
desconhecido. Pelo menos para mim, quanto mais estranho, melhor. Então, o fato de
eu ter escolhido o boxe como um esporte para investigar tem a ver com isso, com não
entender nada do que estava acontecendo no ringue.. E falando agora em dimensões,
creio também que o que acontece, pelo menos junto à Universidade de Buenos Aires,
no Instituto de Investigação Gino Germani da Faculdade de Ciências Sociais, é que o
grupo segue sendo pequeno. Não é um grupo como eu vejo que funciona no Brasil, com
grupos ou núcleos de pesquisa de diferentes universidades. Eu penso que o Brasil está
muito adiantado com o tema. Por exemplo, fazem apenas cinco anos que explodiu toda
a discussão sobre gênero e sexualidades aqui na Argentina. Vocês já estavam discutindo
isso faz tempo. E há outra pergunta que você havia feito, Mônica… Mônica: Vocês dois acabaram falando sobre algo que já estava previsto na entrevista,
que é como vocês foram construindo as suas trajetórias rumo à Antropologia dos
Esportes. Gostaríamos que vocês falassem sobre pertencimento acadêmico, sobre os
grupos de pesquisa aos quais estão associados, de qual lugar estão produzindo ciência. Além disso, o que vocês pretendem pesquisar e desenvolver em um horizonte próximo? Verônica Moreira: No meu caso, faz tempo que eu quero realizar um trabalho sobre
o boxe. Idealizo isso já faz um tempo. Na RAM de Curitiba, em 2011, apresentei um
trabalho sobre isso. Por diferentes motivos, não realizei esse trabalho de campo com
regularidade naquele momento, mas agora estou realizando essa pesquisa com
profundidade. O que acontece na Argentina é que muitas produções são sobre futebol. Daí a importância que tem em se trabalhar com outros esportes. E essas outras
pesquisas estão se multiplicando para temas como corrida, golfe, dentre outros. Em
uma coletânea que fizemos em 2013, há trabalhos sobre diferentes objetos de estudo,
mas o futebol segue sendo o tema que mais atrai nas investigações. Então, no meu
caso, quando eu terminei a minha formação, pensei “eu gostaria de trabalhar com
atletas”. Ou seja, já havia trabalhado com aficionados, sócios, dirigentes, então acreditei
que era o momento de trabalhar com atletas. E em um esporte que para mim era muito
desconhecido. Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina Pelo menos para mim, quanto mais estranho, melhor. Então, o fato de
eu ter escolhido o boxe como um esporte para investigar tem a ver com isso, com não
entender nada do que estava acontecendo no ringue.. E falando agora em dimensões,
creio também que o que acontece, pelo menos junto à Universidade de Buenos Aires,
no Instituto de Investigação Gino Germani da Faculdade de Ciências Sociais, é que o
grupo segue sendo pequeno. Não é um grupo como eu vejo que funciona no Brasil, com
grupos ou núcleos de pesquisa de diferentes universidades. Eu penso que o Brasil está
muito adiantado com o tema. Por exemplo, fazem apenas cinco anos que explodiu toda
a discussão sobre gênero e sexualidades aqui na Argentina. Vocês já estavam discutindo
isso faz tempo. E há outra pergunta que você havia feito, Mônica… Interlocuções esportivas: uma
dobradinha entre Brasil e Argentina E, então, pensando
novamente com a “Butler” não apenas a ideia de sexo, gênero e sexualidade, mas dois
tipo de gêneros diferentes, continuaramos a falar de uma homossociabilidade? E aí eu
desenvolvo o conceito de sociabilidade “homo gênero” e sociabilidade “hétero gênero”
para pensar sociabilidades nos quais, por exemplo, fossem só homens, mas de gênero
diferentes ou só mulheres de gêneros diferentes. Então, isso é um pouco dessa trajetória
que depois fui aprofundando e comecei a desenvolver mais na vela junto com a questão
da corporalidade. Para pensar a questão da identidade e corporalidade nos esportes
adaptados, tive uma influência enorme ao ter sido membro da banca de doutorado da
Mônica Araujo; a leitura da tese da Mônica me inspirou muito. Eu me lembro que eu saí
da defesa falando “algum dia eu vou pesquisar essa questão do esporte para pessoas
com deficiência”, e fiz um trabalho acompanhando a ANDEF, que é a Associação
Niteroiense dos Deficientes Físicos, pensando a questão do esporte de alto rendimento. Em relação a isso, agora estou no momento inicial de uma outra pesquisa sobre políticas
públicas esportivas para pessoas com deficiência e na semana que vem estarei 103 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: Vocês dois acabaram falando sobre algo que já estava previsto na entrevista,
que é como vocês foram construindo as suas trajetórias rumo à Antropologia dos
Esportes. Gostaríamos que vocês falassem sobre pertencimento acadêmico, sobre os
grupos de pesquisa aos quais estão associados, de qual lugar estão produzindo ciência. Além disso, o que vocês pretendem pesquisar e desenvolver em um horizonte próximo? Verônica Moreira: No meu caso, faz tempo que eu quero realizar um trabalho sobre
o boxe. Idealizo isso já faz um tempo. Na RAM de Curitiba, em 2011, apresentei um
trabalho sobre isso. Por diferentes motivos, não realizei esse trabalho de campo com
regularidade naquele momento, mas agora estou realizando essa pesquisa com
profundidade. O que acontece na Argentina é que muitas produções são sobre futebol. Daí a importância que tem em se trabalhar com outros esportes. E essas outras
pesquisas estão se multiplicando para temas como corrida, golfe, dentre outros. Em
uma coletânea que fizemos em 2013, há trabalhos sobre diferentes objetos de estudo,
mas o futebol segue sendo o tema que mais atrai nas investigações. Então, no meu
caso, quando eu terminei a minha formação, pensei “eu gostaria de trabalhar com
atletas”. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: Sim. E quais são os seus horizontes de pesquisa daqui pra frente? Mônica: Sim. E quais são os seus horizontes de pesquisa daqui pra frente? Veronica Moreira: No meu caso, e também como diretora de um projeto de
investigação no Instituto, a ideia é trabalhar sobre diferentes objetos de estudo como
o boxe, a corrida (running), o futebol também, e crossfit. Nesses casos, pensando no
cruzamento entre corpo e gênero, que está como um tema muito presente na agenda
de discussão, também em outras universidades; insisto em dizer que não tanto como 104 Pisani; Araujo no Brasil. Há interesse em se trabalhar outras questões que não tem a ver unicamente
com a violência no futebol, ainda que isso sempre esteja aí como estudo. Trabalhar com
torcidas e violências ainda é uma linha de investigação muito interessante, mas, no meu
caso, a ideia é diversificar o olhar para outros esportes, incluindo a discussão sobre o
capacitismo e o corpo com deficiência. Para mim é um tema rico, um super tema para
investigar. Isso seria como uma aspiração, como um objetivo no futuro. Mônica: E você, Luiz? Mônica: E você, Luiz? Luiz Rojo: Primeiro, assim, eu vou só completar um pouquinho a pergunta anterior. Mônica: Sim. Luiz Rojo: Olhando retrospectivamente, chama a minha atenção algo que fala um
pouco desse processo da implantação da Antropologia dos Esportes no Brasil. Tanto na
minha dissertação de mestrado quanto na tese de doutorado, haviam partes dedicadas
à questão esportiva. E esse foi o ponto de encontro para conversar com a Simone
Guedes. Eu acompanhei uma semana a realização das olimpíadas regionais dos
estudantes de medicina, e então fiz um capítulo sobre isso na dissertação do mestrado. Lá tem um item chamado Mens Pulchra in Corpore Pulchro que acabou sendo meu
primeiro artigo na área de esportes, que é um item do capítulo da tese de doutorado
falando sobre as práticas esportivas entre naturistas. Mas eu escrevi isso sem nenhum
referencial teórico sobre esporte porque simplesmente não chegava até então aos meus
ouvidos. Estava se constituindo, estava avançando. A primeira reunião da RBA com o
grupo de esportes, mostra um pouco como esse processo foi ganhando corpo. E eu
peguei justamente essa transição na hora que a Antropologia do Esportes está
começando a se constituir de forma institucional. Respondendo mais especificamente à
última pergunta, o que eu estou buscando cada vez mais agora é juntar duas paixões. Eu vivi uma paixão muito intensamente antes de mergulhar na antropologia, que foi a
vida política. Em certo momento, houve uma parada quase total quando eu fui me
dedicar a terminar a graduação, mestrado, doutorado, entrar na universidade, realizar
as primeiras pesquisas… E recentemente, já há seis, sete anos, eu fui retomando a
minha vivência política, mas até então como duas coisas muito separadas, a vida política
e a vida acadêmica. E agora, escrevi um artigo, que foi publicado na revista da ALA,
sobre o impacto do giro à direita na América Latina sobre a discussão dos esportes no
Brasil, e também tenho discutido essa questão das políticas públicas esportivas em
relação ao esporte de pessoas com deficiência. Mônica: E você, Luiz? Pensando sobre isso, que foi uma das
coisas que eu estava falando no Chile na outra semana, quando a gente olha hoje para 105 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina o Brasil, o reconhecemos como uma potência do esporte paralímpico, em termos de
quadro de medalhas, em termos de ter medalhas em diversas modalidades, de ter uma
equipe como a de futebol de pessoas com deficiência visual que rivaliza com a Argentina. É um bom tema de pesquisa, a questão do futebol né, mas o futebol de pessoas com
deficiência visual é uma equipe quase que imbatível historicamente. Mas ao mesmo
tempo, se você olha para as ruas, para os parques, para as praias, para os espaços
públicos, é muito, muito raro você encontrar uma pessoa com deficiência praticando
algum esporte. Você olha corridas de rua no Rio de Janeiro ou em outros locais, às vezes
mil, duas mil, cinco mil pessoas correndo e você raramente encontra, quando encontra
são duas, três pessoas, na maioria atletas que estão aproveitando aquele espaço para
um treinamento específico, para alguma coisa, e não pessoas que correm como a
maioria dos demais e estão ali praticando um esporte. Então, o que eu tenho me
dedicado cada vez mais é pensar isso: quais são as motivações, quais são as questões
políticas, sociais, culturais, corporais que envolvem essa inexistência da prática esportiva
- e não diria só de lazer - de pessoas com deficiência e da inexistência de políticas
públicas específicas para esse setor da população. Por exemplo, hoje, é cada vez mais
impossível, felizmente, você ter projetos e atuações que excluem completamente as
mulheres. É cada vez mais difícil, felizmente também, ter políticas públicas que excluam
a população afro-brasileira. Agora, é completamente aceitável que você tenha políticas
públicas que excluam completamente as pessoas com deficiência. Então, estamos em
que momento dessas lutas sociais, dessas questões do próprio movimento nacional de
pessoas com deficiência, da questão da incorporação do esporte e dessas temáticas
dentro das políticas públicas brasileiras? Agora esse é o meu eixo principal de desenvolvimento de pesquisa. Mariane: O campo dos estudos dos esportes, especialmente na área de Antropologia,
tem se expandido e se consolidado nos últimos anos, tendo em vista a publicação de
um livro no Brasil dos vinte anos dos estudos da área de Antropologia dos Esportes,
Lazer e outras práticas. Mônica: E você, Luiz? A gente pode destacar sobretudo nesse movimento de expansão
o trabalho do Conselho Latinoamericano de Ciências Sociais e a União Internacional de
Antropologia e Etnologia, por exemplo. Vocês poderiam comentar como esses espaços
foram sendo construídos e constituídos, e também um pouco da participação de vocês
nesses lugares? Verônica Moreira: Antes de responder a esta pergunta, eu quero destacar o
Movimento Nenhuma a Menos, na Argentina, que é um movimento que denuncia o
número de feminicídios no país, a partir da morte de uma jovem. Isto começou em 2015 106 Pisani; Araujo e a temática sobre a violência de gênero explodiu logo em seguida, assim como toda
uma movimentação nas ruas. Isso impactou muito como eu me entendo na academia
e nas investigações. As perguntas sobre os gêneros e as sexualidades surgiram das
mãos de jovens que estavam começando as suas investigações de doutorado. Isso para
mim é um ato bastante revelador e muito interessante. Agora essas pessoas já estão
formadas e usam as suas teses e outras produções dentro de uma agenda social e
política a nível nacional. Sobre a rede CLACSO… A CLACSO é uma rede de estudo comparativo latinoamericana
e a ideia é que investigadores, investigadoras e pessoas em formação estejam em
contato para discutir diversos temas e assuntos que podem ser as questões de gênero,
mas também discussão sobre políticas públicas. Aliás, este canal especificamente está
bastante obstruído, pois nos custa muito chegar para contribuir e realizar políticas
públicas concretas sobre determinados temas. E ainda sobre esse tema da política
pública, que também está presente na CLACSO, sentimos na nossa própria pele os
desafios quando se trata da questão da violência no futebol. Temos muito material
elaborado sobre o tema, mas tudo muito fragmentado, entende? A rede tem isto: estão
presentes discussões sobre gêneros, sexualidades e políticas públicas como carro chefe
e ao longo do tempo foi-se somando pessoas de diferentes países. Acredito que em
1999 foi a primeira formação do grupo de trabalho dedicado às Ciências Sociais e
esportes. E eu me lembro que nesse momento eram umas quinze pessoas mais ou
menos, com países como Brasil, Argentina, Equador… Bom, eram muitos poucos países. Atualmente a rede tem setenta pessoas e os seguintes países: Argentina, Brasil, Chile,
Bolívia, Colômbia, Porto Rico, Cuba, Equador, México, Paraguai, Peru e Uruguai. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? O que
eu quero dizer com isso é que podemos observar que há uma ampliação da incorporação
de novos países que antigamente não participavam desses congressos que assistimos,
onde se trabalha sobretudo o tema dos esportes. Ou seja, cresceu a produção a nível
de outros países. E de toda maneira, eu chamo a atenção para as dificuldades, para o
fato do quanto é complexo sustentar uma rede que funcione da forma como idealmente
pensamos que deve funcionar. É muito complexo porque todas essas setenta pessoas
estão trabalhando em pares. Algumas pessoas produziram algumas coisas como, por
exemplo, o boletim dedicado à Copa América Feminina. Fizemos uma reunião na
pandemia e, naquele momento, foi bom poder conectar pessoas de diferentes países e
ter diálogos muito enriquecedores. Fizemos dois bate-papos muito interessantes: um
sobre a formação de futebolistas e outro em que discutimos raça. Eu acho que a
CLACSO, sendo um conselho latino americano, possui uma abertura para trabalhar a
questão da raça, do racismo no esporte. Bem… Há outras atividades que podem ser Sobre a rede CLACSO… A CLACSO é uma rede de estudo comparativo latinoamericana
e a ideia é que investigadores, investigadoras e pessoas em formação estejam em
contato para discutir diversos temas e assuntos que podem ser as questões de gênero,
mas também discussão sobre políticas públicas. Aliás, este canal especificamente está
bastante obstruído, pois nos custa muito chegar para contribuir e realizar políticas
públicas concretas sobre determinados temas. E ainda sobre esse tema da política
pública, que também está presente na CLACSO, sentimos na nossa própria pele os
desafios quando se trata da questão da violência no futebol. Temos muito material
elaborado sobre o tema, mas tudo muito fragmentado, entende? A rede tem isto: estão
presentes discussões sobre gêneros, sexualidades e políticas públicas como carro chefe
e ao longo do tempo foi-se somando pessoas de diferentes países. Acredito que em
1999 foi a primeira formação do grupo de trabalho dedicado às Ciências Sociais e
esportes. E eu me lembro que nesse momento eram umas quinze pessoas mais ou
menos, com países como Brasil, Argentina, Equador… Bom, eram muitos poucos países. Atualmente a rede tem setenta pessoas e os seguintes países: Argentina, Brasil, Chile,
Bolívia, Colômbia, Porto Rico, Cuba, Equador, México, Paraguai, Peru e Uruguai. Mônica: E você, Luiz? O que
eu quero dizer com isso é que podemos observar que há uma ampliação da incorporação
de novos países que antigamente não participavam desses congressos que assistimos,
onde se trabalha sobretudo o tema dos esportes. Ou seja, cresceu a produção a nível
de outros países. E de toda maneira, eu chamo a atenção para as dificuldades, para o
fato do quanto é complexo sustentar uma rede que funcione da forma como idealmente
pensamos que deve funcionar. É muito complexo porque todas essas setenta pessoas
estão trabalhando em pares. Algumas pessoas produziram algumas coisas como, por
exemplo, o boletim dedicado à Copa América Feminina. Fizemos uma reunião na
pandemia e, naquele momento, foi bom poder conectar pessoas de diferentes países e
ter diálogos muito enriquecedores. Fizemos dois bate-papos muito interessantes: um
sobre a formação de futebolistas e outro em que discutimos raça. Eu acho que a
CLACSO, sendo um conselho latino americano, possui uma abertura para trabalhar a
questão da raça, do racismo no esporte. Bem… Há outras atividades que podem ser 107 feitas como, por exemplo, o lançamento de boletins. Já a publicação de livros é um
trabalho que demanda mais tempo e esforço. Temos essas reuniões para discutir
assuntos pontuais, mas não podemos fazer muito mais por uma questão de tempo. Luiz Rojo: Bom, Verônica acabou focando bem nesse debate, até porque ela está na
coordenação do nosso grupo da CLACSO. Eu acho que esse processo realmente é muito
difícil porque construir conexões da forma como a gente trabalha, de forma muito
isolada…Ou seja, acho que a gente ainda não conseguiu, pelo menos que eu saiba,
produzir projetos mais comparativos, que é um salto que a gente tem que dar em
equipe. Pensar como que nós podemos trabalhar em equipe para além dos encontros,
dos boletins, dos livros, dos eventos. É um desafio que está posto. É bom quando a
gente tem desafios pois temos mais coisas a enfrentar. E do ponto de vista da IUAES é
um processo semelhante. Conversando isso algumas vezes com a Simone, a gente
falava muito sobre a importância desses projetos de internacionalização. Tanto a
Simone quanto o Pablo Alabarces fizeram esse trabalho forte da consolidação dos
estudos sobre esportes na América Latina. Mônica: E você, Luiz? E, foi como a Verônica falou, desde 98, 99,
não lembro exatamente o ano, houve a iniciativa do Pablo desse grupo da CLACSO e
daí pra frente as viagens que fizeram juntos para a a Colômbia, México e em lugares
para participarem de eventos. E agora eu me lembro de outro momento, de quando eu vi uma chamada de um
congresso da IUAES que ia ter em Dubrovnik, na Croácia. Achei interessantíssimo e falei
“poxa, nunca fui à Croácia!” e era aquele momento da vida em que, (ai que saudade!),
a gente mandava um pedido de passagem, e de hospedagem, e de diária e vinha tudo. Passagem aérea, diária, hospedagem, inscrição… Tinha dinheiro para a gente investir
em ciência, tecnologia, tinha dinheiro para a gente investir nessa parte, e eu acho que
isso impulsionou muito a nossa possibilidade de avançar a nível internacional. Eu fui
para aquele congresso e tinha lá o grupo formado sobre esportes. Ainda não havia um
grupo organizado na IUAES, mas havia um grupo de trabalho. Quando cheguei lá eu
tive uma surpresa gigantesca porque eram três sessões de trabalho, com quinze
trabalhos no total. E tinham dois trabalhos, o meu e o de um doutorando da Finlândia…
O dele sobre Maratonas Solidárias, sobre as pessoas se engajavam para arrecadar
fundos para eventos específicos.Os nossos dois eram os únicos trabalhos de
Antropologia Cultural. O resto era tudo Antropologia Física. “O impacto da lesão não sei
o que…”, parecia que eu estava voltando ao mestrado assistindo aulas de anatomia,
aquela coisa que eu acompanhei lá no trabalho de campo do mestrado. E eu lembro
que a gente conversou, este finlandês e eu, e saímos de lá horrorizados pois ninguém 108 Pisani; Araujo fez pergunta para a gente, a gente não fez pergunta para ninguém, a não ser eu
perguntar do trabalho dele e ele perguntar do meu. Não tinha nem ponte de contato. A
gente ficou conversando sobre isso e, eu lembro que estava a Carmen Rial e a Miriam
Grossi no congresso, elas já estavam à frente da IUAES participando ativamente, e elas
me estimularam para “meter a mão nesta cumbuca”. Já no Congresso do Canadá, eu
fiz uma proposta de grupo,eu comecei a conversar com todo mundo que estava, mandei
e-mail e falei: “vamos construir o grupo dentro da IUAES”. Bem na cara e na coragem
fomos construindo. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? É uma infinidade tão grande de temáticas, Verônica… ica Moreira: Sim, é difícil sistematizar porque está em processo.O que ocorre na 109 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina CLACSO é que temos um perfil construído com foco no debate das desigualdades,
justamente de norte a norte, e, a partir daí, nos organizamos sobre alguns assuntos
como a desigualdade de gênero, a violência, políticas públicas. Há temas que norteiam
e esse processo tem sido muito interessante. Por outro lado, tem toda uma dificuldade
para lidar com as diferentes realidades, por exemplo, como abordar o racismo no Brasil,
que é distinto da Bolivia, da Argentina,... Luiz Rojo: Há que se pensar que a CLACSO já tem uma história de vinte e três anos
discutindo a questão do esporte. Nós somos descendentes, de descendentes, de
descendentes do Pablo, da Simone, então isso já tem uma história, uma trajetória. No
caso da IUAES, nós temos quatro anos de história. Então, é um movimento ainda muito
embrionário que eu espero que vá se consolidar, mas que ainda é passo a passo. Verônica Moreira: Acredito que, se for pensar na pandemia, não há tanto diálogo na
atualidade talvez porque não pudemos nos reunir presencialmente e continuar com as
reuniões que para mim são um clássico do intercâmbio. Pontualmente, falo da RAM. A
“RAM” começou, creio que com a primeira reunião em 2001, em Curitiba, com a
coordenação da Simone e com Arlei Damo, que foi o primeiro congresso que eu me
apresentei junto com José Fassheber. Foi o primeiro em tudo. Foi o primeiro congresso,
primeiro congresso internacional, e a partir daí sempre, no meu caso, participei do grupo
de Esportes e depois foi sendo construído uma mesa paralela, com um tema em
particular. O que sinto é que a pandemia mudou algo, que acredito que possa ser
revertido. Ficou algo pendente para mim também do que disse o Luiz, na questão de
uma dimensão comparativa. Creio que Simone insistiu nisso e faz tempo que há um
projeto para isso, com muitas ideias, mas com o intuito de se montar, por exemplo,
grupos para escreverem sobre um tema pontual, mas fazê-lo com algumas pessoas de
diferentes países. É difícil, às vezes, por uma questão de tempo material que não temos. Mônica: E você, Luiz? O Jerôme Soldani, da França, teve um papel fundamental de abrir o
campo também na Europa, de trazer mais gente; Mariane Pisani participou depois aqui
em Santa Catarina, uma série de pessoas foram se agregando. Se a Verônica fala da
dificuldade da CLACSO, na IUAES a dificuldade é muito maior porque é um campo
mundial. Hoje felizmente já tem gente dos cinco continentes, mas você imagina juntar
pessoas dos Estados Unidos, da África do Sul, do Quênia, da índia, da Indonésia, do
Japão, da Europa, da América do Sul, é uma loucura e ainda não está totalmente
consolidado. Agora teremos o congresso na Índia, estamos trabalhando para isso e vai
ser um momento muito delicado de passagem de bastão. Eu estarei saindo da
coordenação, termino este meu mandato, o Jerôme irá continuar tendo uma pessoa o
acompanhando, da República Tcheca, mas estaremos fazendo essa passagem e aí
conseguindo avançar, mas é um processo lento, é um processo difícil porque envolve
uma quantidade absurda de países, de momentos e de ritmos diferentes, de produção,
de redes e de contatos dentro desse campo. Mas eu acho que é um desafio que estamos
conseguindo colocar em movimento. Espero que para os próximos anos mais gente do
Brasil se junte, mais gente da América Latina se junte para ocupar efetivamente esse
espaço da IUAES que é uma conexão muito importante para gente. Verônica Moreira: Perdão. E de que temas tratam? Já sei que devem ser muito
variados mas, que tipo de problemática colocam? Luiz Rojo: Nós sabemos - até em função do que já relatei sobre o congresso na Croácia
- que alguns países a Antropologia do Esporte está muito vinculada à Antropologia da
Saúde, à Antropologia Física, e uma das questões que nós colocamos é que nós não
queremos ser um grupo de Antropologia Cultural dos Esportes. A gente nasceu assim,
mas já incorporamos um indiano que trabalha, diria, na fronteira entre a Antropologia
Cultural e a Antropologia Física. Então, a ideia é buscar ampliar ainda mais para poder
ver esses diálogos, ver o que cada lado contribui, o que é difícil porque torna essa
agenda ainda mais complexa. Mônica: E você, Luiz? Mas, também, há outros pontos: quem nos financia, quanto dinheiro nos dão para
fazermos nosso trabalho de campo e para viajar, e eu acredito que aí o contexto político
incide sobre o que fazemos, nos impacta. Na Argentina, toda essa questão de discutir
gênero e sexualidades estão legitimadas porque há um Ministério de Mulheres e
Diversidade, há um Ministério de Esportes que tem a agenda de gênero muito presente,
tudo facilita isso, um monte de produções, há mais dinheiro circulando sobre isso. Eu,
como diretora de um centro de formação de Gênero e Esportes na Universidade de
Buenos Aires, tenho o apoio da Secretaria Esportes da Nação. Como o Luiz já tinha
comentando, de que antes tinham a possibilidade de participar de um congresso onde
te davam a passagem e todo o resto e hoje isso se encontra muito limitado… Então, o 110 Pisani; Araujo contexto político dita sim o que fazemos. Eu sempre vi que há um diálogo muito
profundo, mas hoje vejo que isso diminuiu, creio eu, como produto da pandemia. A
vontade é voltar a fazer os intercâmbios, então, agradeço a Mariane e Mônica por me
convidar a participar disso, pois isso é o que eu entendo que temos que fazer e sair
construindo entre todos. Tenho vontade de seguir estabelecendo diálogos e
aprofundando os intercâmbios. Luiz Rojo: Mariane, essa questão que você colocou me fez lembrar do dia em que eu
conheci a Verônica. Não sei se a Verônica se lembra que a gente se conheceu em Buenos
Aires, em uma sala da Universidade de Buenos Aires, num desses encontros que a
Simone e o Pablo organizavam e que foi um grupo daqui, algumas pessoas, para Buenos
Aires, para um fim de semana de conversas. Em uma sala, foi a primeira ida para um
evento assim. A Simone me convidou e eu fui; tava lá Garrica, tava lá Verônica, tava lá
um grupo de pessoas e eu acho que isso, esses encontros, para além dos congressos,
era algo que organizava, inclusive depois com a Simone indo fazer um pós-doutorado
na Argentina, com o Nicolás Cabrera que veio aqui, pra cá, com o Davi Quitian, da
Colômbia, que veio fazer um pós-doutorado aqui. Então, havia mais esse intercâmbio. Verônica Moreira: Qual é a tradução? Luiz Rojo: “Quanto mejor…” Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? Assim, como disse a Verónica a pandemia realmente teve um impacto nisso, mas
mesmo antes a gente já sentia um recuo por conta da questão econômica e política, ou
seja, a dificuldade de verba para viajar, para fazer as coisas. E eu acho que tem uma
outra questão que temos que pensar, e aí é um ponto complicado, vou fazer uma
brincadeira: tinha um bloco aqui em Niterói que dizia “se melhorar, afunda” e… Verônica Moreira: “Se hunde.” Luiz Rojo: Isso. E eu acho que uma parte disso também é fruto exatamente do nosso
crescimento, do nosso sucesso. Porque quando nós éramos poucas pessoas lá em 2005,
2006, fundamentalmente Brasil, Argentina e uma pessoa daqui e uma outra pessoa de
acolá era muito mais fácil se reunir, era muito mais fácil pensar projetos comuns dessa
articulação. Nós tínhamos a RAM e a ABA, um congresso por ano, o que também dava
encontros, mas dava tempo. Se a gente olhar a nossa agenda hoje, nós temos: todos
os anos, a princípio, congresso da IUAES; a cada dois anos uma reunião da Associação
Brasileira de Antropologia, acho que também lá do Congresso de Antropólogos da
Argentina, uma reunião nacional; temos a reunião de Antropologia do Mercosul; temos
a reunião da Associação Latinoamericana de Antropologia; então nós temos hoje uma
sobrecarga de congresso. Além disso, ainda pensando que a gente praticamente não 111 participa da reunião de Antropologia Equatorial, como um grupo, como uma coisa
organizada, e abandonamos praticamente ou totalmente a ANPOCS, no qual também
pessoas da Argentina participavam, iam trocar. Se a gente pensar que em várias das
nossas reuniões de antropologia do Brasil pesquisadores da Argentina vinham
apresentar trabalho, e que muitos de nós íamos apresentar trabalho, olha a quantidade
de congressos e eventos que nós temos. O que foi um crescimento e um fortalecimento
da área também implicou, eu acho, em uma redução desses outros espaços de
encontros mais próprios de sentar e debater mais profundamente, como fizemos na
Argentina, acho que em 2005, 2006. Para conversar, trocar ideias e não para apresentar
trabalho de quinze minutos, depois ter conferência, mesa redonda e seminário. Então,
esses espaços foram se perdendo também. A gente se reúne muito, mas a gente se
encontra pouco. E eu acho que a gente tem que pensar um pouco como a gente não
vai abrir mão desses espaços. Como a Verónica falou - e eu concordo- , isso é importante
para a visibilidade do campo, para o seu fortalecimento , mas como a gente consegue
mediar? Talvez a tecnologia seja uma alternativa. Dá pra gente fazer… É ruim não ser
presencial? Mas você veja, se a gente não tivesse esse espaço, como a gente estaria
juntando Niterói, Teresina, Buenos Aires? Impossível! Então, usar mais a tecnologia para
a gente trocar ideia e conversar, bater papo acadêmico e pensar projetos buscando
recompor os espaços. Verônica Moreira: “Se hunde.” Essa possibilidade que a Verônica aponta lá da Argentina, a gente
espera que no Brasil a partir do ano que vem comecem a surgir essas possibilidades, de
mais bolsas e mais pesquisas para que a gente possa fazer doutorado sanduíche dos
nossos orientandos e das nossas orientandas, pós doutorados entre a gente. Espaços
também dessa circulação, que são tão importantes, para que a gente possa ir se
fortalecendo. Verônica Moreira: Simplesmente isso do curso conseguir financiamento de alguma
agência mundial, que não seja da Argentina ou do Brasil, que financie, que tenha
dinheiro para essas reuniões presenciais com um dia, dois dias de discussão, de
conversa, desses encontros que você menciona, que não são somente reuniões. Também vejo assim os congressos, como uma fábrica de salsichas (risos). Esta é uma
metáfora aqui na Argentina para dizer quando vem uma coisa atrás da outra, e não há
muito tempo para a discussão, para o diálogo, para que as coisas sejam melhor
apuradas. E agora eu fico pensando nisso com pena, pois sinceramente nós perdemos
essa questão do encontro, de estar de maneira presencial dialogando. Então há muito
o que fazer. Pisani; Araujo
Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um
11 Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um 112 Pisani; Araujo artigo né (risos)... Já daria ali uma descrição bem interessante sobre os caminhos que
são tomados a partir disso, uma nova realidade, uma expansão do campo que, por outro
lado, traz um conjunto de desafios, uma complexidade que a gente tem que enfrentar. E o Luiz lembrando do papel da Simone e do Pablo na constituição desse campo, mas
também em um espaço que transbordava. Espaço esse de diálogo, mas também um
espaço de sociabilidade extra acadêmica. Isso me faz lembrar do papel do Nepess e nos
eventos que eram liderado pela Leda Costa e pelo Martin Curi como, por exemplo, a
visita a estádios, combinar saídas para assistir aos jogos… Essas coisas nos trazem um
saudosismo em relação a essas outras atividades que tinham como horizontes,
obviamente, os nossos temas de pesquisa, mas que extrapolava em termos de uma
interação, da mobilização desses afetos. Verônica Moreira: “Se hunde.” Voltando para o nosso roteiro, a gente não tem como fazer uma entrevista dessa
natureza sem falar do impacto da realização dos grandes eventos na cidade do Rio de
Janeiro: Copa do Mundo de 2014 e depois os Jogos Olímpicos e Paralímpicos de 2016. Então, queria que vocês falassem um pouco sobre isso. Luiz Rojo: Respondendo a partir da minha própria vivência, eu acho que sem a
realização dos jogos aqui no Rio de Janeiro, diante dos Jogos Paralímpicos que é o meu
foco, é pouco provável que eu pudesse desenvolver o tipo de pesquisa que eu
desenvolvi sobre a questão do esporte adaptado. Não apenas porque houve visibilidade
gigantesca do tema, mas porque abriu um campo de interesse sobre essa temática. Tem
uma série de análises, foram escritas coletâneas, livros, artigos sobre a questão do
impacto político da Copa principalmente, mas também dos Jogos Olímpicos. Eu não
tenho profundas divergências com a maioria deles, mas eu lembro de ter escrito um
artigo em especial no qual dialogo com o nosso querido, saudoso e amigo, Gilmar
Mascarenhas que tinha um olhar muito crítico para esses mega eventos. E eu falo assim:
“ok mas, não por acaso, esse olhar crítico focava na Copa do Mundo e nos Jogos
Olímpicos.” Em momento algum - e eu li a coletânea toda sobre o impacto dos mega
eventos - há uma única citação à realização dos jogos paralímpicos e eu acho que esse
evento trouxe um tipo de visibilidade. Falava-se tanto do legado, “qual o legado dos
jogos?”, eu digo: a visibilidade dos jogos adaptados no Brasil”, pois é inegável a
transformação que há pré jogos e pós jogos. Então, eu acho que esse é um tema que
fala um pouco das nossas agendas. Voltando à questão feita anteriormente, sobre os
conceitos utilizados… Metodologicamente, as questões que mais me impactaram foi a
leitura do Magnani sobre a observação “de perto e de dentro”. Acho aquele texto de
uma potência, de uma riqueza fantástica, e como todo bom texto, ele permite que você 113 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina se aproprie dele para além de somente ler. E uma das coisas que eu comecei a fazer há
um bom tempo é partir para as considerações do Magnani para pensar a observação de
perto e de dentro como uma alternativa a observação participante. Verônica Moreira: “Se hunde.” Mas não apenas para
a questão urbana, do desenvolvimento, da forma como Magnani usa. Eu uso aquilo de
uma forma um pouco diferente. E para pensar no que ele fala muito ali, do quanto que
a dimensão urbana pouco olha para o ponto de vista das atribuições de significado
nativos. E eu acho que esse olhar, do ponto de vista das pessoas que estavam ali
vivenciando esses mega eventos, ainda faltou na nossa elaboração. Nós fomos de
alguma forma apanhados por essa crítica aos mega eventos esportivos. Ela era
importantíssima de ser feita, havia muitos aspectos indicados, mas ela conseguiu de
alguma forma se impor como “a narrativa”. E de alguma forma ela prejudicou que outras
narrativas pudessem aparecer porque parecia que outras narrativas poderiam legitimar
a realização dos mega eventos. E o olhar crítico já tinha se colocado ali como uma
vertente definitiva, podemos dizer assim. A Simone publicou um texto, tratando do
recente contexto político brasileiro, no qual fala do “segundo sequestro da camisa verde
e amarela”. E se ela foi sequestrada uma segunda vez é porque ela foi resgatada da
primeira vez. A gente precisa de um resgate dos megaeventos esportivos, lançando
outros olhares, outras perspectivas desses eventos, sem abrir mão da visão crítica. Precisamos procurar compreender o que eles significaram não apenas no macro mas, -
nos apropriando do histórico e metodológico da nossa disciplina - impactos micro. Além
disso, no que isto implica, em algum grau que seja, no fortalecimento da
descentralização do monopólio do futebol, no suporte e na visibilidade de outras
vivências e outras relações com a prática esportiva, sem contar as mudanças em relação
às mídias. A maior questão que esses mega eventos trazem para a gente hoje é o reflexo
inclusive sobre isso, sobre a nossa vivência, ou seja, cada um de nós deve ter percebido
o quanto se tornou mais fácil publicar, mais fácil falar, o quanto dessa área ocupou um
espaço, não apenas falando do nosso crescimento orgânico, mas porque o nosso
crescimento orgânico enquanto grupo coincidiu com o fato de que a sociedade brasileira
tava se debruçando sobre a questão do esporte como nunca se debruçou antes na vida. E para além disso, se debruçou simultaneamente sobre futebol em 2014 e sobre os
esportes Olímpicos e Paralímpicos dois anos depois. Verônica Moreira: “Se hunde.” Então acho que a gente é herdeiro
disso, eu sempre lembro a Mônica falando que tinha um projeto de doutorado sobre
dança afro, se não me engano… Pisani; Araujo
Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento
114 Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento 114 Pisani; Araujo Pisani; Araujo esportivo. Luiz Rojo: Isso… E aí foi assistir uma prova de natação nos jogos parapanamericanos
e mudou de tema. Isso é legado dos megaeventos. A tese de doutorado da Mônica é
legado dos Jogos Parapanamericanos. Se não o houvesse, talvez nós tivéssemos mais
uma tese muito boa sobre dança afrobrasileira, mas não teríamos a primeira tese de
doutorado da história da Antropologia Brasileira sobre qualquer tipo de modalidade
adaptada. Então a gente tem que pensar também qual é o impacto, isso também
merecia um artigo, sobre os megaeventos esportivos na consolidação, diversificação e
ampliação do campo da Antropologia dos Esportes no Brasil. Mônica: Então realmente a gente ficou muito refém de uma narrativa que é importante
mas que foi pensada, posso estar sendo injusta, de uma maneira um pouco apressada,
no sentido de dizer, de maneira muito categórica, chamar atenção apenas para os
aspectos negativos como se colocássemos em jogo tudo aquilo que de positivo, de
outros potenciais, a gente estivesse legitimando, de forma acrítica a realização desses
eventos. E nós sabemos de todos os problemas, as questões das remoções, uma série
de aspectos que foram muito complicados e que tiveram impacto concreto na vida de
uma grande parte da população; ninguém está cego para isso, mas eu acho que tem
outras camadas que não foram devidamente abordadas. Acho que ainda tem espaço e
tempo para se fazer isso. Luiz, você começa a falar sobre isso no seu artigo sobre a
questão da visibilidade como legado dos Jogos Paralímpicos, mas tem outra camada que
tem a ver justamente com a produção do campo dos esportes que se amplia e
diversifica.. Acho que também tem a questão da profusão de encontros, antes a gente
tinha uma mesa, agora temos mais de um GT, mesas temáticas, ou seja, um aumento
tem um aumento muito expressivo. Luiz Rojo: Para mim esse foi um momento muito bom para olhar para essa trajetória
e analisar um pouco. . Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Verônica Moreira: “Se hunde.” E acho que o campo precisa disso, ocasionalmente, de fazer
balanços como esse que acabamos de fazer, olhando para o que já foi feito, para as
lacunas, para os ajustes possíveis, O Bordieu já dizia que a gente vai reconstruindo a
memória e a significação dos eventos a partir do ponto que a gente está hoje para narrá-
los, e eu acho que a gente hoje está em uma situação melhor para poder fazer essa
leitura de forma mais crítica, no sentido mais amplo do termo, não crítica só negativa,
mas crítica no sentido mais amplo, mais potente do termo, sobre esses eventos e sobre
a própria construção do campo. Essa entrevista ajudou muito a contar não apenas
trajetórias, mas caminhos futuros para a consolidação e desenvolvimento deste campo
da Antropologia dos Esportes. Então, além de ser um prazer pessoal estar com vocês, 115 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina é um prazer também intelectual estar narrando, observando, pensando sobre. E, claro,
sobre o meu papel nele. Já são dezessete anos estudando na Antropologia dos Esportes. É uma trajetória né. Legal as vezes parar e olhar para ela. Tem coisa aí construída. Mariane: Da minha parte eu só queria reiterar os agradecimentos, não só do Luiz e da
Verônica, mas da Mônica também nessa parceria justamente porque no seio desse grupo
das práticas esportivas que eu me constituí como Antropóloga. A primeira vez que nos
encontramos eu estava apresentando um trabalho da graduação, depois do mestrado,
depois do doutorado e depois como professora universitária. Então, praticamente para
além das orientações das minhas professoras orientadoras, muito da antropóloga que
me constitui hoje e dos meus interesses de pesquisa, nascem nestes grupos de trabalho,
nessas trocas, nesse intercâmbio. A Verónica é uma parceira de trabalho maravilhosa,
desde que eu a conheci a gente vai mantendo contato e a mesma coisa com Luiz, a
mesma coisa com Mônica. Então eu acho que essa entrevista também é fruto de muita
satisfação pessoal, de rever nessa história, dessa área, dessa temática de duas pessoas
como você, Luiz, e Verônica, a consolidação e a possibilitação, a pavimentação de outras
trajetórias como a minha, por exemplo.. É um prazer imenso ter estado junto com vocês
três essa tarde. 116 Pisani; Araujo |
https://openalex.org/W4392090920 | https://www.journals.vu.lt/politologija/article/download/34283/33037 | English | null | Who should Issue a Permit for the Memorial? Administrative Law as a Platform for the Conflict over the Construction of the Monument to the Victims of the Smoleńsk Tragedy in Warsaw | Politologija | 2,023 | cc-by | 11,539 | Received: 31/08/2023. Accepted: 15/12/2023
Copyright © 2023 Piotr Eckhardt. Published by Vilnius University Press. This is an Open Access article distributed
under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and
reproduction in any medium, provided the original author and source are credited. Who should Issue a Permit
for the Memorial? Administrative
Law as a Platform for the Conflict
over the Construction of
the Monument to the Victims of
the Smoleńsk Tragedy in Warsaw Who should Issue a Permit
for the Memorial? Administrative
Law as a Platform for the Conflict
over the Construction of
the Monument to the Victims of
the Smoleńsk Tragedy in Warsaw Piotr Eckhardt
University of Wrocław
E-mail: piotr.eckhardt@uwr.edu.pl Piotr Eckhardt Abstract. Circles associated with the ruling Law and Justice party decided to build a mon-
ument to the victims of the crash of a Polish government airplane in Smoleńsk on April
10, 2010 in Piłsudski Square in Warsaw. However, the authorities of that city, associated
with the political opposition, were not positive about the project. Government bodies in-
strumentally used (and even abused) existing institutions of administrative law to build the
monument despite the opposition of the local self-government. First, control over Piłsudski
Square was taken away from the city authorities. Then the square was declared a closed
area of military importance so that the city authorities could not make it difficult to obtain
permission to build the monument. Finally, the Polish parliament created special legislation
to make it more difficult to remove the monument in the future. fi
Keywords: Smoleńsk air disaster, Smoleńsk monument, instrumentalization of law, mem-
ory laws, construction law. Kas turėtų išduoti leidimą statyti paminklą? Administracinė
teisė kaip konflikto platforma: paminklo Varšuvoje Smolensko
tragedijos aukoms atminti atvejis Politologija
ISSN 1392-1681 eISSN 2424-6034
2023/4, vol. 112, pp. 108–138
DOI: https://doi.org/10.15388/Polit.2023.112.4
Contents lists available at Vilnius University Press Politologija
ISSN 1392-1681 eISSN 2424-6034
2023/4, vol. 112, pp. 108–138
DOI: https://doi.org/10.15388/Polit.2023.112.4
Contents lists available at Vilnius University Press Contents lists available at Vilnius University Press ISSN 1392-1681 eISSN 2424-6034
DOI: https://doi.org/10.15388/Polit.2023.112.4 ISSN 1392-1681 eISSN 2424-6034
DOI: https://doi.org/10.15388/Polit.2023.112.4 Politologija
2023/4, vol. 112, pp. 108–138 Kas turėtų išduoti leidimą statyti paminklą? Administracinė
teisė kaip konflikto platforma: paminklo Varšuvoje Smolensko
tragedijos aukoms atminti atvejis Santrauka. Lenkijos valdančiosios partijos „Teisė ir teisingumas“ atstovai nusprendė Ju-
zefo Pilsudskio aikštėje Varšuvoje pastatyti paminklą 2010 m. balandžio 10 d. Lenkijos
vyriausybinio lėktuvo katastrofos Smolenske aukų atminimui. Tačiau su tuomete politine 108 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... opozicija sieta Varšuvos miesto valdžia projektą įvertino neigiamai. Nepaisant vietos savi-
valdos pasipriešinimo, valstybinės valdžios institucijos pasinaudojo (ir net piktnaudžiavo)
veikiančiomis administracinės teisės institucijomis, kad paminklas būtų pastatytas. Pir-
miausia buvo apribotos miesto valdžios galimybės kontroliuoti Pilsudskio aikštę. Blokuo-
jant miesto valdžios turimus įrankius ir siekiant apsunkinti leidimo statyti paminklą išda-
vimą, ji buvo paskelbta uždara karinės reikšmės teritorija. Galiausiai Lenkijos parlamentas
sukūrė specialius teisės aktus, apsunkinančius galimybę pašalinti paminklą ateityje. opozicija sieta Varšuvos miesto valdžia projektą įvertino neigiamai. Nepaisant vietos savi-
valdos pasipriešinimo, valstybinės valdžios institucijos pasinaudojo (ir net piktnaudžiavo)
veikiančiomis administracinės teisės institucijomis, kad paminklas būtų pastatytas. Pir-
miausia buvo apribotos miesto valdžios galimybės kontroliuoti Pilsudskio aikštę. Blokuo-
jant miesto valdžios turimus įrankius ir siekiant apsunkinti leidimo statyti paminklą išda-
vimą, ji buvo paskelbta uždara karinės reikšmės teritorija. Galiausiai Lenkijos parlamentas
sukūrė specialius teisės aktus, apsunkinančius galimybę pašalinti paminklą ateityje. Reikšminiai žodžiai: Smolensko lėktuvo katastrofa, Smolensko paminklas, įstatymo
instrumentalizacija, atminties įstatymai. 1
Nikolai Koposov, Memory Laws, Memory Wars. The Politics of the Past in Europe
and Russia (Cambridge: Cambridge University Press, 2018), 1.
2
Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias, “Introduction: Memory
Laws: Mapping a New Subject in Comparative Law and Transitional Justice,” in Law
and Memory. Towards Legal Governance of History, eds. Uladzislau Belavusau and
Aleksandra Gliszczyńska-Grabias (Cambridge: Cambridge University Press, 2017), 1.
3
Belavusau and Gliszczyńska-Grabias, 1. 1
Nikolai Koposov, Memory Laws, Memory Wars. The Politics of the Past in Europe
and Russia (Cambridge: Cambridge University Press, 2018), 1. 3
Belavusau and Gliszczyńska-Grabias, 1. 2
Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias, “Introduction: Memory
Laws: Mapping a New Subject in Comparative Law and Transitional Justice,” in Law
and Memory. Towards Legal Governance of History, eds. Uladzislau Belavusau and
Aleksandra Gliszczyńska-Grabias (Cambridge: Cambridge University Press, 2017), 1.
3
B l
d Gli
ń k G bi
1 Introduction The interrelationship of law and social collective memory is usually
investigated in the context of the creation and application of spe-
cialized legal regulations in this area – so-called memory laws. This
term was coined in France in 2000s as a name for legislation penaliz-
ing i.a. Holocaust negationists.1 According to Uladzislau Belavusau
and Aleksandra Gliszczyńska-Grabias “such laws enshrine state-ap-
proved interpretations of crucial historical events. They commemo-
rate victims of past atrocities as well as heroic individuals or events
emblematic of national and social movements.”2 They explain, that
“[m]emory laws affect us in various, often controversial ways. They
sometimes impose criminal penalties on speech or conduct deemed
offensive to the plight of heroes and victims. <…> Children every-
where grow up reading state-approved texts designed to impact not
merely a knowledge, but an interpretation of history. Governments
everywhere designate national memorial ceremonies or authorize the
construction of public monuments.”3 It is clear that the memory laws 109 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) quite often and thoroughly studied by scholars4 are specialized legal
regulations created for the sole purpose of legal governance of his-
tory. Marta Buholc names four areas of particular intense reciprocal
relationship between law and memory in the context of memory ac-
tivism: memory laws (defined as above), truth seeking initiatives,
mnemonic mobilization in the struggles for historical justice, and
constitutional memories.5 Also in the case of this broader area of reg-
ulation, it is easy to see that their impact on social collective memory
has had to be one of the contexts considered by the legislator. There are also such legal acts which do not have the primary in-
tention of shaping collective memory, but it is easy to see that they
can be used for this purpose. The laws regulating street naming can
serve as an example. In the same procedure, a street can be given a
name that is both completely historically neutral or that commemo-
rates a certain person or event. This is being investigated by research-
ers from various countries.6 However, there are situations where only in the practice of apply-
ing the law it becomes apparent that some regulations are relevant to
the implementation of certain projects of shaping social collective
memory. 4
For state of research on memory laws see e.g.: Uladzislau Belavusau, “The Rise of
Memory Laws in Poland an Adequate Tool to Counter Historical Disinformation?,”
Security and Human Rights 29, Issue 1–4 (2018): 37–38.
5
Marta Buholc, “Law,” in The Routledge Handbook of Memory Activism, eds. Yifat
Gutman and Jenny Wüstenberg (London and New York: Routledge, 2023), 150.
6
See e.g.: Michael Hebbert, “The Street as Locus of Collective Memory,” Environment
and Planning D Society and Space 23: 581–596; Vasile Docea, “History, Ideology
and Collective Memory. Reconstructing the Identities of Timisoara by Means of
Monographies and Street Names during the Communist Regime (1947–1989),” Acta
Universitatis Sapientiae European and Regional Studies 1, no. 1 (2010): 83–102;
Bartłomiej Różycki, “Renaming Urban Toponomy as a Mean of redefining Local
Identity: The Case of Street Decommunization in Poland,” Open Political Science 1,
no. 1 (2017): 20–31. 4
For state of research on memory laws see e.g.: Uladzislau Belavusau, “The Rise of
Memory Laws in Poland an Adequate Tool to Counter Historical Disinformation?,”
Security and Human Rights 29, Issue 1–4 (2018): 37–38. 5
Marta Buholc, “Law,” in The Routledge Handbook of Memory Activism, eds. Yifat
Gutman and Jenny Wüstenberg (London and New York: Routledge, 2023), 150. 6
See e.g.: Michael Hebbert, “The Street as Locus of Collective Memory,” Environment
and Planning D Society and Space 23: 581–596; Vasile Docea, “History, Ideology
and Collective Memory. Reconstructing the Identities of Timisoara by Means of
Monographies and Street Names during the Communist Regime (1947–1989),” Acta
Universitatis Sapientiae European and Regional Studies 1, no. 1 (2010): 83–102;
Bartłomiej Różycki, “Renaming Urban Toponomy as a Mean of redefining Local
Identity: The Case of Street Decommunization in Poland,” Open Political Science 1,
no. 1 (2017): 20–31. Introduction An analysis of the content of legislation without the context
of a particular case may lead to the conclusion that it has no relevance
to the subject matter, but later in practice it nevertheless turns out that
it is decisive. Examining the role of such legislation in the implemen- 110 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... tation of the politics of memory is only possible using the case study
method. First, it is necessary to identify a specific conflict, and then
analyze all the legal instruments that were used by both sides of the
dispute. The results of such research make it possible to identify new
areas (often specific to a particular country or region) in which there
is an intense reciprocal relationship between law and memory. The installation of monuments in public space often becomes the
topic of heated disagreements. Situations in which there is a seri-
ous dissension in society about the appropriateness of commemo-
rating a particular person or event (in general or in some specific
way or place) are frequent. Usually these conflicts are analyzed from
the perspective of politics, sociology or history. However, it should
be remembered that in a democratic state under the rule of law, all
major interventions in public space must take place on the basis of
and within the limits of the law. That is why legal regulations can
become a tool in the hands of those who want to press through the
establishment of a certain monument. In turn, opponents of the same
commemoration can use legal institutions to prevent the criticized
initiative. Therefore, such conflicts can be a good subject for a case
study on regulations whose significance for social collective memory
is not obvious. This paper is a study of such a case from Poland. It analyzes the
instrumental use of administrative law to build a Monument to the
Victims of the Smoleńsk Tragedy on Piłsudski Square in Warsaw. Aside from the introduction and conclusion, the paper consists of five
parts. First, relevant information about the Smoleńsk Tragedy, the
place where it was to be commemorated and the monument itself is
briefly gathered. Then the legal regulations governing the construc-
tion of monuments in Poland are presented. 7
This was a war crime committed by the NKVD in the spring of 1940 – the Soviets
executed then at least 21,768 Polish citizens (including many Polish Army officers).
See: Anna M. Cienciala, Natalia S. Lebedeva and Wojciech Materski, eds., Katyn: A
Crime Without Punishment. Annals of Communism Series (New Haven: Yale Univer-
sity Press, 2008). 8
Agnieszka Bejma, „Od afery Rywina do katastrofy smoleńskiej – nowe (utrwalone)
podziały społeczno-polityczne w Polsce,” Studia Politologiczne, nr 29 (2013): 127–
128. Introduction The following sections
analyze how instrumental use of existing and newly created laws has
been used by Poland’s ruling political forces to take control of the site
of the intended commemoration, to authorize the construction of the
monument despite the objections of local authorities, and to protect it
from possible attempts to remove it in the future. 111 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) 9
Arkadiusz Nyzio, „Znacząca nieobecność? Katastrofa smoleńska w kampaniach wy-
borczych 2015 roku,” in Oblicza kampanii wyborczych 2015, eds. Małgorzata Ku-
łakowska, Piotr Borowiec and Paweł Ścigaj (Kraków: Wydawnictwo Uniwersytetu
Jagiellońskiego, 2016), 436. 11
Halina Taborska, „Pomniki smoleńskie w Warszawie – lokalizacje, dzieła, kontrower-
sje,” Zeszyty naukowe PUNO, nr 7 (2019): 15. 1.1. The Smoleńsk Tragedy Smoleńsk Tragedy is the name commonly used in Poland for the
plane crash that took place at Smoleńsk North Airport near the city
of Smoleńsk, Russia, on April 10, 2010. At the time, a Tupolev Tu-
154 M belonging to the Polish Air Force crashed while attempting to
land. There were 96 people on board the machine, all of whom died. Among the delegation going to the ceremonies marking the seven-
tieth anniversary of the Katyń massacre7 were the president of the
Republic of Poland Lech Kaczyński and his wife Maria Kaczyńska,
the last president of the Republic of Poland in exile Ryszard Kac-
zorowski, deputy speakers of the Sejm and Senate, 18 members of
parliament and the most important commanders of the Polish army.l The Smoleńsk Tragedy briefly united society and the political
class. However, it soon proved to be a source of new conflicts and
divisions. The first protests erupted after the announcement that the
presidential couple would be buried at Wawel Castle. Subsequent
tensions arose over the further fate of the cross spontaneously erect-
ed by scouts in front of the Presidential Palace shortly after the ca-
tastrophe, the investigation into the crash or the issue of returning the
wreckage of the plane to Poland. Attitudes toward the disaster over-
laid the lines of Poland’s long-standing political divisions, leading to
an intensification of conflicts.8 The topic of the Smoleńsk catastrophe 112 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... continued to play an important role in the electoral campaign ahead
of the 2015 presidential and parliamentary elections.9 Along with
the catastrophe, the “Smolensk myth” constructed around the figure
of the tragically deceased president was born. Its manifestations in-
clude numerous films, books or exhibitions devoted to the Smoleńsk
Tragedy, marches and happenings related to it or even recitals of
“Smoleńsk songs.”10 This event had a very great impact on Polish
social and political reality. Initiatives to commemorate it in the public
space should therefore come as no surprise to anyone. 10
Paweł Sendyka, „Narodziny „mitu smoleńskiego”,” Prace Etnograficzne, nr 1 (2013):
49. 14
Portal Samorządowy, „Warszawa: Radni zdecydują o lokalizacji pomnika smoleń-
skiego,” April 9, 2015. Accessed August 20, 2023, https://www.portalsamorzadowy.
pl/komunikacja-spoleczna/warszawa-radni-zdecyduja-o-lokalizacji-pomnika-
smolenskiego,69385.html 15
Dziennik Gazeta Prawna, „Sasin: Na początku przyszłego tygodnia podamy nowe
lokalizacje pomników smoleńskich,” January 26, 2018. Accessed August 20, 2023,
https://www.gazetaprawna.pl/wiadomosci/artykuly/1100549,jacek-sasin-na-poczat-
ku-przyszlego-tygodnia-podamy-nowe-lokalizacje-pomnikow-smolenskich.html 13
Michał Wotjczuk, „3 mln zł za dwa pomniki ofiar katastrofy smoleńskiej. „Mają
nie być okazałe, ale bardzo okazałe”,” Gazeta Wyborcza, April 13, 2017. Accessed
August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,21631078,3-mln-
zl-za-dwa-pomniki-ofiar-katastrofy-smolenskiej-maja.html#S.embed_link-K.C-B.1-
L.2.zw 12
Anna Szulc, „Pomnik smoleński przed Pałacem. Co prezydent Duda zlecił w sekre-
cie?”, Newsweek, March 21, 2016. Accessed August 20, 2023, https://www.newsweek.
pl/polska/tajny-projekt-pomnika-lecha-kaczynskiego/ph1lknei 16
Wprost, „Ogłoszono miejsce postawienia warszawskiego Pomnika Ofiar Tragedii
Smoleńskiej,” February 7, 2018. Accessed August 20, 2023, https://www.wprost.
pl/kraj/10102659/ogloszono-miejsce-postawienia-warszawskiego-pomnika-ofiar-
tragedii-smolenskiej.html
17
Eugeniusz Szwankowski, Ulice i place Warszawy (Warszawa: Państwowe Wydawnic-
two Naukowe, 1970), 269.
18
Bartłomiej Kaczorowski (ed.), Encyklopedia Warszawy (Warszawa: Wydawnictwo
Naukowe PWN, 1994), 638. 1.2. Piłsudski Square Regardless of any controversy surrounding the Smoleńsk catastro-
phe, there was no doubt about the unprecedented magnitude of the
tragedy. It is therefore not surprising that discussions about the need
to commemorate it began shortly after the victims’ funerals. The de-
bates focused on three potential locations. Two of them were speci-
fied precisely from the beginning. The first was the crash site at the
Smoleńsk North Airport, while the second was the section of the
Powązki Military Cemetery in Warsaw, where 28 of the crash victims
were buried. The third location was to be some open urban space in
the Polish capital, suitable for a commemoration of this kind.11 Initially, there was even discussion of erecting a monument in
front of the Presidential Palace on Krakowskie Przedmieście Street. It was supposed to commemorate only Lech Kaczyński, replacing
the monument to Prince Poniatowski, that would have to be moved 113 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) to another location, which aroused great controversy.12 Later, loca-
tions (already for two individual monuments: to the victims of the
Smoleńsk catastrophe and separately to Lech Kaczyński) were also
indicated on Krakowskie Przedmieście Street, but at a slightly great-
er distance from the Presidential Palace. This variant was supported
by the chairman of the Law and Justice party, Jarosław Kaczyński
(brother of the president, who died in the crash), and Jacek Sasin –
a Law and Justice party politician particularly involved in the con-
struction of the monuments.13 However, the local government of
Warsaw did not want to agree to this location, pointing out that it was
not accepted by the city’s conservator of monuments. Instead, they
proposed (in agreement with some of the families of the victims of
the crash) to erect the monument at the corner of Trębacka Street and
Focha Street, in the immediate vicinity of Krakowskie Przedmieście
Street.14 In January 2018 Jacek Sasin rather unexpectedly announced that
a new location for the monuments which would be “easier to carry
out” would be announced soon, and according to him, no properties
managed by the authorities of Warsaw can be considered in this con-
text.15 On February 7, 2018, ‘Social Committee for the Construction
of Monuments: The late President of the Republic of Poland Lech 114 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... 21
„Skład Komitetu,” Komitet Społeczny Budowy Pomników: Śp. Prezydenta RP Lecha
Kaczyńskiego oraz Ofiar Tragedii Smoleńskiej 2010 roku. Accessed August 20, 2023,
http://web.archive.org/web/20190121152818/http://komitetspolecznybudowypomni-
kow.pl/sklad-komitetu.html 19
Rzeczpospolita, „Sondaż: Czy pomnik smoleński stawiać na placu Piłsudskiego,”
February 14, 2018. Accessed August 20, 2023, https://www.rp.pl/spoleczenstwo/
art9934341-sondaz-czy-pomnik-smolenski-stawiac-na-placu-pilsudskiego 20
Michał Wojtczuk, „71 proc. warszawiaków w sondażu przeciwko budowie pomnika
smoleńskiego na pl. Piłsudskiego,” Gazeta Wyborcza, November 22, 2017. Accessed
August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22681241,71-
proc-warszawiakow-w-sondazu-przeciwko-budowie-pomnika-smolenskiego.html 19
Rzeczpospolita, „Sondaż: Czy pomnik smoleński stawiać na placu Piłsudskiego,”
February 14, 2018. Accessed August 20, 2023, https://www.rp.pl/spoleczenstwo/
art9934341-sondaz-czy-pomnik-smolenski-stawiac-na-placu-pilsudskiego
20
Michał Wojtczuk, „71 proc. warszawiaków w sondażu przeciwko budowie pomnika
smoleńskiego na pl. Piłsudskiego,” Gazeta Wyborcza, November 22, 2017. Accessed
August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22681241,71-
proc-warszawiakow-w-sondazu-przeciwko-budowie-pomnika-smolenskiego.html
21
„Skład Komitetu,” Komitet Społeczny Budowy Pomników: Śp. Prezydenta RP Lecha
Kaczyńskiego oraz Ofiar Tragedii Smoleńskiej 2010 roku. Accessed August 20, 2023,
http://web.archive.org/web/20190121152818/http://komitetspolecznybudowypomni-
kow.pl/sklad-komitetu.html 1.2. Piłsudski Square Kaczyński and the Victims of the 2010 Smoleńsk Tragedy’ has an-
nounced that the Smoleńsk monument will be built in the immediate
vicinity of Piłsudski Square.16 Marshal Józef Piłsudski Square (this is the full name) is located in
Warsaw’s Śródmieście district, between the Saxon Garden and Moli-
er, Królewska, Tokarzewski-Karaszewicz and Ossolińscy Streets. It
was created as the courtyard of the Saxon Palace (built in 1712–1727
through a major expansion of the manor house that previously existed
there). In the interwar period, the Tomb of the Unknown Soldier was
located under the colonnade of the palace. The fragment of the colon-
nade with this tomb is the only part of the Saxon Palace that survived
after the structure was blown up by German troops in 1944 (measures
have now been taken to rebuild it). During the People’s Poland peri-
od, the square was called Victory Square.17 Piłsudski Square was the
site of many events of a different nature: both the parades of the Ger-
man occupiers during World War II, official celebrations in People’s
Poland (such as the May Day parades), but also manifestations of
the anti-communist opposition or the Mass celebrated by Pope John
Paul II and the funeral ceremonies of Cardinal Stefan Wyszyński.18
Therefore, there is no doubt that this is a place of special significance
for the history of Warsaw and Poland. It is worth mentioning that, according to public opinion research,
the idea of building a Smoleńsk monument in Piłsudski Square has
not gained widespread support. In a poll commissioned by the Rzec-
zpospolita daily newspaper, 60.8% of respondents said that the mon-
ument should not be erected in this location. Only 17.6% of peo-
ple expressed support for its construction in this site. 21.8% had no 115 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) opinion.19 In a poll conducted only among Warsaw residents at the
request of the capital’s City Hall, as many as 71% of people vot-
ed against the construction of a Smoleńsk monument in Piłsudski
Square.20 The location finally designated for the Monument to the
Victims of the Smoleńsk Tragedy was therefore highly controversial
not only among politicians, but also in society. 1.3. Monument to the Victims of the Smoleńsk Tragedy 22
Taborska, „Pomniki smoleńskie w Warszawie – lokalizacje, dzieła, kontrowersje,” 36.
23
Maria Czaputowicz-Głowacka, „Narracje heroiczne w przestrzeni miejskiej”, Stan
Rzeczy, nr 19 (2020): 191.
24
„To nie są tylko schody do nieba”. Jerzy Kalina o pomniku smoleńskim, Polskie Radio
24. Accessed August 20, 2023, https://polskieradio24.pl/130/5927/artykul/2717701,to-
nie-sa-tylko-schody-do-nieba-jerzy-kalina-o-pomniku-smolenskim
25
Ustawa z dnia 7 lipca 1994 r. Prawo budowlane (consolidated text: Dz.U. 2023
poz. 682). 1.3. Monument to the Victims of the Smoleńsk Tragedy The commemoration was initiated by the ‘Social Committee for the
Construction of Monuments: The late President of the Republic of
Poland Lech Kaczyński and the Victims of the 2010 Smoleńsk Trag-
edy,’ established on April 26, 2016, which was also the organizer
of the public fundraising for this purpose. It included many lead-
ing Law and Justice party politicians, including Jarosław Kaczyński,
Mariusz Błaszczak and Marek Kuchciński. It also included relatives
of some of the victims of the crash and right-wing journalists, such
as Bronisław Wildstein and Marcin Wolski.21 Therefore, this social
organization cannot be considered apolitical. The social committee organized a competition to develop a de-
sign for a Monument to the Victims of the Smoleńsk Tragedy. It was
resolved on October 19, 2017 by a jury chaired by Prof. T. J. Żu-
chowski, an art historian from Adam Mickiewicz University in
Poznań. The chosen design was submitted by Jerzy Kalina, a gradu-
ate of the Painting Department of the Academy of Fine Arts in War- 116 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... saw, sculptor, theater and film set designer, as well as creator of doc-
umentary films and theater performances.22 The monument was unveiled on April 10, 2018, the eighth an-
niversary of the catastrophe. It has the form of a black block 6 me-
ters high. Its shape is reminiscent of an airplane passenger boarding
stairs. On its front are 96 names of the victims in alphabetical order.23
The author of the monument said this about his intentions: “I wanted
the usually empty square to resemble an airport waiting for the re-
turn, and in this space there was a gangway with lights.”24 2. Polish legal regulations on
the construction of monuments Before describing the case of the Monument to the Victims of the
Smoleńsk Tragedy, it is necessary to clarify what legal regulations
apply to the erection of monuments in Poland. The key legal act in
this context should be considered the Construction Law.25 Its Article
3 point 3 puts the monuments in the category of structures. Accord-
ing to Article 3 point 1, a structure is one of the types of construction
structures. Article 3 point 7, on the other hand, states that the con-
struction of a construction structure is construction work. According
to Article 28 Section 1 of the Construction Law, construction work
can only be started on the basis of a construction permit decision. The
law provides for many exceptions to this rule, but the construction of
a monument is not one of them. Therefore, an analysis of all these
definitions leads to the conclusion that the erection of a monument
in Poland requires a construction permit in the form of an adminis- 117 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) trative decision. Pursuant to Article 82 Section 2 in conjunction with
Article 28 Section 1a, such a decision is issued by the relevant local
self-government authorities at the level of the powiat.26 Warsaw (like
other large cities in Poland) has the status of a city with the right of
a powiat. This means that it is not part of any powiat, and its local
government authorities perform all the tasks assigned in various laws
to powiat authorities. Consequently, in Warsaw, as a rule, it is the mu-
nicipal authorities that have the authority to issue decisions on con-
struction permits. As will become immediately apparent, in order to
obtain a permit it is necessary to dispose of the land for construction
purposes. Art. 3 point 11 of the Construction Law defines this as the
possession of a legal title arising from ownership, perpetual usufruct,
management, limited right in rem or a contractual relationship pro-
viding for the right to carry out construction work. This means that
the entity authorized to obtain a construction permit is not always the
owner of the land. In certain situations, the right to dispose of real
estate for construction purposes may be held by someone else, based
on one of the above-mentioned legal titles. 26
A powiat (sometimes translated as county) is the second of three levels of local
government in Poland, located above a municipality and below a voivodeship. 26
A powiat (sometimes translated as county) is the second of three levels of local
government in Poland, located above a municipality and below a voivodeship.
27
Ustawa z dnia 8 marca 1990 r. o samorządzie gminnym (consolidated text: Dz.U. 2023
poz. 40).
28
Beata Chanowska-Dymlang, „Rada gminy nie jest upoważniona do wyrażenia zgody
na budowę pomnika,” Legalis administracja, August 23, 2017. Accessed August 20,
2023,
https://gov.legalis.pl/rada-gminy-nie-jest-upowazniona-do-wyrazenia-zgody-
na-budowe-pomnika/ 27
Ustawa z dnia 8 marca 1990 r. o samorządzie gminnym (consolidated text: Dz.U. 2023
poz. 40). 28
Beata Chanowska-Dymlang, „Rada gminy nie jest upoważniona do wyrażenia zgody
na budowę pomnika,” Legalis administracja, August 23, 2017. Accessed August 20,
2023,
https://gov.legalis.pl/rada-gminy-nie-jest-upowazniona-do-wyrazenia-zgody-
na-budowe-pomnika/ 29
Tomasz Urzykowski, „Plac Piłsudskiego. Wojna wojewody z Zarządem Dróg Miej-
skich o „serce stolicy”,” Gazeta Wyborcza, October 27 2017. Accessed August 20,
2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22571263,plac-pilsudskiego-
wojna-wojewody-z-zarzadem-drog-miejskich.html
30
Ustawa z dnia 21 sierpnia 1997 r. o gospodarce nieruchomościami (consolidated text:
Dz.U. 2023 poz. 344).
31
Anna Trembecka, „Trwały zarząd jako forma władania nieruchomościami publicznymi
na przykładzie miasta Krakowa,” Acta Scientiarum Polonorum. Administratio
Locorum 16, nr 3 (2017): 216.
32
Leszek Bielecki, „Zarządzanie nieruchomościami a trwały zarząd nieruchomością,”
Rocznik Administracji Publicznej, nr 1(2015): 10. 2. Polish legal regulations on
the construction of monuments It is necessary to clarify here the meaning of Article 18 Section
2 point 3 of the Law on Municipal Self-Government,27 which stipu-
lates that adopting resolutions on the erection of monuments is the
exclusive competence of the municipal council (and therefore, in the
case of urban municipalities, the city council). It should be pointed
out that this provision is only related to the manner of exercising
ownership rights in the event that the monument in question is to
be located on land owned by the municipality.28 It does not give the
municipal council the right to decide on the erection of monuments 118 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... on land that has other owners (i.e. private or state-owned). It should
be understood as an indication that in the case of the construction of
a monument on land owned by the municipality, it is the municipal
council (and not, for example, the president of the city) that should
make the decision. The entity erecting a monument on its own land is
only required to obtain a construction permit. 32
Leszek Bielecki, „Zarządzanie nieruchomościami a trwały zarząd nieruchomością,”
Rocznik Administracji Publicznej, nr 1(2015): 10. 29
Tomasz Urzykowski, „Plac Piłsudskiego. Wojna wojewody z Zarządem Dróg Miej-
skich o „serce stolicy”,” Gazeta Wyborcza, October 27 2017. Accessed August 20,
2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22571263,plac-pilsudskiego-
wojna-wojewody-z-zarzadem-drog-miejskich.html 3. Struggle for control over Piłsudski Square As outlined above, in order to obtain a building permit, it is necessary
to have the right to dispose of the property on which the project is
to be located for construction purposes. Piłsudski Square is owned
by the State Treasury.29 However, for many years it was the Warsaw
authorities that held the right to dispose of this property for the con-
struction purposes, as described above, necessary to build the monu-
ment. This legal state of affairs requires clarification. The Law on Real Estate Management30 in its Article 43 intro-
duced the institution of the so-called permanent management. This is
a public-legal form of possession of national or municipal real estate
by organizational units without legal personality, distinct from lim-
ited rights in rem or civil law contracts.31 As a rule, state property
can only be put under the management of a state organizational unit,
and local government property only to a local government organi-
zational unit.32 However, the political system reforms carried out in
Poland in the 1990s created exceptions to this rule. The structure of 119 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) local government was then changed. In addition to communes and
voivodships (the number of which was significantly reduced), a new,
intermediate level of local self-government was introduced – powi-
ats.33 As a result, it was necessary to adjust the categories of public
roads. Until then, there were national, municipal and voivodeship
roads, and powiat roads had to be introduced as well. According to
Article 103 of the Introductory Provisions of the Laws Reforming
Public Administration,34 national and provincial roads were listed in
an ordinance of the Council of Ministers. The existing national and
provincial roads not included in this list became powiat roads as of
January 1, 1999. Powiat road authorities became the legal successors
of the previous road authorities through the appropriate application
of Section 2 of Article 49 of the Law on Real Estate Management. This provision stipulates that permanent management should be es-
tablished over real estate in favor of the entities taking over the cor-
responding tasks. 36
Tomasz Żółciak, „Wojna o Plac Piłsudskiego w Warszawie. Władze stolicy mają plan, jak
go odzyskać,” October 31, 2017, Dziennik Gazeta Prawna. Accessed August 20, 2023,
https://wiadomosci.dziennik.pl/wydarzenia/artykuly/561558,spor-plac-pilsudskiego-
wladze-stolicy-kontra-wojewoda.html 33
See: Arkadiusz Ptak, „Territorial Self-government during Transformation in Poland.
Significance, Evolution and Conclusions de lege ferenda,” in Transformacja polska –
oczekiwania i rzeczywistość, eds. Joanna Dzwończyk and Jerzy Kornaś (Kraków: Wy-
dawnictwo Uniwersytetu Ekonomicznego, 2010), 311–321.
34
Ustawa z dnia 13 października 1998 r. Przepisy wprowadzające ustawy reformujące
administrację publiczną (Dz.U. nr 133 poz. 872).
35
„Wykaz dróg powiatowych w Warszawie,” Zarząd Dróg Miejskich w Warszawie. Ac-
cessed August 20, 2023, https://zdm.waw.pl/wp-content/uploads/2018/07/2015-02-20_
DZP_5_PN_5_15_Wykaz_drog_powiatowych_w_Warszawie.pdf
36
Tomasz Żółciak, „Wojna o Plac Piłsudskiego w Warszawie. Władze stolicy mają plan, jak
go odzyskać,” October 31, 2017, Dziennik Gazeta Prawna. Accessed August 20, 2023,
https://wiadomosci.dziennik.pl/wydarzenia/artykuly/561558,spor-plac-pilsudskiego-
wladze-stolicy-kontra-wojewoda.html 34
Ustawa z dnia 13 października 1998 r. Przepisy wprowadzające ustawy reformujące
administrację publiczną (Dz.U. nr 133 poz. 872). 35
„Wykaz dróg powiatowych w Warszawie,” Zarząd Dróg Miejskich w Warszawie. Ac-
cessed August 20, 2023, https://zdm.waw.pl/wp-content/uploads/2018/07/2015-02-20_
DZP_5_PN_5_15_Wykaz_drog_powiatowych_w_Warszawie.pdf 3. Struggle for control over Piłsudski Square Piłsudski Square is included in the list of powiat roads in Warsaw,
as a city with rights of the powiat.35 According to the regulations ana-
lyzed above, that is why the area had been under the permanent man-
agement of the Warsaw City Road Authority since the late 1990s.36
According to Section 2 of Article 43 of the Law on Real Estate Man-
agement, an entity to which real estate has been given into perma-
nent management has the right to carry out construction work on the 120 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... property. Permanent management is one of the legal titles that are the
basis for disposing of real estate for construction purposes according
to Art. 3 point 11 of the Construction Law, discussed in the previous
section. Therefore, in such a legal situation, the Warsaw Municipal
Road Administration was the entity authorized to obtain a building
permit for the investments planned in the area of Piłsudski Square,
even though the owner of the property was the State Treasury. However, on October 25, 2017 the Minister of Infrastructure and
Construction issued a decision to transfer Piłsudski Square into per-
manent management to the Mazovian Voivode.37 It should be noted
here that in the Polish administrative structure there is a kind of dual-
ism at the voivodship level. In addition to local government (headed
by a marshal of the voivodship appointed by the voivodship assem-
bly coming from direct elections), there is also government adminis-
tration, headed by a voivode (representative of the Council of Minis-
ters in the voivodship, appointed by the Prime Minister). This means
that, as a result of the decision of the Minister of Infrastructure and
Construction, the management of Piłsudski Square was taken away
from a local government unit (linked to the political opposition) and
transferred to a body fully dependent on the parliamentary majority. It should be noted that in accordance with Article 46a Section 1
of the Law on Real Estate Management, as a rule, the Minister of
Infrastructure and Construction had the right to issue a decision to
terminate permanent management, and in accordance with Article 60
Section 3 in conjunction with Section 1, was allowed to subsequently
transfer the property to permanent management for the needs of the
voivodship office. Therefore, there is no obvious violation of the law
here. 37
Urzykowski, „Plac Piłsudskiego.” 40
Patrycja Wieczorkiewicz and Paweł Gawlik, „Plac Piłsudskiego podzielony na nowo.
Rzecznik ratusza: Nie było konsultacji,” Gazeta Wyborcza, January 5, 2018. Accessed
August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22861523,plac-
-pilsudskiego-podzielony-na-nowo-rzecznik-ratusza-nie.html 38
„Oświadczenie w sprawie placu Piłsudskiego w Warszawie,” Wojewoda Mazo-
wiecki, October 27, 2017. Accessed August 20, 2023, https://web.archive.org/
web/20180210002409/https://www.mazowieckie.pl/pl/aktualnosci/komunika-
ty/34763,Oswiadczenie-w-sprawie-placu-Pilsudskiego-w-Warszawie.html 39
Żółciak, „Wojna o Plac Piłsudskiego w Warszawie.” 38
„Oświadczenie w sprawie placu Piłsudskiego w Warszawie,” Wojewoda Mazo-
wiecki, October 27, 2017. Accessed August 20, 2023, https://web.archive.org/
web/20180210002409/https://www.mazowieckie.pl/pl/aktualnosci/komunika-
ty/34763,Oswiadczenie-w-sprawie-placu-Pilsudskiego-w-Warszawie.html
39
Żółciak, „Wojna o Plac Piłsudskiego w Warszawie.”
40
Patrycja Wieczorkiewicz and Paweł Gawlik, „Plac Piłsudskiego podzielony na nowo.
Rzecznik ratusza: Nie było konsultacji,” Gazeta Wyborcza, January 5, 2018. Accessed
August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22861523,plac-
-pilsudskiego-podzielony-na-nowo-rzecznik-ratusza-nie.html 3. Struggle for control over Piłsudski Square However, it is worth to analyze the authorities’ communicated
motives for this decision to assess whether the law was instrumental-
ly used in this case to achieve political goals. In a statement published on October 27, 2017, the Mazovian
Voivode stated that the decision to transfer to him Piłsudski Square 121 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) for permanent management was made at his request. He justified it
by the fact that “it is a place that primarily serves the organization of
state ceremonies and therefore should be under the supervision of the
government administration.”38 On the other hand, the authorities of
Warsaw pointed out that so far there have been no problems with the
organization of state ceremonies at the site, and besides, the Tomb
of the Unknown Soldier itself is still located on a separate plot still
owned by the city, so any ceremonies that include the tomb will still
have to be organized in consultation with the authorities of Warsaw. The local government also argued that taking the management of the
property away from the Warsaw Municipal Road Administration is
impossible as long as it includes powiat roads.39 It seems that the
government administration in this case partially conceded to the city
authorities. However, this did not involve returning the management
of Piłsudski Square to the local self-government unit. Instead, an di-
vision of the plot of land was made to exclude streets adjacent to the
square.40 In the manner described above, the government authorities took
control of Piłsudski Square from the local self-government. They
used legitimate means to do so. However, it is significant that they
were employed only at this moment, despite the existence of an
unchanged legal status for many years. When asked by journalists
whether taking control of the square was not a step towards building
a monument there to the victims of the Smolensk catastrophe, the
Mazovian Voivode replied that another location had been chosen for 122 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... it.41 Admittedly, Piłsudski Square was not officially designated as a
place of commemoration until several months later, in early 2018. The issue of permanent management was the most important issue in
the context of Piłsudski Square for only a short time. 41
Urzykowski, „Plac Piłsudskiego.”
42
Decyzja nr 231 Ministra Spraw Wewnętrznych i Administracji z dnia 31.10.2017 r. w
sprawie ustalenia terenu zamkniętego. Accessed August 20, 2023, https://archiwum-
bip.mswia.gov.pl/bip/komunikaty/25079,Decyzja-nr-231-Ministra-Spraw-Wewnetrz-
nych-i-Administracji-z-dnia-31102017-r-w-s.html
43
Ustawa z dnia 17 maja 1989 r. Prawo geodezyjne i kartograficzne (consolidated text:
Dz.U. 2023 poz. 1752). 3. Struggle for control over Piłsudski Square Just a few days
later, further legally momentous events occurred that would eventu-
ally lead to the construction of the Monument to the Victims of the
Smoleńsk Tragedy there. 43
Ustawa z dnia 17 maja 1989 r. Prawo geodezyjne i kartograficzne (consolidated text
Dz.U. 2023 poz. 1752). 4. “Militarization” of Piłsudski Square Taking over the management of Piłsudski Square from Warsaw’s lo-
cal authorities was only the first stage of seizing effective control
over the site by government authorities through legal measures. The
decision issued on October 31, 2017 by the Minister of Internal Af-
fairs and Administration is of the most momentous significance.42
It says that the Minister has declared plots of land encompassing
Piłsudski Square a so-called closed area. The aforementioned decision was issued on the basis of Article 4,
Section 2a of the Geodetic and Cartographic Law,43 which states that
closed areas are established by the competent ministers and heads of
central offices by decision. But what is this „closed area”? The Geo-
detic and Cartographic Law, in its Article 2, contains a glossary con-
sisting of definitions of terms used in the act. Its point 9 specifies that
closed areas are understood to be areas of a restricted character for
reasons of state defense and security, defined by the competent min-
isters and heads of central offices. According to the jurisprudence of
the Polish administrative courts, the very fact of recognizing an area
as a closed area determines the designation of that area for purposes 123 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) related to national defense and security.44 This means that the Min-
ister of Internal Affairs and Administration has recognized Piłsudski
Square as an area of special military significance. The regulations on closed areas for the purposes of national de-
fense and security are quite laconic, but an analysis of their content
allows to understand quite well what was the aim of the legislator
introducing these regulations. There is a number of solutions in the
Geodetic and Cartographic Law that allow for the classification of
information on technical infrastructure, plots of land, buildings and
dwellings located in closed areas. Land and building records main-
tained for an area where a closed area has been designated must im-
mediately be brought into compliance with regulations on the pro-
tection of classified information. The literature indicates that this re-
quirement comes out of the need to ensure security and state defense
readiness.45 It follows that the essence of closed areas should be a
limited access to information about what is located within them. 44
Monika Ziniewicz, „Administracyjnoprawne ograniczenia procesu inwestycyjno-bu-
dowlanego na terenach zamkniętych w Polsce,” Studia Iuridica Toruniensia, t. XXIX
(2021): 490.
45
Mirosław Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo
państwa ustanawiane przez organy administracji rządowej,” Ius Novum, nr 4 (2016):
199.
46
Rozporządzenie Ministra Obrony Narodowej z dnia 18 lipca 2003 r. w sprawie
terenów zamkniętych niezbędnych dla obronności państwa (Dz.U. nr 141 poz. 1368). 44
Monika Ziniewicz, „Administracyjnoprawne ograniczenia procesu inwestycyjno-bu-
dowlanego na terenach zamkniętych w Polsce,” Studia Iuridica Toruniensia, t. XXIX
(2021): 490. 4. “Militarization” of Piłsudski Square This
would be hard to achieve in the case of an open, publicly accessible
space located in the heart of a large city, such as Piłsudski Square. The Ordinance of the Minister of Defense on Closed Areas Neces-
sary for State Defense46 contains a list of closed areas where the Min-
ister of Defense supervises surveying and mapping work. It includes,
inter alia, command posts of the Armed Forces of the Republic in a
state of threat to state security and war, facilities for radio reconnais-
sance and combat and national air and anti-aircraft defense, telecom-
munications facilities for the transmission of classified information
constituting state secrets, war ports, military airports or ammunition
depots and warehouses. It should be borne in mind that this is not a 124 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... complete enumeration of closed areas, because the supervision of the
Minister of National Defense over surveying and mapping work has
not been introduced for all of them, but it clearly comes out from this
enumeration that the legislator was concerned with areas very direct-
ly related to state defense, with strictly military use. There is no doubt
that Piłsudski Square is not such an area. On November 17, 2017, a little more than two weeks after the
decision discussed above was issued, the Ministry of Internal Affairs
and Administration released a written statement,47 informing that
Piłsudski Square will continue to be accessible to residents and tour-
ists, and its area will not be fenced off. This was most likely to dispel
doubts that may have come out of the colloquial understanding of the
term closed area. The Ministry further wrote that “Piłsudski Square
is a place where national holidays and major ceremonies are held.”
It did not indicate what role the area has for state defense. It did not
explain what connection the said state holidays and celebrations have
with state defense. So what was the most likely real purpose of declaring Piłsudski
Square a closed area? The answer must be sought in the already cited
Construction Law. The key is Section 3 point 5 of Article 82, which
stipulates that the architectural and construction administration body
of first instance (i.e. the entity competent to issue decisions on con-
struction permits) in the case of objects and construction work locat-
ed in closed areas is the voivode. 47
„Oświadczenie MSWiA w sprawie placu Piłsudskiego,” Ministerstwo Spraw We-
wnętrznych i Administracji. Accessed August 20, 2023, https://archiwum.mswia.gov.
pl/pl/aktualnosci/16730,Oswiadczenie-MSWiA-w-sprawie-placu-Pilsudskiego.html 4. “Militarization” of Piłsudski Square This is an exception to the already
mentioned general rule, according to which construction permits are
issued in Poland by the head of the powiat (and in the case of cities
with the rights of a powiat – such as Warsaw – by the president of
the city). This means that the recognition of Piłsudski Square as a
closed area automatically shifted the competence to issue building
permits (as described above, required in the case of erecting a mon-
ument) from a local self-government body, controlled by one side of 125 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) the dispute over the Smoleńsk monument, to an authority directly
controlled by the government, coming from the political group that is
the other side of that dispute. The matter of issuing building permits should be considered most
important in the context of the construction of the Monument to the
Victims of the Smoleńsk Tragedy, but it is worth to mention the sec-
ond area in which the competencies of Warsaw’s local authorities
have been drastically reduced in a result of the recognition of Piłsud-
ski Square as a closed area. According to Article 3 Section 1 of the
Law on Spatial Planning and Development,48 the shaping and con-
ducting of spatial policy on the territory of the municipality, includ-
ing the adoption of local spatial plans, is one of the municipality’s
own tasks. However, this does not apply to closed areas. According
to Article 4 Section 1 of this law, the determination of land use, the
location of public purpose investments and the determination of the
ways in which land is used and developed shall be made in a local
spatial plan. However, Article 4 Section 2 point 2 stipulates that with
regard to closed areas, only the boundaries of these areas are estab-
lished in the local spatial plan. What is more, in the case of spatial planning and development,
the recognition of a particular site as a closed area results in a transfer
of authority similar to that of a building permit. According to Arti-
cle 51 of the discussed law, in matters of determining the location
of a public purpose investment, decisions are issued by the head of
the municipality (i.e. the local government). However, if it is a pub-
lic purpose investment in a closed area, the voivode (i.e. 48
Ustawa z dnia 27 marca 2003 r. o planowaniu i zagospodarowaniu przestrzennym
(consolidated text: Dz.U. 2023 poz. 977). 4. “Militarization” of Piłsudski Square the rep-
resentative of the government) is authorized to issue the decision. Importantly, such a decision is necessary precisely when the area in
question is not covered by a spatial plan (and, as described above,
such a plan is not drawn up for a closed area). Therefore, recognizing
Piłsudski Square as a closed area not only made it impossible for the
Warsaw authorities to determine the manner of its development in 126 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... the local spatial plan, but also deprived them of the authority to issue
a decision to determine the location of a public purpose investment
necessary in the absence of a plan. Referring the provisions of the
Law on Spatial Planning and Development to the case of the Mon-
ument to the Victims of the Smoleńsk Tragedy, it should be pointed
out that the application for a decision establishing the location of a
public purpose investment was submitted by Jacek Sasin on behalf of
the social committee on January 29, 2018, and the Mazovian Voivode
issued the decision on February 2. It became binding on February 5,
2018.49 It is worth recalling that the location of the monument was
made public by the social committee on February 7, 2018, that is,
when much of the paperwork required for its construction had al-
ready been completed. Therefore, it can be considered that the recognition of Piłsudski
Square as a closed area was another step towards the construction of
a Monument to the Victims of the Smoleńsk Tragedy in Warsaw, in
defiance of the local authorities of that city. After the “militarization”
of the square, the state authorities could not only freely dispose of the
property (which they ensured for themselves by taking over the man-
agement of the square by the voivode), but also gained the certainty
that there would be no problems with obtaining a building permit,
since the competence to issue one was also given to the voivode. It
seems that in the case of the decision to declare Piłsudski Square a
closed area, legal measures were used in the political dispute in a
much more instrumental way than in the matter of taking over the
management of the square. 49
Portal Samorządowy, Wojewoda mazowiecki zatwierdził lokalizację Pomnika Ofiar
Tragedii Smoleńskiej, February 7, 2018. Accessed August 20, 2023, https://www.por-
talsamorzadowy.pl/polityka-i-spoleczenstwo/wojewoda-mazowiecki-zatwierdzil-lo-
kalizacje-pomnika-ofiar-tragedii-smolenskiej,103790.html 53
Michał Wojtczuk, „Jest decyzja prokuratury w sprawie przejęcia placu Piłsudskiego
przez rząd,” Gazeta Wyborcza, September 27, 2021. Accessed August 20, 2023, https://
warszawa.wyborcza.pl/warszawa/7,54420,27620065,plac-pilsudskiego-wziety-w-
kamasze-jest-decyzja-prokuratury.html 50
Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo państwa usta-
nawiane przez organy administracji rządowej,” 197. 52
Kamil Siałkowski, „Spór o pl. Piłsudskiego. Prokuratura musi jeszcze raz zba-
dać, czy Mariusz Błaszczak nie przekroczył uprawnień,” Gazeta Wyborcza, Oc-
tober 30, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warsza-
wa/7,54420,24111978,spor-o-plac-pilsudskiego-prokuratura-musi-jeszcze-raz-zba-
dac.html 51
„Zawiadomienie o możliwości popełnienia przestępstwa,” Miasto Stołecz-
ne Warszawa, Accessed August 20, 2023, https://um.warszawa.pl/document-
s/39703/7003459/2018_03_27_m._st._warszawa_zawiadomienie.pdf/adb2c111-d-
0df-e4f0-ce39-83af5329713a?t=1634498830960 50
Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo państwa usta-
nawiane przez organy administracji rządowej,” 197.
51
„Zawiadomienie o możliwości popełnienia przestępstwa,” Miasto Stołecz-
ne Warszawa, Accessed August 20, 2023, https://um.warszawa.pl/document-
s/39703/7003459/2018_03_27_m._st._warszawa_zawiadomienie.pdf/adb2c111-d-
0df-e4f0-ce39-83af5329713a?t=1634498830960
52
Kamil Siałkowski, „Spór o pl. Piłsudskiego. Prokuratura musi jeszcze raz zba-
dać, czy Mariusz Błaszczak nie przekroczył uprawnień,” Gazeta Wyborcza, Oc-
tober 30, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warsza-
wa/7,54420,24111978,spor-o-plac-pilsudskiego-prokuratura-musi-jeszcze-raz-zba-
dac.html
53
Michał Wojtczuk, „Jest decyzja prokuratury w sprawie przejęcia placu Piłsudskiego
przez rząd,” Gazeta Wyborcza, September 27, 2021. Accessed August 20, 2023, https://
b
l/
/7 54420 27620065
l
il
d ki
i t 4. “Militarization” of Piłsudski Square Indeed, the claim that in this situation a
legal institution was used contrary to its intended purpose envisaged
by the legislator is not groundless. The law in this case has become
an instrument for achieving political goals. Similar doubts were ex-
pressed by the authorities of Warsaw. 127 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) It should be noted that the decision to establish a closed area is
not an administrative decision. This means that it cannot be appealed
or challenged in an administrative court.50 In such a situation, the
authorities of Warsaw took another option. On March 27, 2018, they
filed a notice of possible commission of a crime by the Minister of
Internal Affairs and Administration Mariusz Blaszczak of exceeding
his powers to the prosecutor’s office. The Warsaw authorities indicat-
ed that the recognition of Piłsudski Square as a closed area despite
the absence of factual grounds related to defense and state security
reasons is an abuse of legal institutions. The notice stated that the
real purpose of these actions was to deprive the local authorities of
the powers they are entitled to under the binding law related to de-
cision-making in the field of spatial planning and development.51
However, the District Prosecutor’s Office in Warsaw refused to open
an investigation, stating that no crime had been committed in this
situation.52 The authorities of Warsaw filed a complaint against this
decision with the competent court. The latter recognized the com-
plaint and ordered the prosecutor’s office to launch an investigation. However, it was discontinued in 2021. The prosecutor’s office again
cited the absence of the elements of a criminal act.53 It should be
pointed out that the position of Attorney General at the time was held
by Zbigniew Ziobro – one of the members of the ‘Social Committee 128 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... for the Construction of Monuments: The late President of the Repub-
lic of Poland Lech Kaczyński and the Victims of the 2010 Smoleńsk
Tragedy.’ The application of regulations created to protect military areas,
such as firing ranges and naval bases, to an open, public space in the
center of the Polish capital made it possible to build the Monument
to the Victims of the Smoleńsk Tragedy at a site designated by a
committee associated with the politicians of Law and Justice party. 54
Oficjalna strona Prezydenta Rzeczypospolitej Polskiej, „Prezydent podpisał deklarację
o restytucji Pałacu Saskiego.” Accessed August 20, 2023, https://www.prezydent.
pl/aktualnosci/polityka-historyczna/100-rocznica-odzyskania-niepodleglosci-rp/
aktualnosci/11-listopada---symboliczny-poczatek-odbudowy-palacu-saskiego,8259 4. “Militarization” of Piłsudski Square In this place it is worth reminding that Minister of Internal Affairs
and Administration Mariusz Błaszczak, who issued the controversial
decision, was one of the members of this committee. However, this
was not the last situation in which regulations were creatively used in
relation to this monument. The ruling majority decided to reach for
such extraordinary legislative solutions that were designed to secure
the monument for the future. 55
Tomasz Żółciak, „Lex Saski receptą na ewentualny opór władz Warszawy,” Dzien-
nik Gazeta Prawna, 20 November 2018. Accessed August 20, 2023, https://www.
gazetaprawna.pl/wiadomosci/artykuly/1356455,lex-saski-recepta-na-ewentualny-
opor-wladz-warszawy.html 56
Druk nr 1388 Przedstawiony przez Prezydenta Rzeczypospolitej Polskiej projekt usta-
wy o przygotowaniu i realizacji inwestycji w zakresie odbudowy Pałacu Saskiego,
Pałacu Brühla oraz kamienic przy ulicy Królewskiej w Warszawie, July 7, 2021. Ac-
cessed August 20, 2023, https://www.sejm.gov.pl/Sejm9.nsf/druk.xsp?nr=1388 57
Ustawa z dnia 11 sierpnia 2021 r. o przygotowaniu i realizacji inwestycji w zakresie
odbudowy Pałacu Saskiego, Pałacu Brühla oraz kamienic przy ulicy Królewskiej w
Warszawie (Dz.U. 2021 poz. 1551). 58
Ustawa z dnia 21 sierpnia 1997 r. o gospodarce nieruchomościami (consolitated text:
Dz.U. 2023 poz. 344). 60
Katarzyna Żaczkiewicz-Zborska, „Odbudowa Pałacu Saskiego z poważnymi uster-
kami w ustawie,” Prawo.pl, July 23, 2021. Accessed August 20, 2023, https://www.
prawo.pl/samorzad/bledy-i-niedomowienia-w-ustawie-o-odbudowie-palacu-saskie-
go,509608.html; Business Insider Polska, „Odbudowa Pałacu Saskiego może przebie-
gać w atmosferze skandalu. Problematyczna specustawa,” August 16, 2021. Accessed
August 20, 2023, https://businessinsider.com.pl/wiadomosci/odbudowa-palacu-
saskiego-moze-przebiegac-w-atmosferze-skandalu/r7798pe 59
Katarzyna Domagała, „Ciąg dalszy kontrowersji wokół odbudowy Pałacu Saskiego.
Eksperci piszą otwarty list sprzeciwu, projekt wraca do Komisji Kultury,” Architektu-
ra i Biznes, July 22, 2021. Accessed August 20, 2023, https://www.architekturaibiznes.
pl/odbudowa-palacu-saskiego-list-otwarty-ekspertow,8380.html 5. Monument protected by a special law In the section on the history and architecture of Piłsudski Square, it
was mentioned that preparations are underway to rebuild the Saxon
Palace, which was once located there. This project also has a legal
dimension. Both the genesis and content of the regulations for the
planned reconstruction are related to the history of the Monument to
the Victims of the Smoleńsk Tragedy. The decision to reconstruct the Saxon Palace was made by Presi-
dent Andrzej Duda when he made the solemn declaration on Novem-
ber 11, 2018, as part of the celebration of the centennial of Polish in-
dependence.54 Just a few days later, the newspaper Dziennik Gazeta
Prawna, citing anonymous sources connected with the government,
reported that the authorities were considering enacting a special law 129 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) separately regulating the rules for the implementation of only this
one investment. According to unnamed ruling party politicians, such
a solution was to be necessary because the Saxon Palace was to be
rebuilt on land belonging to the city, and the story of the construction
of the Monument to the Victims of the Smoleńsk Tragedy showed
that the Warsaw authorities are unwilling to cooperate on govern-
ment projects.55i A draft of the new legislation was submitted to the first chamber
of the Polish parliament on July 7, 2021.56 Just over a month later, the
Act of August 11, 2021 on the preparation and implementation of in-
vestments in the reconstruction of the Saxon Palace, the Brühl Palace
and the townhouses on Królewska Street in Warsaw was passed.57 The new law has ruthlessly resolved the problem of ownership of
the land on which the Saxon Palace is to be reconstructed. According
to its Article 37 Section 1, real estate in the area where the recon-
struction will be carried out automatically becomes the property of
the State Treasury by force of law, after the voivode issues a decision
on determining the location of the investment. This is a special mode
of property acquisition by the state. The provisions of the Real Es-
tate Management Act58 allow expropriation of real estate for public
purposes only after a separate procedure, to which the entire Chapter
4 of this law is dedicated. In the case of the reconstruction of the
Saxon Palace, it was decided to speed up the proceedings not only 130 Piotr Eckhardt. 59
Katarzyna Domagała, „Ciąg dalszy kontrowersji wokół odbudowy Pałacu Saskiego.
Eksperci piszą otwarty list sprzeciwu, projekt wraca do Komisji Kultury,” Architektu-
ra i Biznes, July 22, 2021. Accessed August 20, 2023, https://www.architekturaibiznes.
pl/odbudowa-palacu-saskiego-list-otwarty-ekspertow,8380.html
60
Katarzyna Żaczkiewicz-Zborska, „Odbudowa Pałacu Saskiego z poważnymi uster-
kami w ustawie,” Prawo.pl, July 23, 2021. Accessed August 20, 2023, https://www.
prawo.pl/samorzad/bledy-i-niedomowienia-w-ustawie-o-odbudowie-palacu-saskie-
go,509608.html; Business Insider Polska, „Odbudowa Pałacu Saskiego może przebie-
gać w atmosferze skandalu. Problematyczna specustawa,” August 16, 2021. Accessed
August 20, 2023, https://businessinsider.com.pl/wiadomosci/odbudowa-palacu-
saskiego-moze-przebiegac-w-atmosferze-skandalu/r7798pe 5. Monument protected by a special law Who should Issue a Permit for the Memorial? Administrative Law as a Platform... in terms of expropriating the necessary real estate. Procedures for
determining compensation for their former owners were also simpli-
fied, as well as those for the construction supervision of the ongoing
investment. As a result, the law has stirred up controversy in various
circles. Architectural historians have issued an open letter against it. Their concerns included the exclusion of the rebuilt Palace from the
supervision of the monument protection service.59 Legal community
criticized the law for drafting errors and ambiguities, in addition to
severe restrictions on the powers of local government.60 Therefore, the reconstruction of the Saxon Palace involves a
similar dispute between government authorities and local self-gov-
ernment as the construction of the Monument to the Victims of the
Smoleńsk Tragedy. However, the government learned from the first
conflict and did not rely solely on already existing legal instruments. In this case, it has decided to create completely new regulations that
will allow the implementation of the intended project without the
possibility of resistance from local authorities. The dispute over the construction of the Monument to the Vic-
tims of the Smoleńsk Tragedy was one of the reasons for the special
law on the reconstruction of the Saxon Palace. At the same time, its
provisions also directly regulate the legal situation of the monument
itself. Article 36 of the analyzed act gave special legal protection to
Marshal Józef Piłsudski Square with the following objects located
there: Tomb of the Unknown Soldier, Monument to Józef Piłsudski,
Papal Cross, Monument to Lech Kaczyński and Monument to the 131 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) Victims of the 2010 Smoleńsk Tragedy. According to this provision,
the urban layout encompassing the square and these objects is invio-
lable (of course, including the reconstructed Saxon Palace). This is a situation unprecedented in the Polish legal system, con-
sisting of general and abstract norms as a rule, in which the legis-
lator decided to secure the future of several specific monuments at
the level of an act of statutory rank. This demonstrates the great im-
portance attached to these objects by the political force that formed
the parliamentary majority at the time the discussed law was passed. 5. Monument protected by a special law The legislation lists all the objects located in Piłsudski Square, but
the presence there of the Tomb of the Unknown Soldier, the Papal
Cross or the Monument to Józef Piłsudski does not raise any dispute
in principle. Therefore, it can be presumed that the main purpose of
introducing the discussed provision in the Law on the Reconstruc-
tion of the Saxon Palace was to protect the controversial Monument
to the Victims of the Smoleńsk Tragedy and the Monument to Lech
Kaczyński. Conclusions On the basis of the analysis presented above, it can be concluded that
the instrumental use of administrative law allowed the construction
of a monument desired by the political forces controlling the gov-
ernment administration in the very center of the city, whose local
authorities expressed open opposition to commemoration at this par-
ticular site. First, the voivode took control of the site where the monument
was to be erected. He exercised his authority in this case, and there
is no violation of the law in this case. However, the justification for
this decision cannot be considered convincing. The claim that it was
issued solely to facilitate the construction of the Monument to the
Victims of the Smoleńsk Tragedy seems justified. Shortly thereafter, legal instruments created to ensure the national
security and defense were used to circumvent the requirement to ob- 132 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... tain positive decisions from local authorities before building a monu-
ment under construction law and spatial planning law. Finally, special provisions drafted to protect the Smolensk Trag-
edy Victims Monument have been introduced into the newly creat-
ed legislation, so that its removal will be difficult even if there is a
change in the balance of political forces in the future. It is therefore clear that the instrumental use of the law can be a
way to break the resistance of opponents to the implementation of
a certain memory policy in the public space even when these oppo-
nents are democratically elected local self-government authorities. l The pattern in which the conflict over the monument’s construc-
tion revolves between the right-wing populist central government
and the liberal local municipal authorities linked to the opposition to
the forces establishing illiberal democracy can be observed not only
in Poland. A very similar case took place in Hungary ruled by Viktor
Orbán’s Fidesz. Right-wing state authorities intended to erect a new
monument to the victims of the German occupation of Hungary in
Liberty Square in Budapest. The city authorities originating from po-
litical circles opposing Fides resisted against that project. Therefore,
the Orbán government issued a decree declaring the project an issue
of particular importance with regard to the national economy. 61
Ágnes Erőss, ““In Memory of Victims”: Monument and counter-monument in
LibertySquare, Budapest,” Hungarian Geographical Bulletin 65, no. 3 (2016): 241. Conclusions As a
result, construction of the monument could begin not only without
the required permits, but also without a tender process.61 The story of the legal dispute over the Monument to the Victims
of the Smoleńsk Tragedy proves that a democratic state needs mech-
anisms to prevent the circumvention of the law and the extremely
instrumental use of legal institutions contrary to their intended pur-
pose by the legislator in order to achieve current political goals. Even
the issue of building a monument in a certain square may be a sit-
uation in which such mechanisms for protecting the rule of law as
an independent prosecutor’s office, a constitutional judiciary or tools
for enforcing compliance with the principles of good legislation will 133 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) be crucial. Their functioning is necessary so that disputes over the
placement of controversial commemorations in the public space can
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https://openalex.org/W3007007446 | https://europepmc.org/articles/pmc7063879?pdf=render | English | null | Effects of Routine Checkups and Chronic Conditions on Middle-Aged Patients with Diabetes | Advances in preventive medicine | 2,020 | cc-by | 5,657 | Hindawi
Advances in Preventive Medicine
Volume 2020, Article ID 4043959, 8 pages
https://doi.org/10.1155/2020/4043959 Hindawi
Advances in Preventive Medicine
Volume 2020, Article ID 4043959, 8 pages
https://doi.org/10.1155/2020/4043959 Hindawi America E. McGuffee
, Kailyn Chillag, Amber Johnson, Regan Richardson,
Hallie Williams, and Jessica Hartos epartment of Physician Assistant Studies, University of North Texas Health Science Center, Fort Worth, TX, USA Received 18 June 2019; Accepted 28 August 2019 Academic Editor: Gerardo E. Guillén Nieto Copyright © 2020 America E. McGuffee et al. This is an open access article distributed under the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly
cited. Purpose. Middle-aged males and females with diabetes are more likely to have poor physical (PH) and mental health (MH); however,
there is limited research determining the relationship between MH and PH and routine check-up in diabetic middle-aged adults,
especially by gender. The purpose of this study was to determine whether PH and MH status differ by routine check-up in middle-
aged (age 45–64) adults with diabetes in the general population. Methods. This cross-sectional analysis used data from the 2017
BRFSS conducted by the CDC for adults aged 45–64 who reported having diabetes in Florida (𝑁= 1183), Kentucky (𝑁= 617),
Maryland (𝑁= 731), New York (𝑁= 593), and Ohio (𝑁= 754). Multiple logistic regression by state and gender was used to
determine the relationship between MH and PH status and routine check-up while controlling for health-related, socioeconomic, and
demographic factors. Results. Across states, up to one-half reported good PH (32–50%), over one-half reported good MH (46–67%),
and most reported having a routine check-up (87–93%). Adjusted analysis indicated that MH and PH were not significantly related
to routine check-up, but both were inversely related to having diabetes plus two other health conditions. Conclusions. Overall, routine
check-up was not related to good PH and MH in this target population; however, a number of health conditions were inversely
related to good PH and MH status. In a primary care setting for this target population, there may be a low to moderate prevalence
of good PH and MH and a high prevalence of having a routine check-up and having multiple health conditions. It is recommended
to automatically screen this target population for PH, MH, other chronic conditions, and physical activity and treat concurrently. 1. Introduction report having DM) [2]. Because this condition is chronic and
progressive, it can lead to other physical and mental health
complications over time [10–12, 14] . In addition, those with
diabetes report lower HRQoL ratings than do individuals
without chronic illnesses [10]. Thus, annual or more frequent
checkups would be necessary for persons with diabetes as
research indicates that preventative care decreases both the
prevalence and progression of this condition [6]. Through utilization of preventative health examinations and
routine checkups, the most common chronic physical and
mental health conditions can be prevented, delayed, or treated
more effectively [6, 11]. Visits of this type are linked with
improved physical and mental health outcomes [4, 5, 14] as
well as to improvements in health-related quality of life
(HRQoL) and control over diseases [10]. However, research
indicates that both engagement in preventative health checks
and overall perception of one’s health differ based on demo-
graphic factors, socioeconomic status, health insurance cover-
age, lifestyle factors, and disease burden [4, 5, 9, 10, 12–14].i However, research for associations between routine check-
ups and physical or mental health tends to focus on older
adults/Medicare users [4–6], with no studies assessing these
relations for differences by gender [9, 12–14] or by diabetes
status [4, 7, 8]. Therefore, the purpose of this study is to assess
whether physical and mental health differ by receiving a rou-
tine checkup in middle-aged males and females with
diabetes. Diabetes is a significant component of the disease burden
in the US as it affects up to 30 million adults, and of those, up
to 7 million may be undiagnosed (not aware of or did not Advances in Preventive Medicine 2 Table 1 (a): Participant characteristics by state: diabetic males. 1. Introduction Advances in Preventive Medicine 3 Table 1: Continued. (b): Participant characteristics by state: females with diabetes. 1. Introduction Variable
Florida (𝑁= 516)
Kentucky (𝑁= 236)
Maryland (𝑁= 311)
New York (𝑁= 300)
Ohio (𝑁= 323)
푁
%
푁
%
푁
%
푁
%
푁
%
Good mental health
516
100
236
100
311
100
300
100
323
100
Yes
333
65
131
56
207
67
199
66
209
65
No
183
35
105
44
104
33
101
34
114
35
Good physical health
516
100
236
100
311
100
300
100
323
100
Yes
232
45
87
37
154
50
141
47
142
44
No
284
55
149
63
157
50
159
53
181
56
Routine checkup
516
100
236
100
311
100
300
100
323
100
Yes
451
87
213
90
280
90
268
89
292
90
No
65
13
23
10
31
10
32
11
31
10
Health conditions
475
92
218
92
296
95
286
95
302
93
0 or 1 other health
condition
101
21
34
16
67
23
84
29
55
18
2 other health
conditions
374
79
184
84
229
77
202
71
247
82
Physical activity
461
89
214
91
270
87
248
83
300
93
Inactive
195
42
101
47
90
33
95
38
126
42
Insufficiently active
90
20
48
22
60
22
52
21
62
21
Active/Highly active
176
38
65
30
120
44
101
41
112
37
Weight status
487
94
230
97
295
95
287
96
315
98
Underweight or normal
53
11
27
12
34
12
32
11
34
11
Overweight
149
31
64
28
83
28
99
34
83
26
Obese
285
59
139
60
178
60
156
54
198
63
Tobacco use
495
96
229
97
296
95
277
92
315
98
Never
221
45
78
34
149
50
151
55
154
49
Former
182
37
82
36
90
30
85
31
113
36
Current
92
19
69
30
57
19
41
15
48
15
Alcohol use
495
96
228
97
298
96
293
98
313
97
None
299
60
157
69
146
49
138
47
182
58
Light
57
12
27
12
42
14
46
16
42
13
Moderate or excessive
139
28
44
19
110
37
109
37
89
28
Age
516
100
236
100
311
100
300
100
323
100
45–54
176
34
76
32
107
34
103
34
83
26
55–64
340
66
160
68
204
66
197
66
240
74
Ethnicity/Race
506
98
234
99
304
98
288
96
313
97
White
328
65
186
79
191
63
162
56
272
87
Other
178
35
48
21
113
37
126
44
41
13
Marital status
511
99
235
99
310
100
299
100
321
99
Married
292
57
130
55
187
60
145
48
190
59
Not married
219
43
105
45
123
40
154
52
131
41
Education level
515
100
233
99
310
100
297
99
321
99
Graduated college
126
25
56
24
209
33
93
31
75
23
Did not graduate
college
389
76
177
76
101
67
204
69
246
77
Income level
464
90
182
77
272
87
272
91
287
89
$50,000 or more
142
31
65
36
164
60
103
38
123
43
Less than $50,000
322
69
117
64
108
40
169
62
164
57
Employment status
512
99
235
99
309
99
291
97
322
99
Employed
217
42
94
40
181
59
147
51
154
48
Other
295
58
141
60
128
41
144
49
158
52 (a): Participant characteristics by state: diabetic males. 1. Introduction Variable
Florida (𝑁= 667)
Kentucky (𝑁= 381)
Maryland (𝑁= 420)
New York (𝑁= 293)
Ohio (𝑁= 431)
푁
%
푁
%
푁
%
푁
%
푁
%
Good mental health
667
100
381
100
420
100
293
100
431
100
Yes
331
50
197
52
232
55
134
46
205
48
No
336
50
184
48
188
45
159
54
226
52
Good physical health
667
100
381
100
420
100
293
100
431
100
Yes
258
39
123
32
193
46
96
33
162
38
No
409
61
258
68
227
54
197
67
269
62
Routine checkup
667
100
381
100
420
100
293
100
431
100
Yes
580
87
353
93
372
89
267
91
391
91
No
87
13
28
7
48
11
26
9
40
9
Health conditions
605
91
355
90
398
95
274
94
395
92
0 or 1 other health
condition
115
19
51
14
78
20
52
19
62
16
2 other health
conditions
490
81
304
86
320
80
222
81
333
84
Physical activity
610
91
344
90
365
87
250
85
401
93
Inactive
294
48
189
55
150
41
107
43
198
49
Insufficiently active
116
19
872
21
74
20
5
22
83
21
Active/Highly active
200
33
83
24
141
39
88
35
120
30
Weight status
589
88
335
88
378
90
270
92
388
90
Underweight or normal
91
15
44
13
4343
11
41
15
31
8
Overweight
147
25
92
27
90
24
73
27
94
24
Obese
351
60
199
59
245
65
156
58
263
68
Tobacco use
643
96
375
98
398
95
275
94
422
98
Never
325
51
180
48
232
58
143
52
211
50
Former
166
26
108
29
105
26
78
28
111
26
Current
152
24$
87
23
61
15
54
20
100
24
Alcohol use
656
98
379
99
410
98
284
97
420
97
None
473
72
303
80
227
55
143
60
307
73
Light
68
10
35
9^
85
21
78
14
64
15
Moderate or excessive
115
18
41
11
98
24
54
26
49
12
Age
667
100
381
100
420
100
293
100
431
100
45–54
234
35
140
37
140
33
120
41
134
31
55–64
433
65
241
63
280
67
173
59
297
69
Ethnicity/Race
651
98
377
99
416
99
279
95
427
99
White
426
65
309
82
230
55
162
58
348
82
Other
225
35
68
18
186
44
117
42
79
19
Marital status
666
100
379
99
417
99
288
98
429
100
Married
300
45
196
52
200
48
118
41
205
48
Not married
366
55
183
48
217
52
170
59
224
52
Education level
667
100
380
100
420
100
291
99
429
100
Graduated college
137
21
83
22
142
34
92
32
95
22
Did not graduate college
530
79
297
78
278
66
199
68
334
78
Income level
544
82
268
70
357
85
256
86
372
86
$50,000 or more
130
24
94
35
179
50
86
34
117
31
Less than $50,000
414
76
174
65
178
50
170
66
255
69
Employment status
662
99
379
99
418
100
287
98
430
100
Employed
235
36
133
35
213
51
128
45
164
38
Other
427
65
246
65
205
49
159
55
266
62
Table 1: Continued. 1. Introduction (b): Participant characteristics by state: females with diabetes. Advances in Preventive Medicine Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). All models controlled for
physical activity, weight status, tobacco use, alcohol use, age, ethnicity/race, marital status, education level, income level and employment status. (a): Results of multiple logistic regression analyses across states: males. Predicting good mental
health (yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.27
0.64
2.50
4.43
1.07
18.45
2.06
0.73
5.82
2.02
0.68
5.98
0.95
0.35
2.61
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.24
0.10
0.54
1.04
0.25
4.25
0.51
0.20
1.28
0.23
0.92
0.55
0.78
0 .33
1.84
Predicting good physical
health (yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
Ref
—
—
Ref
—
—
Yes
0.59
0.29
1.18
2.39
0.53
10.77
1.39
0.50
3.86
2.55
0.84
7.76
1.48
0.54
4.03
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.18
0.09
0.37
0.08
0.01
0.48
0.41
0.18
0.96
0.39
0.18
0.88
0.95
0.42
2.11
Table 2 Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). All models controlled for
physical activity, weight status, tobacco use, alcohol use, age, ethnicity/race, marital status, education level, income level and employment status. (a): Results of multiple logistic regression analyses across states: males. Predicting good mental
health (yes vs. 1. Introduction no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
e check-up
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
1.36
0.65
2.87
2.16
0.55
8.49
0.77
0.33
1.80
0.54
0.17
1.71
1.06
0.40
2.77
conditions
other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
r health conditions
0.33
0.18
0.61
0.11
0.04
0.33
0.59
0.30
1.17
0.14
0.05
0.39
0.35
0.16
0.78
Table 2: Continued. (b): Results of multiple logistic regression analyses across states: females. Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). Predicting good mental health
(yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.39
0.71
2.73
1.05
0.31
3.61
0.56
0.22
1.41
4.58
1.24
16.91
0.85
0.34
2.10
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.27
0.14
0.52
0.26
0.09
0.76
0.35
0.16
0.77
0.51
0.21
1.29
0.30
0.13
0.67
Predicting good physical
health (yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.36
0.65
2.87
2.16
0.55
8.49
0.77
0.33
1.80
0.54
0.17
1.71
1.06
0.40
2.77
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.33
0.18
0.61
0.11
0.04
0.33
0.59
0.30
1.17
0.14
0.05
0.39
0.35
0.16
0.78
Table 2: Continued. (b): Results of multiple logistic regression analyses across states: females. Note. 1. Introduction no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.27
0.64
2.50
4.43
1.07
18.45
2.06
0.73
5.82
2.02
0.68
5.98
0.95
0.35
2.61
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.24
0.10
0.54
1.04
0.25
4.25
0.51
0.20
1.28
0.23
0.92
0.55
0.78
0 .33
1.84
Predicting good physical
health (yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
Ref
—
—
Ref
—
—
Yes
0.59
0.29
1.18
2.39
0.53
10.77
1.39
0.50
3.86
2.55
0.84
7.76
1.48
0.54
4.03
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.18
0.09
0.37
0.08
0.01
0.48
0.41
0.18
0.96
0.39
0.18
0.88
0.95
0.42
2.11
Table 2 5 Advances in Preventive Medicine 5 (b): Results of multiple logistic regression analyses across states: females. OR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). ting good mental health
. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
e check-up
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
1.39
0.71
2.73
1.05
0.31
3.61
0.56
0.22
1.41
4.58
1.24
16.91
0.85
0.34
2.10
conditions
other health condition
Ref
—
—
Ref
—
—
—
—
Ref
—
—
Ref
—
—
r health conditions
0.27
0.14
0.52
0.26
0.09
0.76
0.35
0.16
0.77
0.51
0.21
1.29
0.30
0.13
0.67
ting good physical
(yes vs. 3. Results Because these responses
were highly skewed toward 0 days in each state and because we
wanted to predict “good” health, we reversed and dichotomized
these values to represent “yes” (30 days of good health in the
past 30 days) or “no” (fewer than 30 days of good health in the
past 30 days) separately for “good mental health” and “good
physical health.” The factor of interest, routine check-up, was
measured as yes/no to having a checkup in the past year. 3.2. Participant Characteristics: Females with Diabetes. Table 1(b) lists participant characteristics for middle-aged
females with diabetes. Most participants reported having a
routine checkup within the past year (87–93%). About half of
the participants reported good mental health (46–55%) and less
than half reported good physical health (32–46%). Regarding
health conditions, most participants had diabetes plus two or
more chronic conditions (80–86%) and were obese (58–68%),
and about one-third to one-half reported being inactive (41–
55%). Regarding health behaviors, the majority of participants
reported no tobacco (48–58%) or alcohol use (55–80%). For
demographics, a range of participants reported their race as
white (55–82%) and around one half were married (41–52%). As for socioeconomic status, the majority of respondents had
not graduated from college or technical school (66–79%) and
earned an income of less than $50,000 (50–76%), while one-
third to one-half of participants were employed (35–51%). 3.2. Participant Characteristics: Females with Diabetes. Table 1(b) lists participant characteristics for middle-aged
females with diabetes. Most participants reported having a
routine checkup within the past year (87–93%). About half of
the participants reported good mental health (46–55%) and less
than half reported good physical health (32–46%). Regarding
health conditions, most participants had diabetes plus two or
more chronic conditions (80–86%) and were obese (58–68%),
and about one-third to one-half reported being inactive (41–
55%). Regarding health behaviors, the majority of participants
reported no tobacco (48–58%) or alcohol use (55–80%). For
demographics, a range of participants reported their race as
white (55–82%) and around one half were married (41–52%). As for socioeconomic status, the majority of respondents had
not graduated from college or technical school (66–79%) and
earned an income of less than $50,000 (50–76%), while one-
third to one-half of participants were employed (35–51%). All models controlled for physical activity, weight status,
tobacco use, alcohol use, education level, income level,
employment status, age, ethnicity/race, and marital status. 2. Methods interest. As such, similar results in three out of five states were
considered reliable evidence for relations. Any observations
with missing data for any variable were excluded from the
adjusted analysis and all analyses were conducted in STATA
Version 15.1 (Copyright 1985–2017 StataCorp LLC). 2.1. Design. This study is a cross-sectional analysis that used
data from the 2017 Behavioral Risk Factor Surveillance System
(BRFSS) conducted by the Centers for Disease Control and
Prevention (CDC) [3]. BRFSS is an annual telephone survey
system that uses random digit dialing techniques for both
landlines and cell phones across all 50 states in the US and the
District of Columbia. This survey gathers data about US adult
residents’ health-related behaviors, chronic health conditions,
and use of preventative services. The CDC compiles all BRFSS
data and makes deidentified data available for secondary
analysis by researchers. This study was given exempt status
by the Institutional Review Board of The University of North
Texas Health Science Center. 1. Introduction AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). Predicting good mental health
(yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.39
0.71
2.73
1.05
0.31
3.61
0.56
0.22
1.41
4.58
1.24
16.91
0.85
0.34
2.10
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.27
0.14
0.52
0.26
0.09
0.76
0.35
0.16
0.77
0.51
0.21
1.29
0.30
0.13
0.67
Predicting good physical
health (yes vs. no)
Florida
Kentucky
Maryland
New York
Ohio
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
AOR
95% CI
Low
High
Low
High
Low
High
Low
High
Low
High
Routine check-up
No
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Yes
1.36
0.65
2.87
2.16
0.55
8.49
0.77
0.33
1.80
0.54
0.17
1.71
1.06
0.40
2.77
Health conditions
0 or 1 other health condition
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
Ref
—
—
2 other health conditions
0.33
0.18
0.61
0.11
0.04
0.33
0.59
0.30
1.17
0.14
0.05
0.39
0.35
0.16
0.78
Table 2: Continued. 6 Advances in Preventive Medicine 3. Results 3.1. Participant Characteristics: Males with Diabetes. Table 1(a)
lists participant characteristics for middle-aged males with
diabetes. The majority of participants had attended a routine
medical checkup within the past year (87–90%) and reported
good mental health (56–67%), but less than half reported good
physical health (37–50%). Regarding health conditions, most
participants had diabetes plus two or more chronic illnesses
(71–84%) and were obese (54–63%), yet less than half reported
being inactive (33–47%). Regarding health behaviors, one-third
to one-half of participants did not use tobacco products (34–
55%) or alcohol (47–69%). For demographics, the majority of
participants were married (48–60%) and reported their race as
white (56–87%). As for socioeconomic status, the majority of
respondents had not graduated from college or technical school
(67–77%), approximately half were employed (40–59%), and up
to two-thirds earned an income of $50,000 or more (40–69%). 2.2. Sample. The samples in the study include males and females
with diabetes between the ages of 45 and 64 in Florida (𝑁= 1183),
Kentucky (𝑁= 617), Maryland (𝑁= 731), New York (𝑁= 593),
and Ohio (𝑁= 754) that had data for mental health, physical
health, and routine checkup. These states were chosen because
they had a large diabetic population and higher rates of fair/poor
health status when compared to the other states [1]. 2.3. Data. The original BRFSS variables for mental and physical
health were determined by asking participants to self-report
the number of “poor health days” in the past 30 days separately
for mental health and physical health. Because these responses
were highly skewed toward 0 days in each state and because we
wanted to predict “good” health, we reversed and dichotomized
these values to represent “yes” (30 days of good health in the
past 30 days) or “no” (fewer than 30 days of good health in the
past 30 days) separately for “good mental health” and “good
physical health.” The factor of interest, routine check-up, was
measured as yes/no to having a checkup in the past year. 2.3. Data. The original BRFSS variables for mental and physical
health were determined by asking participants to self-report
the number of “poor health days” in the past 30 days separately
for mental health and physical health. 3. Results Health conditions were measured as the number of “yes”
responses to whether participants had any of the following:
heart attack, coronary heart disease, stroke, asthma, skin can-
cer, cancer, COPD, arthritis, depression, kidney disease, and
diabetes. The resulting numbers were then categorized as “dia-
betes only,” “diabetes plus one other chronic condition,” and
“diabetes plus two other chronic conditions.” Alcohol use was
measured in BRFSS as number of drinks per day and we cat-
egorized the numbers as “none,” “light” (<1), and “moderate
or excessive” (1–4+ females, 1–5+ males). All variables and
their categories are shown in Table 1(a). 3.3. Mental Health: Males. As shown in Table 2(a), the results
of multiple logistic regression analysis for middle-aged males
with diabetes indicated that after controlling for all other
variables in the model, good mental health was significantly
related to having had routine checkups in only 1 out of 5 states,
which was not considered a reliable finding across states as was
defined in the methods section. 2.4. Analysis. Frequency distributions by state were used
to describe the samples. Multiple logistic regression was
conducted by state and gender to determine the relationship
between mental and physical health status and routine check-
up while controlling for health-related, socioeconomic, and
demographic factors. The state and gender data were analyzed
separately to determine the relationship between the variables
across multiple similar samples within our population of 3.4. Physical Health: Males. Also shown in Table 2(a), the
results of multiple logistic regression analysis for middle-
aged males with diabetes indicated that after controlling for
all other variables in the model, good physical health was not
significantly related to routine checkups across in any state. However, those who reported having diabetes plus two or 7 Advances in Preventive Medicine (instead of “general” health) and separately for males and
females (instead of together), which allowed us to determine
whether patterns in variable relations were similar for
different facets of health and by gender. In addition, BRFSS
also provided current information, given that our dependent
variables (mental and physical health) were measured within
the last 30 days. 4. Discussion The purpose of this study was to determine whether physical
and mental health status differ by routine checkup in mid-
dle-aged males and females with diabetes. For this target popu-
lation, both good mental and physical health did not significantly
differ related to having routine checkups across states. These
results differ from prior research which showed that preventative
care is related to both improved depressive symptoms and the
perception of good overall health [4, 5, 11]. The differences in
findings may be due to differing target populations. While our
results focus on patients with diabetes, previous research focused
on the general population as a whole. Therefore, it is possible
that prevention efforts were in place as most of the patients were
already under medical care. Thus, to our knowledge, our study
is the first to focus only on middle-aged patients with diabetes
as related to regular checkups. Conflicts of Interest The authors declare that they have no conflicts of interest. However, the results of this study did show that for mid-
dle-aged males and females with diabetes, good physical and
mental health were inversely related to having diabetes plus
two or more other health conditions. This is generally consist-
ent with prior research that showed chronic illnesses to be
related to lower overall health in the general population [12]. As prior research focused primarily on the general population,
our study focuses solely on middle-aged people with diabetes. For this target population, the comanagement and treatment
of multiple chronic conditions may have a significant impact
on their mental and physical health, and the assessment of
comorbid conditions should be a focus for their care. 5. Conclusions Because this study used population-based data, the results may
generalize to males and females aged 45–64 with diabetes. Regarding the optimization of patient’s mental and physical
health, we recommend automatic mental and physical health
screening for adults aged 45–64 with diabetes as well as screen-
ing for other chronic health conditions. General practitioners
should assess comorbid conditions and treatments, refer to
specialists as needed, and educate patients on the importance
of proper management of diabetes in combination with any
other chronic illnesses for maintaining good mental and phys-
ical health. 3. Results However, BRFSS did not include variables
that provided information about (1) current treatment and
management of any mental or physical health condition, (2)
current treatment and management of diabetes specifically, or
(3) current management and severity of the chronic illnesses in
addition to diabetes, all of which could have an impact upon
mental and physical health. Future studies should include
information about the current management and treatment of
any mental and physical health conditions and should consider
the influence of specific disease management and medication
use in relation to its impact on mental and physical health in
diabetics. more other chronic conditions were about 2.5–12.5 times less
likely to report good physical health compared to those who
reported diabetes only across states. 3.5. Mental Health: Females. As shown in Table 2(b), the results
of multiple logistic regression analysis for middle-aged females
with diabetes indicated that after controlling for all other
variables in the model, good mental health was significantly
related to having routine checkups in only 1 out of the 5 states,
which was not considered a reliable finding across similar
samples. However, compared to those with only diabetes, those
who reported having diabetes plus two or more other chronic
conditions were approximately three to four times less likely
to report good mental health compared to those who reported
having diabetes only in a majority of the states. 3.6. Physical Health: Females. Also shown in Table 2(b), the
results of multiple logistic regression analysis for middle-aged
females with diabetes indicated that after controlling for all
other variables in the model, good physical health was not
significantly related to routine checkup across states. However,
those who reported having diabetes plus two or more other
chronic conditions were about 3–9 times less likely to report
good physical health compared to those who reported having
diabetes only in the majority of the states. Data Availability BRFSS 2017 data is available online from the CDC at
https://www.cdc.gov/brfss/annual_data/annual_2017.html. References [1] Center for Disease Control and Prevention (CDC), “BRFSS
prevalence and trends data,” 2017a, https://www.cdc.gov/brfss/
brfssprevalence/index.html. [2] Centers for Disease Control and Prevention (CDC), “National
diabetes statistics report,” 2017b, https://www.cdc.gov/diabetes/
data/statistics/statistics-report.html. [3] Center for Disease Control and Prevention (CDC), “Behavioral
risk factor surveillance system,” 2018, https://www.cdc.gov/
brfss/index.html. [4] D. Culica, J. Rohrer, M. Ward, P. Hilsenrath, and P. Pomrehn,
“Medical checkups: who does not get them?” American Journal
of Public Health, vol. 92, no. 1, pp. 88–91, 2002. 4.1. Limitations. The use of BRFFS data provided large,
multiple samples to evaluate both physical and mental health Advances in Preventive Medicine 8 [5] R. Dryden, B. Williams, C. McCowan, and M. Themessl-Huber,
“What do we know about who does and does not attend general
health checks? Findings from a narrative scoping review,” BMC
Public Health, vol. 12, no. 723, pp. 1–23, 2012, http://www. biomedcentral.com/1471-2458/12/723. [6] H. Eyre, R. Kahn, and R. M. Robertson, “Preventing cancer,
cardiovascular disease, and diabetes: a common agenda for the
American cancer society, the American diabetes association,
and the American Heart Association,” Diabetes Care, vol. 27,
no. 7, pp. 1812–1824, 2004. [7] I. Ganguli, J. Souza, and J. McWilliams, “Trends in use of the
U.S. Medicare annual wellness visit, 2011–2014,” Journal of
American Medical Association, vol. 317, no. 21, pp. 2233–2235,
2017. [8] A. Mehrota, A. M. Zaslavsky, and J. Z. Ayanian, “Preventative
health
examinations
and
preventative
gynecological
examinations in the United States,” Archives of Internal Medicine,
vol. 167, no. 17, pp. 1876–1883, 2007. [9] A. Molarius, K. Berglund, C. Eriksson et al., “Socioeconomic
conditions, lifestyle factors, and self-rated health among men
and women in Sweden,” European Journal of Public Health,
vol. 17, no. 2, pp. 125–133, 2006. [10] R. R. Rubin and M. Peyrot, “Quality of life and diabetes,” Diabetes
and Metabolism Research and Reviews, vol. 15, no. 3, pp. 205–
218, 1999, https://www.ncbi.nlm.nih.gov/pubmed/10441043. [11] A. L. Siu, K. Bibbins-Domingo, D. C. Grossman et al., “Screening
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A. H. Mokdad, “The associations between life satisfaction
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pp. 68–74, 2005. |
https://openalex.org/W2400584292 | https://www.matec-conferences.org/10.1051/matecconf/20165804006/pdf | English | null | Temperature Approach Optimization in the Double Pipe Heat Exchanger with Groove | MATEC web of conferences | 2,016 | cc-by | 2,438 | INTRODUCTION through internally grooved pipe. Sunu (2015) investigated
increased pressure drop on internal wall surface in pipe
with rectangular groove. Sunu et al (2015) revealed the
effect of groove numbers on pressure drop in pipe flows. Investigation about pressure drop characteristics in a
periodically grooved was conducted by Adachi et al
(2009). The investigation on pipe bend with rough surface
produced 4 % drag reduction (Nakao, 1995). Lee and Jang
(2005) studied v-shaped groove over curved body. Choi
and Orchard (1997) reveal about turbulence management
using passive device for momentum transfer. Ding et al
(2009) present a correlation to predict frictional pressure
drop of R410A-oil mixture inside internal spiral grooved
microfin tube. Alam and Yong Kim (2012) conducted
mixing analysis in microchannel with rectangular grooves. A number of studies have been carried out to optimize the
enhancement the heat transfer of rough surface geometry. Investigation of turbulent channel flow conducted by
Katoh et al (2000), reveal the relationship between drag
and thermal enhancement by rough surface. Aroonrat et al
(2013) investigated the relationship of heat transfer and
flow characteristics in horizontal internally grooved tube
made by stainless steel. The result showed the thermal
enhancement factor is 1.4 to 2.2 for grooved tube. Graham
et al (1999) studied of pressure drop and heat transfer in
copper tube with axially grooved. Lorenz et al (1995)
investigated the distribution of the heat transfer coefficient
in a channel with periodic transverse grooves. A heat exchanger is a heat transfer device that
exchange heat between two or more process fluids at
different temperature. Heat exchangers have widespread
applications in industrial such as industry process,
petroleum transportation, power, heat recovery, RHVAC
and many domestic applications. One of the simply heat
exchanger is double pipe heat exchanger (DPHE). Their
usual application is for small duties and they are suitable
for high pressure and temperature. Another advantage is
the design of DPHE serviceable easily than the other heat
exchanger and can be connected in series or parallel. Heat
exchangers have to fulfill some requirement such as
effective
temperature
difference. The
effective
temperature driving force is a measure of the potential for
heat transfer that exists at the design conditions. Effective
temperature difference is defined by the log mean
temperature difference (LMTD). Other simply method to
measure thermal performance of heat exchanger is using
temperature approach. ABSTRACT Heat transfer in double pipe heat exchanger with circumference-rectangular grooves has been investigated
experimentally. The volume flowrate of cold and hot water were varied to determine its influence on the approach
temperature of the outlet terminals. In this experimental design, the grooves were incised in annular room that is placed on
the outside surface of the inner pipe. The shell diameter is 38.1 mm and tube diameter 19.4 mm with 1 m length, which is
made of aluminum. The flow pattern of the two fluids in the heat exchanger is a parallel flow. The working fluid is water
with volume flow rate of 27.1, 23.8 and 19.8 l/minute. The temperature of water on the inlet terminals are 50±10C for hot
stream and 30±10C for cold stream. Temperature measurements conducted on each terminal of the inlet and outlet heat
exchanger. The results showed that the grooves induced the approach temperature. The change of the approach temperature
from the grooves compared to that of without grooves decreased by 37.9%. This phenomenon indicates an increase in heat
transfer process and performance of the heat exchanger. Groove improves the heat surface area of the inner pipe,
increasing the momentum transfer and in the other hand, reducing the weight of heat exchangers itself. Keywords: Approach temperature, groove, heat exchanger, optimization INTRODUCTION Temperature approach referred to
difference of temperature between hot and cold outlet of
heat exchanger. g
The need for lightweight, space-saving, and
economical heat exchangers has driven the development of
compact surfaces. Many engineering techniques have been
developed for enhancing the rate of heat transfer through
the wall surface of heat exchanger. The enhanced of heat
transfer accompanied by pressure drop and drag increase. One of the flow surface applications to increase heat
transfer in turbulence flow is groove. Using grooves is
well known as passive flow control. The passive flow
control as concerned wide consideration as it need no
auxiliary power, increase surface area, induced pressure
drop, simplicity and hence give more benefits (Sunu et al.,
2015). Changing the surface of pipe with circumference
rectangular groove can be used to control flow separation. The groove provided as vortex generator and increased the
boundary layer momentum. In the several paper describe above, most studies
focus on heat transfer, flow characteristics and the both
relationship inside/outside grooved tube. The studies of
heat transfer through grooved pipe in a room between tube
and shell has received little attention. Consequently, the
objective of this present study is to optimize the
temperature approach of double pipe heat exchanger with
groove placed in annulus room. TEMPERATURE APPROACH OPTIMIZATION IN THE DOUBLE PIPE
HEAT EXCHANGER WITH GROOVE Putu Wijaya Sunu, Daud Simon Anakottapary, Wayan G. Santika
Department of Mechanical Engineering, Bali State Polytechnic, Badung-Bali, Indonesia. E-mail: wijayasunu@pnb.ac.id © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Co
License 4.0 (http://creativecommons.org/licenses/by/4.0/). DOI: 10.1051/
conf/2016
matec
5804006 DOI: 10.1051/
conf/2016
matec
5804006 ,
Web of Conferences
MATEC
58 04006 (2016)
BISSTECH 2015 ished by EDP Sciences. This is an open access article distributed under the terms of the Creative
Commons Attribution
eativecommons.org/licenses/by/4.0/). © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative
Commons Attribution
License 4.0 (http://creativecommons.org/licenses/by/4.0/). METHODOLOGY The flow pattern of the two fluids in a general
heat exchanger can vary depending on the heat exchanger Over the years, numerous researchers have
carried out experimental studies on flow characteristics DOI: 10.1051/
conf/2016
matec
5804006 ,
Web of Conferences
MATEC
58 04006 (2016)
BISSTECH 2015 outlet temperature of one stream and the outlet
temperature of the other stream design. One of the flow patterns is a parallel flow, which is
the hot fluid and cold fluid move in the same direction. This investigation used parallel flow in the flow direction. The hot side inlet temperature is in contact with the cold
side inlet temperature, the two fluid progresses through the
heat exchanger and at the other terminal point the cold
side outlet temperature is in contact with the hot side
outlet temperature. In a parallel flow heat exchanger, the
approach temperatures are the difference between the The experiment was performed using the
experimental apparatus shown schematically in Fig.1. The
experiment installation consisted two centrifugal pump
which was stabilized by electric stabilizer to circulate hot
and cold water through a loop. The control valve used to
vary flow rate through the test section and the water tank
t
h ld
t
f
th
t hold o
hold approach temperatures are the difference between the
to
hold
water
from
the
system. Figure-1. Experiment set-up
The hot water temperature was 50±10C and the cold water
was 30±10C. The volume flow rate was varied by control
valve set some distance from test section as 27.1, 23.8 and
19.8 l/minute respectively. The tube test outer diameter is
19.4 mm which has circumference rectangular groove 40 x
0.4 mm. While, the shell test section has 38.1 mm outer
diameter. All of the tube made of aluminum pipes. to approach temperatures are the difference between the
to
hold
water
from
the
system. Figure-1. Experiment set-up Figure-1. Experiment set-up 19.4 mm which has circumference rectangular groove 40 x
0.4 mm. While, the shell test section has 38.1 mm outer
diameter. All of the tube made of aluminum pipes. The hot water temperature was 50±10C and the cold water
was 30±10C. The volume flow rate was varied by control
valve set some distance from test section as 27.1, 23.8 and
19.8 l/minute respectively. The tube test outer diameter is Figure-2. Groove geometry Figure-2. METHODOLOGY Groove geometry Temperatures were measured by thermocouples
placed in the inlet and outlet terminal of hot and cold
water from the test section. A data logger digitalized
signal from thermocouples before being recorded in a
computer memory. The approach temperature (AT) was
determined using the data point from hot and cold
terminals of 750 s. The percentage of approach temperature (% AT)
from the grooves was compared to that of a smooth pipe
(without grooves) and estimated by using the equation
bellow: (
)
(
)
%
100%
(
)
smooth
groove
smooth
AT
AT
AT
x
AT
Eq.1 Eq.1 2 DOI: 10.1051/
conf/2016
matec
5804006 ,
Web of Conferences
MATEC
58 04006 (2016) ,
Web of Conferences
MATEC
58 04006 (2016)
BISSTECH 2015 RESULTS AND DISCUSSIONS The rate of approach temperature (a) Qhot= Qcold= 27.1 l/min; (b) Qhot= 27.1 l/min, Qcold= 23.8 l/min; (c)
Qhot= 27.1 l/min, Qcold= 19.8 l/min; (d) Qhot= 23.8 l/min, Qcold= 27.1 l/min; (e) Qhot= 19.8 l/min, Qcold= 27.1 l/min higher momentum convection and energy transfer
through interchange of fluid particles. The rate of approach temperature as a
function of approach temperature is presented in
figure 5. Marked with circle indicates the condition
of smooth pipe (without groove) and marked with
rectangular point represent with grooved pipe. Negative sign on ordinate axis, indicating the
occurrence of a decrease in approach temperature and
indicates greater of heat transfer process. For dT/dt
grooved pipe, the rate of approach temperature for
each approach temperature is more negative then that
the smooth pipe. The greater the flow rate, the more
negative the value dT/dt will be. Increased flowrate is
accompanied by an increase in Re. Greater Re will
increase the randomness of fluid motion, resulting in RESULTS AND DISCUSSIONS This data was then used as a comparison to the data from
the double pipe heat exchanger with groove. The approach
temperature data in DPHE are shown in fig. 3 and 4. Preliminary experiments were done on the double pipe
heat exchanger without groove (smooth pipe) to establish
the time series temperature and approach temperature. Figure-3. Average approach temperature for hot water flowrate variation. Figure-3. Average approach temperature for hot water flowrate variation. Figure-4. Average approach temperature for cold water flowrate variation. Figure-4. Average approach temperature for cold water flowrate variation. Fig. 3 shows the average value of approach
temperature at various hot water flowrate with constant
cold-water flowrate. While figure 4 shows the average
value of approach temperature at various cold-water
flowrate with constant hot water flowrate. The rectangular
pointed denotes the average approach temperature in
smooth pipe DPHE. The percentage values on the plot
show percentage approach temperature estimated using
equation 1. For variation in hot water supply 19.8, 23.8,
27.1 l/min, the approach temperature data of grooved
DPHE indicates reduction of about 10.6%, 34.9%, and
37.9% respectively. For variation in cold water supply
19.8, 23.8, 27.1 l/min, the approach temperature data of
grooved DPHE indicates reduction of about 28.9%,
37.2%, and 37.9% respectively. This phenomenon
indicates the increases of heat transfer process between
two fluids. It was observed that approach temperature
decreased with increasing flow rate in all case. The
approach temperature obtained from the circumference-
rectangular grooved was lower than that those from the
smooth pipe. This occurred because the grooved pipe
provided the enhancement of heat transfer by increasing
recirculation region of the flow. Groove produced swirl
effect on the fluid near to the pipe surface in the annulus
room which lacerating the boundary layer. The fluid
thermal boundary layer became thinner and the increasing
fluid mixing process increased the rate of heat transfer
which represented by the rate of approach temperature. 3 DOI: 10.1051/
conf/2016
matec
5804006 ,
Web of Conferences
MATEC
58 04006 (2016) ,
Web of Conferences
MATEC
58 04006 (2016)
BISSTECH 2015 BISSTECH 2015 Figure-5. The rate of approach temperature (a) Qhot= Qcold= 27.1 l/min; (b) Qhot= 27.1 l/min, Qcold= 23.8 l/min; (c)
Qhot= 27.1 l/min, Qcold= 19.8 l/min; (d) Qhot= 23.8 l/min, Qcold= 27.1 l/min; (e) Qhot= 19.8 l/min, Qcold= 27.1 l/min Figure-5. CONCLUSIONS Heat transfer in double pipe heat exchanger with
circumference-rectangular grooves was investigated
using experimental method. The results showed that
the grooves induced the approach temperature. Groove improves the heat surface area of the inner
pipe (tube side), increasing the momentum transfer,
produced swirl effect on the fluid near to the pipe
surface in annulus room. The change of the approach
temperature from the grooves compared to that of 4 DOI: 10.1051/
conf/2016
matec
5804006 ,
Web of Conferences
MATEC
58 04006 (2016)
BISSTECH 2015 Nakao, S.I. 1995. Effects of riblet bends on pipe
flows. Applied Scientific Research 54: 237-247. without grooves decreased by 37.9%, which indicates
an increase in heat transfer process and performance
of the heat exchanger. Sunu P.W. 2015. The characteristics of increased
pressure drop in pipes with grooved. Adv .Studies
Theor. Phys. 9(2):
57-61. Sunu P.W. 2015. The characteristics of increased
pressure drop in pipes with grooved. Adv .Studies
Theor. Phys. 9(2):
57-61. http://dx.doi.org/10.12988/astp.2015.412152 REFERENCES Adachi Takahiro, Yamato Tashiro, Hirofumi Arima,
Yasuyuki
Ikegami. 2009. Pressure
drop
characteristics of flow in a symmetric channel with
periodically
expanded
grooves. Chemical
Engineering Science 64: 593-597 Sunu P.W., ING Wardana, A.A.Sonief, Nurkholis
Hamidi. 2015. The effect of wall groove numbers on
pressure drop in pipe flows. Int. J. Fluid Mech. Resch., 42(2): 119 - 130 Alam Afroz, Kwang-Yong Kim. 2012. Analysis of
mixing in a curved microchannel with rectangular
grooves. Chemical Engineering Journal 181–182:
708–716. Aroonrat, K., Jumpholkul, C., Leelaprachakul, R.,
Dalkilic, A.S., Mahian, O., Wongwises, S. 2013. Heat transfer and single-phase flow in internally
grooved tube. International Communication in Heat
and Mass Transfer 42: 62-68. Choi, K.S and Orchard D.M. 1997. Turbulence
Management Using Riblets for Heat and Momentum
Transfer. Experimental Thermal and Fluid Science
15: 109-124. Ding G., Haitao Hu, Huang X., Bin Deng, Yifeng
Gao. 2009. Experimental
investigation
and
correlation of two-phase frictional pressure drop of
R410A–oil mixture flow boiling in a 5 mm microfin
tube. International Journal of Refrigeration 32: 150–
161. Graham D., J.C. Chato, T.A. Newell. 1999. Heat
transfer and pressure drop during condensation of
refrigerant 134a in an axially grooved tube,
International Journal of Heat and Mass Transfer 42:
1935–1944. Katoh K., Choi, K.S.,Azuma, T. 2000. Heat-transfer
enhancement and pressure loss by surface roughness
in turbulent channel flows. International Journal of
Heat and Mass Transfer, 43: 4009-4017. Lee, S.J. and Jang, Y.G. 2005.Control of flow around
a naca 0012 airfoil with a micro-riblet film. Journal
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https://openalex.org/W3172085540 | https://europepmc.org/articles/pmc8556635?pdf=render | English | null | Clinic Time Required for Remote and In-Person Management of Patients With Cardiac Devices: Time and Motion Workflow Evaluation | JMIR cardio | 2,021 | cc-by | 8,433 | Corresponding Author: Corresponding Author:
David Lanctin, MPH
Medtronic
8200 Coral Sea Ct NE
Mounds View, MN, 55112
United States
Phone: 1 800 633 8766
Email: david.lanctin@medtronic.com Abstract Background: The number of patients with cardiac implantable electronic device (CIED) is increasing, creating a substantial
workload for device clinics. number of patients with cardiac implantable electronic device (CIED) is increasing, creating a substanti
clinics. Objective: This study aims to characterize the workflow and quantify clinic staff time requirements for managing patients with
CIEDs. Objective: This study aims to characterize the workflow and quantify clinic staff time requirements for managing patients with
CIEDs. Methods: A time and motion workflow evaluation was performed in 11 US and European CIEDs clinics. Workflow tasks were
repeatedly timed during 1 business week of observation at each clinic; these observations included all device models and
manufacturers. The mean cumulative staff time required to review a remote device transmission and an in-person clinic visit were
calculated, including all necessary clinical and administrative tasks. The annual staff time to manage a patient with a CIED was
modeled using CIED transmission volumes, clinical guidelines, and the published literature. Results: A total of 276 in-person clinic visits and 2173 remote monitoring activities were observed. Mean staff time required
per remote transmission ranged from 9.4 to 13.5 minutes for therapeutic devices (pacemaker, implantable cardioverter-defibrillator,
and cardiac resynchronization therapy) and from 11.3 to 12.9 minutes for diagnostic devices such as insertable cardiac monitors
(ICMs). Mean staff time per in-person visit ranged from 37.8 to 51.0 and from 39.9 to 45.8 minutes for therapeutic devices and
ICMs, respectively. Including all remote and in-person follow-ups, the estimated annual time to manage a patient with a CIED
ranged from 1.6 to 2.4 hours for therapeutic devices and from 7.7 to 9.3 hours for ICMs. Conclusions: The CIED patient management workflow is complex and requires significant staff time. Understanding process
steps and time requirements informs the implementation of efficiency improvements, including remote solutions. Future research
should examine heterogeneity in patient management processes to identify the most efficient workflow. (JMIR Cardio 2021;5(2):e27720) doi: 10.2196/27720 (JMIR Cardio 2021;5(2):e27720) doi: 10.2196/27720 Original Paper Original Paper JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 1
(page number not for citation purposes) Clinic Time Required for Remote and In-Person Management of
Patients With Cardiac Devices: Time and Motion Workflow
Evaluation Amber Seiler1, NP, MSN, FHRS, CEPS, CCDS; Eliana Biundo2, MSc; Marco Di Bacco3, PharmD, MS; Sarah
Rosemas3, MPH; Emmanuelle Nicolle3, MSc, MD; David Lanctin3, MPH; Juliette Hennion2, MSc; Mirko de Melis3,
PhD; Laura Van Heel4, BSN 1Cone Health Medical Group, Greensboro, NC, United States
2Deloitte, Brussels, Belgium
3Medtronic, Mounds View, MN, United States
4Centracare, St. Cloud, MN, United States https://cardio.jmir.org/2021/2/e27720 JMIR CARDIO JMIR CARDIO Seiler et al Data Collection The number of patients receiving and living with cardiac
implantable electronic devices (CIEDs), including permanent
pacemakers, implantable cardioverter-defibrillators (ICD),
cardiac resynchronization therapy (CRT) devices, and insertable
cardiac monitors (ICMs), has increased significantly in the past
several years [1-3]. Accordingly, the burden for device clinics
to manage follow-up visits has increased. Such follow-up visits,
consisting of device interrogation and subsequent care changes
(ie, reprogramming device settings and acting upon clinical
findings), have traditionally been performed in person. Their
frequency, essentially based on clinical guidelines, may vary
depending on the facility, physician and patient preferences,
and available resources [4]. As an alternative or complement
to in-person visits, remote monitoring (RM) has become a
guideline-recommended method for managing patients with
CIEDs [5,6]. RM capabilities are a standard feature of modern
CIEDs, and data are continuously transmitted through landlines
or mobile networks, which supplies health care providers with
critical clinical (eg, arrhythmias) and device-related (eg, battery
longevity) information that allows them to adjust and optimize
patient treatment accordingly. In the 2015 Heart Rhythm Society
(HRS) Consensus Statement on remote interrogation and
monitoring for CIEDs, endorsed by European Heart Rhythm
Association and other international societies, RM combined
with an annual in-person visit is recommended rather than
in-person evaluation alone, with the strongest (class I)
recommendation and the highest level of evidence (A) [5]. This
recommendation is primarily because of earlier detection of
clinical events, including atrial fibrillation, ventricular
arrhythmias, and pause arrhythmias, to which RM enables faster
clinical response and appropriate medical action [7-9]. Several
studies have confirmed the clinical and economic benefits of
RM, including improved patient outcomes and reduced health
care use [5,9-13]. A time and motion workflow evaluation was performed in 11
CIED clinics internationally to characterize the discrete activities
and associated time required for all tasks related to managing
patients with CIEDs. Among the participating clinics, 6 were
located in the United States, and 5 were located in Europe (3
in the United Kingdom, 1 in France, and 1 in Germany). Participating clinics were actively managing an average of 5758
(range: 870-22,000) patients with CIEDs, an average of 4217
patients in the United States and 7606 in Europe. All 11 clinics
used guideline-recommended RM in combination with in-person
device follow-up. Half (3) of the US clinics were located within
academic institutions, and 3 of the 5 European clinics were
academic. KEYWORDS rdiac implantable electronic devices; remote monitoring; patient management; clinic efficiency; digital he cardiac implantable electronic devices; remote monitoring; patient management; clinic efficiency; digital health; mobile phone JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 1
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 JMIR CARDIO Seiler et al Data Collection A third-party observer prospectively collected data for one
business week (5 days) at each clinic, recorded the tasks
performed by the staff, and measured each task's duration with
a stopwatch. Workflow measurements included all CIED types
(permanent pacemaker, ICD, CRT, ICM) across any device
manufacturer found within the clinic during the study week
(Abbott, Biotronik, Boston Scientific, Medtronic, and
Microport). The observations included all activities related to managing
patients with CIEDs and were categorized into 3 groups of
activities: in-person clinic visits, remote transmission review,
and other patient management activities not attributable to a
specific patient device check (eg, patient triage and scheduling,
identifying patients lost to follow-up, and telephone
communication with patients). Owing to insufficient data
collection on remote transmission review workflow activities
at the German site, these observations were excluded from the
analysis. Staff Time Per Device Check for Remote and In-Person
Device Follow-ups Furthermore, the literature has shown that the review of an RM
transmission requires less staff time than an in-office
interrogation, and RM is associated with greater patient
adherence to device follow-up checks and a reduction in
scheduled, often nonactionable in-office visits [10,14,15]. However, implementation in clinical practice of an overall
management process for patients with CIEDs, incorporating
both RM and in-person visits, can be challenging because of
the scarcity of information on organizational models and
requirements. The specific steps involved and the health care
professional time required for these activities are poorly
understood, which may hinder the implementation of optimal
follow-up strategies, including remote solutions. Multimedia Appendix 1 lists all observed workflow steps
occurring within each activity category (in-person clinic visit,
remote transmission review, and other patient management
activities). The differences in observed steps between categories
are because of differences in device check scope; for example,
assessing patient vitals or reprogramming device therapy are
specific to in-person clinic visits. These lists are comprehensive
of all possible steps observed, but all steps may not have
occurred during each device check or in sequence as listed, as
practices and workflow vary widely. Thus, to quantify the
workload associated with an average patient device check
(remote or in-person), the unit steps were weighted based on
each step's likelihood of occurring in a given device check. The
weighting factors are listed in Multimedia Appendix 2
[5,14,16-21] and were based on study observations where
possible, supplemented by data from the literature. The mean
time per remote and in-person device checks was calculated,
including all clinical tasks and any administrative tasks related Statistical Analysis Staff Time Per Device Check for Remote and In-Person
Device Follow-ups JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 2
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Annual Staff Time for Other Patient Management
Activities The annual time spent on other patient management activities
not attributable to a specific patient device check was calculated
based on observed clinic norms for performing tasks (eg, weekly
identification of patients with disconnected monitors), whereas
the frequency of telephone calls between the clinic and patient
was based on a previous workflow study [21]. The per-patient
workflow for in-person clinic visits, remote transmission review,
and other patient management activities were extrapolated to
the clinic level based on the average size of the clinics
participating in the study (5758 patients). Annual Staff Time Per Patient for Remote and In-Person
Device Follow-ups Annual Staff Time Per Patient for Remote and In-Person
Device Follow-ups A total of 54 distinct workflow steps were observed and timed
during the management of patients with CIEDs: 31% (17/54)
for remote transmission review, 39% (21/54) for in-person clinic
visits, and 30% (16/54) for other patient management activities
such as patient phone calls and patient triage. The average time
associated with each step is reported in Multimedia Appendices
3-5. During 11 total business weeks of data collection,
observations included 276 in-person clinic visits (124/276,
44.9% the United States and 152/276, 55.1%, Europe), 1948
(1269/1948, 65.14% the United States and 679/1948, 34.86%
Europe) individual remote transmission review tasks (not every
step could be observed for each given transmission, as they
often did not occur sequentially), and 440 other patient
management tasks (the United States only). Considering all
individual time recordings, approximately 50.21% (2424/4828)
of the observations were in patients using pacemakers, 17.13%
(827/4828) were in patients using ICD, 20.89% (1009/4828)
were in patients using CRT, and 11.76% (568/4828) were in
patients using ICM. On the basis of the calculated mean time per activity category,
the annual staff time required to manage each patient with a
CIED was modeled. The volume of remote transmissions per
patient per year was based on real-world device transmissions
from the calendar year 2016-2017 and included routine and
alert-driven transmissions (Multimedia Appendix 2). For
in-person clinical visits, it was assumed that each patient would
have a routine visit per year according to clinical guidelines [6]
and a number of unscheduled visits (ie, device alert or
symptom-driven) based on the frequencies reported in the
remotely monitored arm of published RM trials for each CIED
type [16-20]. Objective This study aims to characterize the workflow processes and
clinic staff time required for remote and in-person device
follow-up of patients with CIEDs. https://cardio.jmir.org/2021/2/e27720 XSL•FO
RenderX JMIR CARDIO Seiler et al programmer was used versus visits in which a tablet programmer
was not used. to that device check (eg, software access, documentation,
scheduling follow-up, and sending information for billing). For remote transmission review tasks, consideration of the
transmission type and review process enabled further analyses. Transmissions were classified as nonactionable versus actionable
(ie, requiring clinical follow-up because of either abnormal
device functioning or a clinical patient event, such as an
arrhythmia). It was assumed that 27% of transmissions would
be actionable, based on a previously published time and motion
evaluation [14]. Scenario analyses were performed to test the
sensitivity of this parameter using additional literature-derived
estimates [14,22,23]. We also estimated staff time spent on first-
and second-line review of remote transmission data, considering
that transmissions sometimes require escalation to more
experienced staff for review and clinical decision-making. We
assumed that 8.2% of transmissions would be sent for
second-line review based on the aforementioned time and
motion study [14]. For in-person clinic visits, 21.8% (27/124)
of the visits were actionable based on study observations. Ethical Considerations As this study was a workflow process evaluation that collected
no patient or clinical data and only collected staff time
measurements, the study protocol did not require approval from
a local ethics committee or institutional review board. This
study adhered to the General Data Protection Regulation and
Health Insurance Portability and Accountability Act data privacy
guidelines in Europe and the United States, respectively. The
included sites consented to participate in the data collection
process in accordance with their privacy requirements. Participating sites were required to have more than one
employee of any given type (eg, nurse, physiologist, and
physician) to preserve employee privacy, with all workflow
data pooled across a staff of the same type. Staff Time per Device Check for Remote and In-Person
Device Follow-ups Mean cumulative staff time required to review a remote device
transmission ranged from 9.4 to 13.5 minutes (16.1-21.7 minutes
for actionable and 6.1-11.2 minutes for nonactionable
transmissions) for therapeutic devices (pacemaker, ICD, or
CRT) and 11.3 to 12.9 minutes (17.3-20.3 minutes for actionable
and 8.0-11.3 minutes for nonactionable transmissions) for ICMs. https://cardio.jmir.org/2021/2/e27720 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 3
(page number not for citation purposes) Predictors of Clinic Efficiency Prespecified subanalyses were performed to identify efficient
clinical practices. Leveraging the same approach described
above for modeling staff time per remote and in-person device
check, the staff time per device check was modeled separately
for the 3 US clinics in which vendor-neutral CIED management
software (Medtronic Paceart Optima) was used during on-site
observations, in comparison with 3 US clinics without
management software. Similarly, the staff time per in-person
visit was modeled separately for observations in which a tablet Participating
clinics
generally
used
a
two-level
transmission-review process. A nurse or device technician
performed a preliminary review (first-line review) to determine
if the transmission requires the intervention of an advanced
practitioner (second-line review performed by a nurse
practitioner, physician assistant, or medical doctor). The staff
time for a first-line review ranged from 11.9 to 13.0 minutes in
the United States and 9.63 to 11.1 minutes in Europe, depending
on device type. A second-line review ranged from 7.2 to 7.9 XSL•FO
RenderX Seiler et al JMIR CARDIO minutes in US clinics and 6.72 to 9.23 minutes in European
clinics (Table 1). minutes in US clinics and 6.72 to 9.23 minutes in European
clinics (Table 1). observations (n=165) were performed by clinical staff, including
nurses, physiologists, and other advanced practitioners (Table
2). Cumulative staff time per in-person clinic visit ranged from
37.8 to 51.0 minutes and 39.9 to 45.8 minutes for therapeutic
devices and ICM, respectively (Table 1). For both remote
transmission review and in-person clinic visits, the overall
percentage of labor performed by each staff type (nurses,
technician or medical assistants, medical doctors, physician
assistants, or nurse practitioners, administrative assistants, and
physiologists) is characterized by country in Table 2. Furthermore, the staff performing administrative tasks differed
by site and region. In the United States, 46.3% (348/751) of all
administrative workflow observations were performed by
medical and administrative assistants, whereas 53.7% (403/751)
of administrative tasks were performed by clinical practitioners. In the United Kingdom, all administrative workflow Given that the estimated time to review an average remote
transmission was dependent on the likelihood of a transmission
being actionable, a series of scenario analyses were performed
to test the sensitivity of this parameter. JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 4
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Predictors of Clinic Efficiency On the basis of the range
of available literature-derived estimates (ranging from 8% to
27%), the time to review a transmission in the United States
ranged from 11.9 to 13.5 minutes for patients with pacemakers,
10.8 to 12.7 minutes for patients with ICDs, 10.8 to 11.9 minutes
for patients with CRTs, and 11.7 to 12.9 minutes for patients
with ICMs. In Europe, the time ranged from 7.7 to 9.4 minutes
for patients with pacemakers, 9.8 to 11.6 minutes for patients
with ICDs, 10.7 to 12.4 minutes for patients with CRTs, and
9.6 to 11.3 minutes for patients with ICM. Table 1. Mean cumulative staff time required per remote transmission review and in-person clinic visit. Table 1. Mean cumulative staff time required per remote transmission review and in-person clinic visit. Europe
United States
Workflow activity
ICM
CRT
ICD
PM
ICMd
CRTc
ICDb
PMa
Remote device transmission review
11.3
12.4
11.6
9.4
12.9
11.9
12.7
13.5
Staff time per average transmissione, minutes
35.6
5.9
5.1
3.6
38.9
5.1
4.6
3.7
Number of transmissions per year (both scheduled and unscheduled
transmissions)f
6.7
1.2
1.0
0.6
8.4
1.2
1.0
0.8
Annual staff time for remote transmissions per patient, hours
In-person clinic visits
39.9
40.9
37.8
41.2
45.8
43.4
51.0
50.1
Staff time per visit, minutes
1.3
1.7
1.7
1.5
1.3
1.7
1.7
1.5
Number of visits per year (both routine and event-driven visits)
1.0
1.1
1.1
1.0
1.0
1.2
1.4
1.3
Annual staff time for clinic visits per patient, hours
7.7
2.4
2.0
1.6
9.3
2.4
2.4
2.1
Total annual per patient staff time, hours
Type of remote device transmission
Staff time required to review actionable versus nonactionable transmissions, minutes
20.3
21.7
20.6
18.3
17.3
16.1
20.1
19.8
Staff time per actionable transmission
8.0
9.0
8.3
6.1
11.3
10.3
9.9
11.2
Staff time per nonactionable transmission
Distribution of staff time for first-line versus second-line review of remote transmissions, minutes
10.7
11.1
10.4
9.6
12.5
11.9
12.2
13.0
Staff time for first-line transmission review (relevant for all trans-
missions)
8.0
9.2
6.7
8.0
7.8
7.2
7.9
7.8
Staff time for second-line transmission review (required for only
8.2% of transmissions) https://cardio.jmir.org/2021/2/e27720 XSL•FO
RenderX XSL•FO
RenderX JMIR CARDIO Table 2. Annual Staff Time for Other Patient Management
Activities In-person clinic visit staff time was modeled separately for visits
in which a tablet-based CIED programmer was used (n=599
total observations) compared with visits in which a legacy
programmer—which is large and cumbersome—was used
(n=794). A tablet-based programmer was associated with an
average of 5.2 minutes lower staff time (54 vs 49 minutes; 9.6%
reduction) for a clinic visit, driven by reduced time for
programmer device transport to a patient room and improved
data connectivity with the electronic health record. The staff time required for other patient management tasks such
as calling patients, troubleshooting device connectivity issues,
identifying loss to follow-up, and triaging patients or
transmissions (full task list provided in Multimedia Appendix
5) was estimated to be 17.3 minutes per patient annually. At
the clinic level (based on the average 5758-patient clinic size
of participating clinics), this translates to 1659.2 hours of staff
time per year (31.9 hours per week). Predictors of Clinic Efficiency Percentage of cardiac implantable electronic devices management workload by staff type and region.a
Physiologistb, n
Administrative assis-
tant, n
Medical doctor, physi-
cian assistant, or nurse
practitioner, n
Technician or medi-
cal assistant, n
Nurse, n
Staff type and region
In-person clinic visits
0
2
45
29
24
United States
52
0
46
0
2
United Kingdom
Remote transmission review
0
3
35
10
53
United States
100
0
0
0
0
United Kingdom
Other patient management (eg, calls and connectivity troubleshooting)c
0
1
0
51
48
United States
Time contribution by staff type: overall
0
2
34
20
44
United States
80
0
19
0
1
United Kingdom
aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. Table 2. Percentage of cardiac implantable electronic devices management workload by staff type and region.a aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. Annual Staff Time Per Patient for Remote and
In-Person Device Follow-ups The staff time required per remote and in-person device check
was modeled separately for the 3 US clinics in which
vendor-neutral CIED management software (Medtronic Paceart
Optima) was used during on-site observations in comparison
with the 3 US clinics without management software. On average,
the total staff time to review a remote transmission was 2.1
minutes lower at sites with management software (11.5 vs 13.6
minutes). The staff time associated with an in-clinic visit was
2.2 minutes lower at clinics with management software (50.4
vs 52.6 minutes). For both remote transmission review and
in-person clinic visits, the time savings were driven by the steps
involved in electronic health record documentation. When
extrapolated to an average clinic size of 5758 patients, the use
of such software was associated with an estimated 10.1
cumulative staff hours saved during a clinic day (50.7 hours per
week) based on 171 weekly clinic visits and 1335 weekly remote
transmissions. Annually, this translates to 2639 hours of staff
time saved, equivalent to 1.4 annual full-time equivalents. The mean number of transmissions per year per patient
(including scheduled and unscheduled transmissions) ranged
from 3.6 to 5.9 for therapeutic devices and 35.6 to 38.9 for ICMs
(Table 1). In contrast, the number of expected in-person clinic
visits per year ranged from 1.3 to 1.7 per patient. Although we
seek to model time for an average clinic, the frequency of
in-person and remote device checks will vary significantly
between clinics depending on device programming practices,
patient indications, and patient education. Multiplying the staff time for each expected remote and
in-person device check by the annual frequencies of device
checks per year yielded an estimated total annual staff time of
1.6 to 2.4 hours to manage a patient with a therapeutic device
and 7.7 to 9.3 hours for a patient with an ICM (Table 1). The
higher staff time to manage a patient with an ICM was attributed
to the increased transmission volume observed. https://cardio.jmir.org/2021/2/e27720 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 5
(page number not for citation purposes) Principal Findings Similar to most sites in this study, a two-tiered remote
transmission review structure was leveraged, in which nurses
(or other similar practitioners) performed the initial transmission
review and escalated critical events to a physician. However,
this model may not apply to all device clinics, depending on
the size, RM infrastructure, and staff resources available. Our study observed a significant workload associated with
fielding patient calls and troubleshooting connectivity, which
is consistent with a recent study that found that more than 40%
of patient calls received by CIED clinics pertain to
troubleshooting RM equipment and transmission status [21]. Strategies to improve device connectivity—for instance,
Bluetooth-enabled, smartphone-paired, or widespread use of
other wireless monitors—could alleviate this significant
workload burden on CIED clinics. Furthermore, optimizing the
appropriate staffing types for each activity (eg, administrative
tasks performed by administrative staff) could help clinics
balance operational costs and resource availability. Although different organizational models, staff types, and
workflows may exist in practice depending on the setting and
available resources, the essential tasks required to manage
patients with CIEDs remain similar. This evaluation sets a
baseline by describing the essential activities performed by
clinical staff to manage a population of patients with CIEDs
and the time required to execute it. It also underscores the
complexity of the current management of patients with CIEDs,
identifying 54 distinct workflow tasks across three categories
(remote transmission review, in-person clinic visits, and other
patient management activities, such as patient phone calls and
triaging). A number of studies have previously estimated the time to
perform remote and in-person device checks, yielding a wide
range of time estimates, suggesting that there may be significant
clinic-to-clinic variability [14,31-33]. To our knowledge, this
study is the first multicenter, multinational study to describe
comprehensive work requirements for managing patients with
CIEDs. Considering the significant time-consuming activities
related to follow up patients with CIEDs, appropriate funding
needs to be in place to ensure that this crucial part of the patient
care pathway is not overlooked. As RM is considered a
guideline-recommended standard of care for all patients with
CIEDs, hospital or clinic budget holders, payers, and
reimbursement authorities should financially support its
implementation and day-to-day practice. Funding and
reimbursement of RM are variable and remain a challenge in
many geographies today, as all stakeholders involved in this
continuous service provision are often not remunerated or
insufficient. Principal Findings This study characterized the staffing resources necessary for
cardiac device clinics to manage patients with CIEDs, including
detailed time associated with each workflow step and
breakdowns by device, geographic region, and staffing types. Although differences were observed across device types and
geographic regions, the overall workload was found to be
consistently substantial, regardless of CIED type and region. As revealed by the predictors of efficiency analysis described
above, even small improvements in the efficiency of CIED
clinics can have a significant positive impact on time savings. Although our study observed meaningful time savings associated
with the use of patient management software and tablet-based
programmers, further research is needed to identify other
strategies for optimal patient follow-up. For instance, the
growing number of technologies capable of transmitting patient
data to CIED clinics represents a challenge for data management
[25,26]. Further innovation on solutions for integrating and
storing data from this multitude of sources could enhance the
efficient management of patients with CIEDs. This software
also presents an opportunity for closer clinical care and patient
safety; previous studies using the triaging and analytic
capabilities of the PaceArt Optima system showed an improved
enrollment of patients in RM [27] and identification and
successful interventions for patients with suboptimal ICD
programming [28] and low CRT pacing [29,30]. As CIED technology advances, so do device data capabilities
to inform and optimize patient care. The benefits of RM have
been illustrated in several clinical studies, including faster event
detection, improved patient outcomes, and reduced health care
use. However, data alone will not result in clinical and economic
benefits unless timely clinical action is taken. Clinical workflows
must be optimized to capture the value of the device data. The HRS consensus statement on RM outlined the importance
of implementing a streamlined organization with clear roles and
responsibilities to manage RM data in parallel with in-person
follow-ups [5]. However, there is limited literature on how
patients with CIEDs are managed in practice, including the
workflow steps and the staffing requirements associated with
each task, creating implementation challenges for new RM
users. Protocols for remote management of patients with CIEDs
have been developed, including the HomeGuide registry study
[24], which implemented a dedicated nurse-physician team
strategy. Predictors of Clinic Efficiency A series of prespecified subanalyses were conducted to identify
the predictors of clinic efficiency. JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 5
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 XSL•FO
RenderX JMIR CARDIO Seiler et al devices) because of increased device transmissions both for
routine data review and programmable automatic device alerts. However, it should be noted that the magnitude of the device
transmission frequency with ICMs is highly dependent on the
alert programming settings, patient indications, and patient
education. The overall annual time required to follow and
manage a patient with a CIED is lower for a patient with a
therapeutic device (1.6-2.4 hours) than a patient with a
diagnostic device (ICM: 7.7-9.3 hours). JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 6
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Principal Findings Such a barrier affects RM adoption and its
implementation as a standard of care. For this time and motion Mean staff time required per remote transmission review and
in-person clinic visit ranged from 9.4 to 13.5 minutes and 37.8
to 51.0 minutes, respectively, depending on device type. This
validates previous research demonstrating the efficiency
opportunities for RM [14]. The annual time per patient required
for in-person device checks was relatively consistent across
device types (1.0-1.4 hours), perhaps because of the low
frequency of office visits required for patients being
continuously monitored with RM. The annual time per patient
for RM was higher in patients with diagnostic devices (ICMs:
6.7-8.4 hours per year vs only 0.6-1.2 hours for therapeutic JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 6
(page number not for citation purposes) XSL•FO
RenderX JMIR CARDIO Seiler et al different device populations and staffing resources is unknown. However, this is the first attempt at characterizing cardiac device
clinic workflow in full and provides a first step in filling the
knowledge gap around patient management practices and
resource requirements. evaluation, countries where RM reimbursement is available
were selected to avoid the influence of this lack of financial
incentives on patient management organizations, which could
be reflected in time measures. However, local reimbursement
challenges persist, including limitations on specific cardiac
devices, settings, and health care professionals in France and
Germany. RM may not be suitable for every patient for different
reasons (technical, clinical, or patient preference) but should be
proposed to all eligible patients, in line with the medical
recommendations and considering the current environment
[34,35]. With the COVID-19 pandemic, RM benefits have been
reinforced, also underlining the need to establish an appropriate
infrastructure to manage patients remotely, which requires
human, time, and financial investment. In addition, as the time and motion methodology was designed
as a clinic-perspective workflow characterization and did not
follow patients longitudinally, we were unable to measure
patient clinical metrics, such as device connectivity success and
patient adherence to follow-ups. Finally, extrapolations were
made using externally published data (eg, proportion of device
checks requiring second-line assessment) and HRS guidelines
for patient follow-up, and these assumptions may not be
generalizable to all clinics. A series of sensitivity analyses were
performed to test the impact of our assumption on transmission
actionability. Acknowledgments Acknowledgments
The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection
and analysis were funded by Medtronic. Conflicts of Interest
MDB, SR, EN, DL, and MM are Medtronic employees and shareholders. Data collection for this study, performed by Deloitte,
was funded by Medtronic. Multimedia Appendix 1
Workflow steps observed during the management of cardiac implantable electronic devices patients. [DOCX File , 46 KB-Multimedia Appendix 1]
Multimedia Appendix 2
Modeling inputs. [DOCX File , 17 KB-Multimedia Appendix 2]
Multimedia Appendix 3
Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3]
JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7
https://cardio.jmir.org/2021/2/e27720
(page number not for citation purposes)
FO
erX The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection
and analysis were funded by Medtronic. The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection
and analysis were funded by Medtronic. Principal Findings Although device check-level and annual resource
use will be dependent on individual workflow practices,
individual workflow step measurements can readily be used to
create a workflow framework that is highly customizable to
individual centers and circumstances. Although it is widely acknowledged today that RM is a valuable
tool for optimal follow-up of patients with CIEDs, to achieve
this objective, infrastructure investments are required, including
equipment (eg, additional computer or monitors) and setting up
a specific clinic workflow organization involving sufficient
human resources. As this infrastructural investment might not
be an option in all settings, outsourcing remote patient
management to other clinics or third-party arrhythmia review
services could be an alternative to in-house implementation, as
has been shown previously [36]. Conclusions This observational study confirmed the complexity of the
management of patients with CIEDs. The associated workflows
require significant clinical and administrative staff time across
in-person clinic visits, remote transmission review, and other
patient management tasks. RM is an efficient component of
managing patients with CIEDs, allowing for continuous
follow-up of patients with reduced staff time required per device
check. Detailed recommendations on organizational models for
managing patients with CIEDs are warranted to ensure
homogeneous follow-up, support RM implementation, and
enable optimal patient care. Limitations This study had several limitations. Owing to the real-world
observational nature of this analysis, study measurements were
reliant on the workflow taking place during the data collection
week and were not systematically controlled for patient or center
characteristics. This study describes the workflow observed at
11 centers in the United States and Europe, but the
generalizability of these observations to other centers with Conflicts of Interest MDB, SR, EN, DL, and MM are Medtronic employees and shareholders. Data collection for this study, performed by Deloitte,
was funded by Medtronic. Multimedia Appendix 1 Workflow steps observed during the management of cardiac implantable electronic devices patients. [DOCX File , 46 KB-Multimedia Appendix 1] JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7
(page number not for citation purposes) Multimedia Appendix 2 Modeling inputs. Modeling inputs. [DOCX File , 17 KB-Multimedia Appendix 2] g
p
[DOCX File , 17 KB-Multimedia Appendix 2] Multimedia Appendix 3
Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3] Multimedia Appendix 3
Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3] Multimedia Appendix 3 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7
(page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 https://cardio.jmir.org/2021/2/e27720 XSL•FO
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https://openalex.org/W44170285 | https://inria.hal.science/hal-01501817/document | English | null | Usability and Utility Needs of Mobile Applications for Business Management among MSEs: A Case of Myshop in Uganda | Lecture notes in computer science | 2,013 | cc-by | 5,423 | To cite this version: Rehema Baguma, Marko Myllyluoma, Nancy Mwakaba, Bridget Nakajubi. Usability and Utility
Needs of Mobile Applications for Business Management among MSEs: A Case of Myshop in Uganda. 14th International Conference on Human-Computer Interaction (INTERACT), Sep 2013, Cape Town,
South Africa. pp.764-773, 10.1007/978-3-642-40480-1_54. hal-01501817 Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-01501817
https://inria.hal.science/hal-01501817v1
Submitted on 4 Apr 2017 L’archive ouverte pluridisciplinaire HAL, est
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abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License Usability and Utility Needs of Mobile Applications for
Business Management among MSEs: A case of Myshop in
Uganda Rehema Baguma1, Marko Myllyluoma2, Nancy Mwakaba2 and Bridget Nakajubi3
1 College of Computing & Information Sciences, Makerere University
rbaguma@cit.mak.ac.ug
2 Nokia Research Centre Nairobi
[marko.myllyluoma, ext-nancy.mwakaba]@nokia.com
3 Grameen Applab-Uganda Office
bridget@applab.org 1 College of Computing & Information Sciences, Makerere University
rbaguma@cit.mak.ac.ug
2 Nokia Research Centre Nairobi
[marko.myllyluoma, ext-nancy.mwakaba]@nokia.com
3 Grameen Applab-Uganda Office
bridget@applab.org Abstract. This paper discusses the usability needs of mobile applications for basic business
management for Micro and Small Scale Enterprises (MSEs) in developing countries. This is
based on results from a user study carried out in Uganda on 30 MSEs. The study was carried
out on MyShop, an easy to use mobile business management application for cash transactions
and book keeping designed for micro-entrepreneurs. The study investigated learning to use
MyShop, the support MyShop gives to the user and its usefulness, and value addition to users. The study also covered the pleasure and stimulation MyShop gives to users. Results from the
study show that MSE owners/shopkeepers would like an application that is easy to use such as
have an intuitive navigation and a simple and clear language. They would also like an applica-
tion that supports their unique context like multiple people operating a shop, selling goods on
credit, ownership of multiple businesses, use of low end phones and regular load shedding. In
terms of value addition, MSEs would like the application to assist them in managing the daily
operations and developing the business in the long term such as marketing, time saving and
control over business. Keywords: Usability, mobile applications, utility, MSEs, MyShop, business manage-
ment. Keywords: Usability, mobile applications, utility, MSEs, MyShop, business manage-
ment. 1
Introduction Micro and Small Scale Enterprises (MSEs) play important roles in the economic
growth and sustainable development of every nation (Moore et al., 2008). The devel-
opment and growth of MSEs can provide solutions to the problem of high unemploy-
ment facing many countries especially developing countries. Maseko and Manyani
(2012) noted that MSEs have low start-up costs, low risk and can exploit untapped
knowledge bases of creativity in the population for new product development. Ac-
cording to East African Community (EAC) (2010), MSEs are often considered a key
source of productivity, growth and job creation. They promote equitable distribution
of income because they are owned by relatively low income entrepreneurs, most of
whom are women. MSEs are therefore important instruments for both income distri- bution and equitable participation in the process of economic development. For gov-
ernments, well-managed and healthy MSEs are a source of revenue in form of taxes. Uganda has 0.8 million MSEs that contribute 20% to GDP and employ over 1.5 mil-
lion people (EAC, 2010). In Uganda, MSEs are categorized according to number of
employees, value of capital investments and turn over as follows: Table 1: MSE Definition used in Uganda
Number of Em-
ployees (Max)
Capital Investments (Max
in UGX)
Revenue (Max in UGX)
Micro
4
12m (USD 4800)
12m (USD 4800)
Small
50
360m (USD 144000)
360m (USD 4800)
From EAC (2010) As mobile phones are multiplying in the developing world, many social economic
services and applications are being innovated by Mobile Network Operators (MNOs),
not for profit and for profit organizations. Hellstrom (2010) noted that in a region
where the vast majority have limited resources among other constraints, mobile phone
solutions provide a means of extending a number of services to the poor who are in
rural and remote areas. However, Corbett (2008) remarked that as sales, access, and
coverage continue to grow, it is yet to be seen whether the mobile phone technology
will play a significant, sustained role in alleviating poverty in the developing world. In most developing countries such as Uganda, while operators’ focus has been people
with a high disposable income and revenue generating services like urban youth and
entertainment, services and development oriented applications have not been priori-
tised. Therefore the number of relevant applications for economic and social devel-
opment is still limited. 1
Introduction p
On the other hand, efforts to develop mobile applications for banking and manag-
ing business internationally have been focused on applications for high end phones
such as iPhone (e.g. Mint and Splash Money), Android (Xero) and ipad (quickbooks
mobile). These sophiscated mobile applications are out of reach for MSEs in develop-
ing countries due to their high cost, hi-tech nature (most MSE owners are computer
illiterate), energy efficiency (battery consumption) and data dependency (online con-
nection). As a result there is need for applications that can run on low end phones that
most MSEs in developing countries use. In addition, most available applications are
mainly about personal financial activities such as banking than managing business
activities of a business. For example iPhones’s Ledger Docs is used for digital captur-
ing of ledger receipts. Mint, another iPhone application, updates account balances,
transmits real-time alerts to the phone for low account balances, over-budget, and
tracks strange buying and selling activity. Android’s Xero keeps the user updated
about business finances and cashflow, creates real time reports as well as integrated
invoicing for precision management. To-date, most research on MSEs and mobile phone usage has been focused on the
communication function of the phone and mobile commerce. Examples of such in-
clude; Kwaka (2012) who reports about mobile phone usage by MSEs in semi-rural
Ghana; Melchioly and Aebø (2010) reports about added value concerning economic
growth and entrepreneurship to SMEs in terms of communication with suppliers and
customers, market solicitation, social cohesion and operational cost reduction; Es- selaar et al (2008) reports on ICT usage and its impact on profitability of SMEs in 13
African Countries. Others are Escobari and Donner (2009), Matambalya and Sussana
(2012), Dorflinger et al (2009), Edim and Muyingi (2010) and Giridher et al (2009). selaar et al (2008) reports on ICT usage and its impact on profitability of SMEs in 13
African Countries. Others are Escobari and Donner (2009), Matambalya and Sussana
(2012), Dorflinger et al (2009), Edim and Muyingi (2010) and Giridher et al (2009). Hence little so far has been done about using mobile phones for business manage-
ment. Palsey (2011) reports about a mobile book keeping application developed as
part of her Honours studies to enable MSEs keep records of their business transac-
tions and automatically generate financial reports. However, the application in ques-
tion is not available in the public domain. 1
Introduction Therefore it is not clear whether it went
beyond the university laboratory to be used by the target users. Business management for MSEs like other business types is important for plan-
ning, budgeting and forecasting, taxation, access to finance among other functions. EAC (2010) noted that the quality of information that a firm produces and maintains
determines its access to finance. However, EAC (2010) found out that majority of
Micro and Small Scale Enterprises do not keep proper records due to lack of appro-
priate skills. Therefore efforts to provide simple business management tools tailored
to the needs and characteristics of MSEs are greatly needed. This paper discusses attributes for an easy to use and beneficial (utility) mobile ap-
plication for business management among MSEs in developing countries. This is
based on results of a user study carried out in Uganda on MyShop. MyShop is mobile
business application for cash transactions and book keeping designed for micro-
entrepreneurs. The study covered ease of use and utility evaluation of MyShop. It
investigated learning to use MyShop and the phone (Nokia c3-01), support MyShop
gives to the user, the pleasure and stimulation MyShop gives to users and the useful-
ness, and value addition of MyShop to users. y
Nielsen (2012) refers to usability as a quality attribute that assesses how easy the
user interfaces are to use. According to Schumacher and Lowry (2010), usability is
the effectiveness, efficiency and satisfaction with which specified users can achieve
specified goals in a particular environment. Utility on the other hand refers to the
design's functionality i.e. whether a product or service does what users need (Nielsen,
2012). Ease of use and utility are equally important and together determine whether
something is useful. Nielsen (2012) noted that it matters little that something is easy
to use if it is not what you want and it is also no good if the system can hypothetically
do what you want, but you cannot make it happen because the user interface is too
difficult. Therefore the attributes discussed in this work are concerned with ease of
use and utility needs of mobile applications for business management among MSEs. In particular, this is discussed in the perspective of the MyShop application. 2
Methodology The ease of use and utility evaluation of MyShop was carried out on a sample of 30
MSEs dealing in products and services in and around Kampala city, Uganda. The
study was conducted between November 2011 to March 2012. The study areas in-
cluded one urban location and three peri-urban areas namely: Kampala city centre,
Kawempe trading centre, Kyaliwajjala trading centre and Natete trading centre. The rationale for selecting one urban location versus 3 peri-urban ones was because most
MSEs in Uganda operate in peri-urban and rural areas. g
p
p
The 30 participants were chosen purposively based on the following attributes: p
p
p
p
y
g
ability to read and write in English. The minimum requirement was completion of
Ordinary Level (Middle School) but completion of Advanced Level (High School)
was preferred. This attribute was important because the application was in English. The second requirement was ability to use Short Message Service (SMS) or mobile
money service. This gave an indication of experience with data applications. In addi-
tion, some individual user characteristics were preferred in order to be sure that the
participant would perform and fulfill all expected tasks. These included: able to at-
tend trainings, willingness to use the application in day to day business, willingness to
commit at least 1 hour daily to update information and commitment to meet data col-
lection requirements. Other desired attributes included: located 10 - 15 kms from
central Kampala, small scale dealing in products and services, 1+ years of operation;
10+ transactions/day, owner operated or employing not more than 5 people and be-
tween 200 and 2000 USD start up capital. p
p
Three weeks to the beginning of the study, participants were trained (half day) in
using the application and phone. After the training, they were given phones loaded
with the application to use for three weeks before beginning of interviews. In addi-
tion, they were given a user guide covering using the main menu and application set-
tings, and a summary of how each of the application’s functions work. The study was conducted through weekly field visits to the study sites during which,
the study team observed how participants were using the application in their cash and
book keeping activities. In addition, 3 questionnaires on ease of use, reliability and
enjoyment, and utility were administered to participants to elicit quantitative and
more detailed qualitative data. 2
Methodology There was no requirement for approval from an Institu-
tional Review Board before running the study. 3.1
About MSEs that Participated The study covered one urban area and three peri-urban areas around Kampala city. The study population was 30 MSEs dealing in products and services. Of the 30 partic-
ipants, 53% were male and 47% female. Fifty percent had a degree or diploma, 33%
had completed Advanced Level (High School) while 17% had completed Ordinary
Level (Middle School). All the participants could read and write in English and could
use SMS or mobile money. The business premises were located 10-15 KMs from
central Kampala and 83% had been in operation for 1+ years. All participating busi-
nesses had 10 + transactions/day, were owner operated or employing not more than 5
people and 59% of the businesses were worth 10 million Uganda Shillings and above
(approximately $4,200 USD). In the findings discussed below, the names given are
not actual names of participants for purposes of protecting the identity and businesses
of participants. 3.1
Usability and Utility Needs of Mobile Applications for Business
Management among MSEs: A case of Myshop in Uganda This section discusses ease of use and utility needs of mobile applications for business
management among MSEs in developing countries. This is based on results from a
user evaluation study of MyShop. MyShop was developed by Nokia and has four
main functionalities: selling stock (called “Sell”), recording sales and expenses (called
“Records”), purchases and inventory management (called “Stock”), and monitoring of
business performance over time (called “Reports”). It is available for free in Nokia’s
online store on http://store.ovi.com/content/249179. p
The needs discussed are categorized into: ease of use, support to the user, usefulness
and value addition to MSE owners/shopkeepers and the pleasure, and stimulation to
the user. According to the Webster online dictionary, ease of use is the property of a
product or thing that a user can operate without having to overcome a steep learning
curve. High ease of use makes products or systems intuitive to use to the average user. In the context of computer/mobile applications, ease of use simply means an applica-
tion that is effortless to understand, find what is needed and do what one wants to do. In addition, the user’s context such as characteristics of the environment, language
preference, cultural or community practices, unique business characteristics, etc.,
need to be understood and supported for better usability. These attributes are catego-
rized as support to the user in this work. 3.1
About MSEs that Participated Further more, for a product, service or sys-
tem to be useful, it should be both easy to use and of value to the users (Nielsen,
2012). Hence value attributes are also important and are classified as value to the
users in this work. Besides ease of use, supporting users’ context and being of value, a
product, service or system should be pleasing and motivating to users to succeed. 3.1.1
Ease of Use This subsection discusses attributes that can make mobile applications for business
management effortless to use for MSE owners/shopkeepers. These include: Using the application as transactions happen: MSE owners/shopkeepers prefer to
use the application as transactions happen. In the MyShop usability evaluation study,
80% of the shopkeepers interviewed preferred to use the application as transactions
happen. They noted that this helps them avoid forgetting details of transactions per-
formed as Mariam, a shopkeeper from Kyaliwajjala trading centre remarked: “I use it
as I transact my business throughout the day because I need to ensure that all records
have been entered”. In line with this need, developers of mobile applications for
business management among MSEs need to focus on making it easier and faster to
record transactions because efficiency is very important to shopkeepers. Auto computation of tasks such as profits and losses: MSE owners like the auto
computation of tasks by computer/mobile applications. This is much easier and less
error prone compared to manual computations on paper. Jolly a shopkeeper in
Kawempe trading centre equipped: “auto calculation of sales, profits and losses
makes my life easy”. Intuitive navigation: MSE owners want a well organized interface that they can
easily navigate and find functions needed. Participants in the MyShop study found it
easy to use the simple navigation structure of MyShop (4 items at the first level and 3- 6 items inside each of the screens on the second level). Betty a saloon operator in
Kawempe trading centre said: “I like the fact that it is easy to navigate through the
application and know where to find what function when I need it”. 6 items inside each of the screens on the second level). Betty a saloon operator in
Kawempe trading centre said: “I like the fact that it is easy to navigate through the
application and know where to find what function when I need it”. Simple and clear language: MSE owners/shopkeepers would like mobile applica-
tions written in simple and clear business management language. This is preferred
because most of them have low levels of education and do not have formal training in
book keeping. In the MyShop study, 68% strongly agreed that the language used in
MyShop is clear and simple which made the application easy to use. 3.1.1
Ease of Use Violet, a drug
shop attendant in Kawempe trading centre noted: “the application uses simple busi-
ness language and the English is clear”. g
g
g
Representative icons: Using icons that are a clear representation of intended function
makes such applications easy to use for MSEs. In the MyShop study, most partici-
pants found the icons used meaningful in relation to the intended function. Jumba, an
operator of a crafts shop in Kyaliwajjala trading centre said: “the icons explain well
what function they represent e.g. using a symbol of money notes to mean sell clearly
shows that whatever is under that function is money coming in”. A key thing about
the understandability of the icons is that they are not global abstract metaphors but
tangible everyday items. For example, instead of a shopping cart, there is a basket
and for stock, the initial metaphor of a delivery truck, was replaced with a pile of
boxes. Easy to learn: MSEs find applications that are easy to learn easy to use. In the
MyShop research study, 24% strongly agreed and 48% agreed that learning MyShop
was easy which made use of the application easy. This was attributed to the ease of
finding functions, simple and clear language, representative icons and an easy to op-
erate phone. 3.1.2
Support to the User This subsection discusses usability attributes that address contextual needs of MSEs
from mobile applications for business management. These include; Multiple user accounts: Some MSE owners have employees hence it is important for
the mobile application to support multiple user accounts with varying privileges. This
will enable shop owners/managers to restrict access to information on certain aspects
such as reports. In the MyShop study, 80% of the participants preferred using the
application alone (which meant running a parallel manual system) because the version
used did not support multiple user accounts. Portability: MSEs prefer the mobile application to a computer application due to its
portability. This helps them carry out offsite business management activities like re-
stocking more easily. In the MyShop study, 35% strongly agreed and 57% agreed that
they enjoy using MyShop in business partly due to its portability. Agnes, a grocery
shop attendant in Kampala city centre noted: “I go with it when shopping for new
stock and I use it to remind me about restocking needs”. Easy to operate phone: The phone(s) on which the application works must be easy
to operate. In the MyShop study, 28% strongly agreed and 40% agreed that the phone
on which MyShop was loaded, was easy to use. This was attributed to the semi-touch
screen phone (small touch screen and large physical keys) and participants’ previous
experience with other Nokia models. Isaac, a video library operator in Kawempe trad- ing centre noted that: “It is very easy to find functions with the touch screen”. This
finding is not isolated because White (2010) noted that less educated and less tech-
nology savy mobile phone users find touch screens easier to use because they directly
manipulate interface objects rather than using third party interaction aids like a mouse
and keyboard. y
Short introduction to bookkeeping: EAC (2010) in a study about MSEs in E. Afri-
can countries found that majority of micro and small enterprises do not keep proper
records due to lack of appropriate skills. In the MyShop study, the “Reports” module
was used less because most participants confused the “Records” module to offer simi-
lar functions to “Reports” and or did not understand how it works. 3.1.2
Support to the User For example Chris-
tine, a beverages shop operator in Kyaliwajjala trading centre said: “I really did not
understand how the reports function works and since I can assess the business per-
formance with records then I do not need to use reports”. The user manual in the
version of MyShop used did not cover book keeping. Including an introduction to
book keeping in the help module, can benefit those new to book keeping concepts. Provide cloud or local backup storage: To prevent against data loss in case of loss
of the phone or a problem with the hardware or software, it is important to provide for
data back up locally or in the cloud. The MyShop version that was used in the study
did not have this provision. p
Device independence: It is important to make such applications compatible with low
end phones so that users are not limited on device choice. In the study, the Nokia c3-
01 used had a short battery life (which was a problem to participants due to regular
load shedding). In addition, Nokia c3-01 costs approximately USD 200 hence is ex-
pensive for most MSE owners but the current version of MyShop runs on lower end
Nokia devices that cost as low as USD 50. Provide for selling services: The MSE sector has both product and service business-
es with varying operational procedures. Therefore it is important for such applications
to provide for both. One way is to have a product and service version with services
offered and details of offering in the place of stock. The MyShop version used was
only applicable to MSEs dealing in physical products such as retail shops. Therefore
it was a challenge using it on businesses dealing in services like video libraries. g
g
g
Provide for credit transactions: Selling on credit is a common practice especially
for retail shops in Uganda and other African countries. The MyShop version used in
the study did not have this provision and participants expressed a need for it. Betty, a
cosmetics shop operator in Kawempe trading centre said: “It is very difficult to keep
track of items sold on credit, yet we sometimes offer goods to on credit”. f
y
ff
g
Local language version: Most MSE owners are not comfortable with English due to
low levels of education. 3.1.2
Support to the User UNESCO (2007) reported that one of the challenges of deliv-
ering mobile phone based services is that 41% of the population in developing coun-
tries is non-literate and even the literate among the poor are typically novice users of
computer technologies. Due to this limitation, the study purposively selected partici-
pants whose level of education ranged from Ordinary Level (Middle School) and
above. Therefore for this application to succeed in the market like Uganda there is
need for it to have a version in a language. In the study, participants requested for a
version in Luganda, the most dominant local language in Uganda. Use one install for two or more businesses: Multiple business ownership is common
among business people in Uganda and Africa. Ronald, a video library operator in Natete trading centre said: “I have a video library and a phone accessories shop
hence I would prefer being able to use one copy of MyShop for both businesses”. Therefore it is important to make it possible for one install to be used for two or more
businesses for example through a multi business edition. p
g
Link application to mobile money: Like other business people, MSEs make a lot of
financial transactions such as paying suppliers, utilities, employees, receiving pay-
ments from customers, etc. However, the banking infrastructure in Uganda like other
developing countries is still severely limited and very few people can meet require-
ments of banking institutions (FinScope, 2007). Participants in the study revealed that
some of the payments they make in their businesses such as paying suppliers, rent,
and receiving payment from some customers are settled using mobile money. There-
fore such a function would make the application more useful and relevant for MSEs. 3.1.3 This subsection discusses attributes that address relevancy and value addition attrib-
utes MSEs desire from mobile applications for business management. Marketing function: MSEs would like an application that can on top of basic book
keeping, perform related functions such as marketing. This can be achieved through
mass dissemination of marketing information via Short Message Service (SMS) or
multimedia messaging. During the study, some participants used the phone camera to
take pictures of their stock for marketing to potential customers. Moses, an operator
of an arts and crafts shop in Kyaliwajjala trading centre noted: “I take pictures of
current stock and sold out items to show to potential customers”. Reduction of workload: MSEs would like an application that reduces their work load
thereby making work easier. 60% of the study participants agreed that using MyShop
had made work easier in their business such as in stock taking and tracking profits and
losses. Deborah, a supermarket operator in Kyaliwajjala remarked: “I track the stock
automatically within the application which less tiresome”. y
pp
Time saving: MSEs desire applications that help them save time in the management
of their businesses creating more efficiency. In the study, over 60% agreed that
MyShop saves time in business management because of automated functions. Joshua
an airtime supplier from city centre remarked that: “MyShop has promoted efficiency
in business information recording/book keeping”. f
g
p g
Safe keeping of business information: MSEs would like an application that keeps
their business information safe and secure. Katende, a shopkeeper in Kawempe trad-
ing centre remarked: “My business is individual therefore I like it that MyShop keeps
my business information away from third parties”. Therefore it is important for such
applications to restrict access to some information like reports. Control over business: MSEs would like the mobile application to help them better
control their business such as keeping track when away and easy assessment of per-
formance. Jackson, a mobile video and disco operator in Natete trading centre noted:
“the business’ performance is easily assessed since everything is automated“. This
can be further enhanced by making the app an online service that syncs across multi-
ple shopkeepers so that the business owner can monitor while away. 3.1.4
Pleasure and Stimulation to the User This subsection discusses attributes that will make mobile applications for business
management pleasing and motivating to use for MSE owners/shopkeepers. g
p
g
g
p
p
Exciting experience: MSE would be attracted to an application that gives them an
exciting experience. This can be achieved through adaptation of the application to
their business needs. In the MyShop usability study, 17% had an extremely exciting
experience while 62% had an exciting experience. This was attributed to relevancy of
MyShop and the semi-touch screen phone which most of them were using for the first
time. Miriam a shopkeeper in Kyaliwajjala trading centre said: “MyShop helps me
make business decisions based on facts e.g. every day, I look at MyShop to find out
what needs restocking before I restock”. g
f
Enjoy using the application: MSEs would like an application that they enjoy using. To achieve this, the application must be relevant to their needs and context. In the
MyShop study, 35% strongly agreed and 57% agreed that they enjoy using MyShop
in business due to its portability and auto computation of tasks. Doris, a mini super-
market operator in Kyaliwajjala said: “I go with it when shopping for new stock and I
use it to remind me about restocking needs”. Conclusion The potential value of Mobile applications for business management among MSEs is
enormous but for this to be realized such applications must be usable and have high
utility to the target MSEs. For MSEs in developing countries such as Uganda, such
applications must be effortless to use, relevant to the needs and context of MSEs add
value to their businesses and be pleasurable and stimulating to use. Future efforts on
such applications should focus on usability and utility for the target market segments. References 1. Donner, J. & Escobari, M. (no date). A review of the research on mobile use by micro
and small enterprises (MSEs) ICTD 2009, Qatar, 17-19 April. p
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2. Dorflinger, J. et al (2009). Mobile Commerce in Rural South Africa-Proof of Concept of
Mobile Solutions for the Next Billion Mobile Consumers. Proc. WOWMOM’09. \ 3. Dim, A. E. & Muyingi, H., N., A. (2010). Mobile Commerce Application for Rural
Economy Development: A case study for Dwesa. Proc. SAICSIT’10. ACM Press (2010). 4. Esselaar, S., Stork, C., Ndiwalana, A. & Een-Swarray, M. (2008). ICT Usage and Its Im-
pact on Profitability of SMEs in 13 African Countries. 5. Faris, S. (2012). Bookkeeping Made Easy…And Mobile With The Help Of Some Great
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6. Gilbert, C. (2012). Usability Evaluation. In: Soegaard, Mads and Dam, Rikke Friis
(eds.). "Encyclopedia of Human-Computer Interaction". Aarhus, Denmark: The Interac-
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http://www.interaction-
design.org/encyclopedia/usability_evaluation.html 7. Giridher, T. et al. (2009). Mobile Applications for Informal Economies. Proc.IMCSIT'09. IEEE (2009). 7. Giridher, T. et al. (2009). Mobile Applications for Informal Economies. Proc.IMCSIT'09. IEEE (2009). 8. Hellström, J. (2010). The Innovative Use of Mobile Applications in East Africa, Sida
Review 2010:12, published by Edita 2010. 9. Kwakwa, A. P. (2012). Mobile Phone Usage by Micro and Small Scale Enterprises in
Semi-Rural Ghana, International Review of Management and Marketing Journal, Vol. 2,
No.3, 2012. 10. Melchioly, R. S. & Sæbø, Ø. (2010). ICTs and Development: Nature of Mobile Phones
usage for SMEs Economic Development - An Exploratory Study in Morogoro, Tanzania. IFIP, Technical Commission 9 – Relationship between Computers and Society. Work-
shop at Makerere University, Uganda. 22-23 March 201. 11. Maseko, N. & Manyani, O. (2012). Accounting practices of SMEs in Zimbabwe: An in-
vestigative study of record keeping for performance measurement (A case study of Bin-
dura). Journal of Accounting and Taxation Vol. 3(8), pp. 171-181, Dec. 2011. 12. Moore et al. (2008). Managing small business: An entrepreneurial emphasis, 14th ed. 13. Nielsen, J. (2012). Usability 101: Introduction to Usability retrieved on 1st October 2012
from: http://www.useit.com/alertbox/20030825.html 14. Schumacher, R. M. & Lowry, S. Z. (2010).NIST Guide to the Processes Approach for
Improving the Usability of Electronic Health Records, National Institute of Standards
and Technology. 15. SMEs get productivity from mobile applications. Retrieved on 25th September from:
http://www.computerweekly.com/news/2240088236/SMEs-get-productivity-from-
mobile-applications. 16. References The East African Community (EAC), (2010). Study on the Promotion of Micro, Small
and Medium Enterprises (MSMEs) in the East African Region, consolidated report by
Ernst and Young. Retrieved on 30th June from: www.ugandainvest.go.ug. 17. UNESCO (2007). UNESCO Institute of Statistics Data Centre, regional literacy rates. Retrieved on 12th June 2012 from
http://stats.uis.unesco.org/unesco/TableViewer/tableView.aspx?ReportId=y201. http://stats.uis.unesco.org/unesco/TableViewer/tableView.aspx?ReportId=y201. 18. Wamuyu, E.& Maharaj (2011). Usage of mobile technologies in Kenya, The African
Journal of Information Systems. 19. Webster Online Dictionary. Retrieved on 2nd October 2012 from: http://www.websters-
online-dictionary.org. 20. White, G. (2010). Designing Mobile services for the Non-literate communities. In the
Proceedings of the 2nd International Conference on M4D 2010, Kampala, Uganda. 21. Xero
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http://www.getapp.com/xero-application Acknowledgements We extend our sincere thanks to Nokia that allowed us to use results from an original-
ly non-academic usability evaluation study on MyShop in Uganda. We also extend
thanks to Grammeen Applab-Uganda Office in particular Sean Paavo Krepp, the
Country Director and Annete Bogere, the Content and Services Manager. Grammen-
Applab coordinated the study in Uganda as a local partner on behalf of Nokia. Our
since thanks also go to Gabriel White who worked as a User Experience Consultant
and Richard Nuwagaba, and Andrew Gagwera who worked as Research Assistants
on the study. |
https://openalex.org/W4293102489 | https://molecular-cancer.biomedcentral.com/counter/pdf/10.1186/s12943-022-01639-0 | English | null | Retraction Note to: MiR-143-3p functions as a tumor suppressor by regulating cell proliferation, invasion and epithelial–mesenchymal transition by targeting QKI-5 in esophageal squamous cell carcinoma | Molecular cancer | 2,022 | cc-by | 651 | He et al. Molecular Cancer (2022) 21:170
https://doi.org/10.1186/s12943-022-01639-0 Open Access Publisher’s Note Publisher’s Note Retraction note to: Mol Cancer 15, 51 (2016)
https://doi.org/10.1186/s12943-016-0533-3 Retraction note to: Mol Cancer 15, 51 (2016)
https://doi.org/10.1186/s12943-016-0533-3 Publisher s Note
Springer Nature remains neutral with regard to jurisdictional claims in pub-
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of significant concerns regarding a number of Figures
presented in this work, which question the integrity of
the data. The Editor-in-Chief therefore no longer has
confidence in the integrity of the data in this article. All
authors agree to this retraction. Retraction Note to: MiR‑143‑3p functions
as a tumor suppressor by regulating cell
proliferation, invasion and epithelial–
mesenchymal transition by targeting QKI‑5
in esophageal squamous cell carcinoma Zhenyue He1†, Jun Yi2†, Xiaolong Liu2†, Jing Chen1, Siqi Han1, Li Jin1, Longbang Chen1* and The original article can be found online at https://doi.org/10.1186/s12943-
016-0533-3
†Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com
1 Department of Medical Oncology, Jinling Hospital, Medical School
of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002,
People’s Republic of China
Full list of author information is available at the end of the article The original article can be found online at https://doi.org/10.1186/s12943-
016-0533-3 †Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. †Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com 1 Department of Medical Oncology, Jinling Hospital, Medical School
of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002,
People’s Republic of China Full list of author information is available at the end of the article © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
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1D
f 1 Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing
University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002, People’s
Republic of China. 2 Department of Cardiothoracic Surgery, Jinling Hospital,
Medical School of Nanjing University, 305 Zhongshan East Road, Nanjing,
Jiangsu 210002, People’s Republic of China. © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
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https://openalex.org/W3083888041 | https://www.journal-vniizht.ru/jour/article/download/438/318 | Russian | null | On the double-deck transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation | Vestnik naučno-issledovatelʹskogo instituta železnodorožnogo transporta/Vestnik Naučno-issledovatelʹskogo instituta železnodorožnogo transporta | 2,020 | cc-by | 5,867 | О двухъярусной перевозке крупнотоннажных
контейнеров: начало работ, приостановка
программы, мероприятия по ее пролонгации
Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина
Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»),
Москва, 129626, Россия ных контейнерных перевозок активизировали в нача-
ле 2000-х гг. освоение такого способа перевозок и на
железных дорогах России. ных контейнерных перевозок активизировали в нача-
ле 2000-х гг. освоение такого способа перевозок и на
железных дорогах России. Аннотация. В начале XXI в. с целью повышения конкурен-
тоспособности контейнерных перевозок на железных дорогах
России были проведены комплексные исследования по воз-
можности перевозки крупнотоннажных контейнеров, погру-
женных в два яруса. В отличие от мирового опыта в освоении
такого способа перевозок, где они осуществляются на линиях с
тепловозной тягой, возможность перевозки контейнеров, по-
груженных в два яруса, на электрифицированных отечествен-
ных магистралях определяется наличием контактного прово-
да, что создает дополнительное ограничение для увеличения
высоты груза. р
Условия перевозок на российских железных до-
рогах существенно отличаются от действующих в
указанных странах. Протяженность электрифици-
рованных линий составляет более 50 % общей экс-
плуатационной длины. Из-за наличия контактного
провода имеется дополнительное ограничение для
двухъярусной перевозки по высоте груза [1, 2, 3, 4, 5]. Тем не менее в 2001 г. ВНИИЖТ было поручено
провести комплексные исследования по созданию спе-
циализированной платформы для перевозки крупно-
тоннажных контейнеров с погрузкой в два яруса. В ре-
зультате этих исследований учеными и специалистами
института были разработаны технические требования к
платформе, а в 2003 г. на Брянском машиностроитель-
ном заводе (ОАО «БМЗ-вагон») впервые в отечествен-
ной практике был создан опытный образец специали-
зированной колодцевой платформы (модель 13-3124)
на типовых грузовых тележках модели 18-100 для двухъ
ярусной перевозки крупнотоннажных контейнеров. Условия перевозок на российских железных до-
рогах существенно отличаются от действующих в
указанных странах. Протяженность электрифици-
рованных линий составляет более 50 % общей экс-
плуатационной длины. Из-за наличия контактного
провода имеется дополнительное ограничение для
двухъярусной перевозки по высоте груза [1, 2, 3, 4, 5]. В статье рассматриваются результаты многолетних ком-
плексных исследований по созданию специализированной
колодцевой платформы и разработке технологии перевозки
в ней крупнотоннажных контейнеров с погрузкой в два яруса,
выполненных ВНИИЖТ в начале 2000-х гг. Представлены осо-
бенности конструкции колодцевой платформы, схемы раз-
мещения в ней контейнеров, виды проведенных испытаний
и данные об опытной перевозке платформы, груженной кон-
тейнерами в два яруса. Приведены сведения о приостановке
работ по внедрению двухъярусной перевозки контейнеров и
предложены мероприятия, которые необходимо выполнить в
случае возобновления работ по внедрению на сети российских
железных дорог такого способа перевозок. Тем не менее в 2001 г. ВНИИЖТ было поручено
провести комплексные исследования по созданию спе-
циализированной платформы для перевозки крупно-
тоннажных контейнеров с погрузкой в два яруса. E-mail: lazarenko_um@list.ru (Ю. М. Лазаренко) © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2
224 Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
224 О двухъярусной перевозке крупнотоннажных
контейнеров: начало работ, приостановка
программы, мероприятия по ее пролонгации
Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина
Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»),
Москва, 129626, Россия 224 – 229 Параметры
контейнеров
Тип контейнеров
1АА
1А
1СС
1С
1ААА
Длина, фут
мм
40
12 192
40
12 192
20
6058
20
6058
40
12 192
Высота, мм
2591
2438
2591
2438
2896
Ширина, мм
2438
2438
2438
2438
2438
Масса брутто, т
30,48
30,48
24,0
24,0
30,48
Высота двух ярусов, мм
5182
4876
5182
4876
5792
Т а б л и ц а 1
Размерно-весовые параметры контейнеров
T a b l e 1
Dimensions and weight parameters of containers • грузоподъемность при применении тележки
модели 18-100 — 67 т; О двухъярусной перевозке крупнотоннажных
контейнеров: начало работ, приостановка
программы, мероприятия по ее пролонгации
Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина
Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»),
Москва, 129626, Россия В ре-
зультате этих исследований учеными и специалистами
института были разработаны технические требования к
платформе, а в 2003 г. на Брянском машиностроитель-
ном заводе (ОАО «БМЗ-вагон») впервые в отечествен-
ной практике был создан опытный образец специали-
зированной колодцевой платформы (модель 13-3124)
на типовых грузовых тележках модели 18-100 для двухъ
ярусной перевозки крупнотоннажных контейнеров. Проведенные учеными и специалистами ВНИИЖТ исследо-
вания по внедрению перевозок крупнотоннажных контейнеров
типа 1АА, 1А, 1СС и 1С с погрузкой в два яруса на колодцевой
платформе показали высокую эффективность разработанной
технологии перевозки. Она по-прежнему сохраняет свою ак-
туальность и может быть внедрена в настоящее время. Пере-
численные в статье мероприятия, подлежащие реализации для
возобновления работ по внедрению данной технологии, пред-
лагается включить в программу внедрения такого вида пере-
возок. При выполнении указанных работ учитывались
размерно-весовые параметры контейнеров четырех
типов (табл. 1). Типаж крупнотоннажных контейнеров: Типаж крупнотоннажных контейнеров: 40-футовые (длина 12 192 мм) — 1АА, 1А; 20-футовые (длина 6058 мм) — 1СС, 1С. Ключевые слова: крупнотоннажный контейнер; колод-
цевая платформа; двухъярусная перевозка; габариты погрузки;
технология перевозки Характеристики колодцевой платформы модели
13-3124 для двухъярусной перевозки крупнотоннажных
контейнеров. Платформа конструируется без хребто-
вой балки. Рама вагона формируется из продольных
боковых балок, которые образуют в межтележечном
пространстве колодец для размещения контейнера. Продольные балки изготавливаются из двух профи-
лей: двутавра со срезами в консольных частях и при-
варенного к нему Z-образного профиля (рис. 1, 2). На
нижние полки Z-образного профиля укладываются
листы пола, стягивающие балки. О О
пыт применения двухъярусной перевозки крупно-
тоннажных контейнеров за рубежом, основания
для начала работ. Положительный опыт зарубежных
железных дорог США, Канады, Китая, Австралии,
Индии и других стран по перевозке крупнотоннажных
контейнеров, погруженных в два яруса, на линиях с
тепловозной тягой, а также возросшая актуальность
повышения конкурентоспособности железнодорож- Платформа модели 13-3124 имеет следующие
основные параметры: © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
224 следовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. • грузоподъемность при применении тележки
модели 18-100 — 67 т; Размерно-весовые параметры контейнеров ;
• масса тары — 27,6 т; • грузоподъемность при применении новых пер-
спективных тележек с нагрузкой на ось 25 т — 72 т; • нагрузка на ось — 23,5 т на тележках модели 18-100; • погонная нагрузка — 4,65 кН/м для тележек мо-
дели 18-100, 4,95 кН/м — для новых тележек. На колодцевую платформу в два яруса может быть
погружено: На колодцевую платформу в два яруса может быть
погружено: • четыре 20-футовых контейнера типа 1С (высота
2438 мм) или 1СС (высота 2591 мм), имеющих загруз-
ку до 17 т каждый (среднесетевая загрузка — 14 – 15 т)
(рис. 3); Примечание. Контейнеры типа 1ААА были исключены из подготовки
к двухъярусной перевозке, так как они использовались только в транзитных
перевозках и возможность их перевозки в два яруса потребовала бы подъема
контактной сети на высоту не менее 6400 мм, что сопряжено с ростом рас-
ходов на реконструкцию устройств подвески контактной сети и сделало бы
двухъярусную перевозку экономически нецелесообразной. • два 40-футовых контейнера типа 1А (высота
2438 мм) или 1АА (высота 2591 мм), имеющих полную
загрузку и массу брутто каждого 30,48 т (рис. 4). Параллельно с разработкой конструкции и изготов-
лением опытного образца колодцевой платформы была
проработана конструкция межъярусного крепления кон-
тейнеров. Все известные способы крепления для контей-
неров первого и второго ярусов были неприемлемы. Рис. 1. Колодцевая часть платформы:
1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме-
таллическая стенка колодца; 4 — направляющий металлический
элемент; УГР — уровень головки рельса; пунктирная
линия — внешний контур контейнера
Fig. 1. Well part of the platform:
1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well;
4 — guiding metal element; УГР — rail head level; dashed line — outer
contour of the container
280
17
1071
310
130
10
20
791
1
2
3
4
13,5
10
50
2438
12
13
1325 УГР
224 УГР
254 УГР 280
17
1071
310
130
10
20
791
1
2
3
4
13,5
10
50
2438
12
13
1325 УГР
224 УГР
254 УГР 280
17
1071
310
130
10
20
791
1
2
3
4
13,5
10
50
2438
12
13
1325 УГР
224 УГР
254 УГР Номинальное габаритное пространство инфра-
структуры характеризуется следующими нормативами: • габарит приближения строений С (ГОСТ 9238–83
«Габариты приближения строений и подвижного со-
става железных дорог колеи 1520 (1524) мм»); 791 • высота подвески контактного провода — 5750 мм. • грузоподъемность при применении тележки
модели 18-100 — 67 т; Основные варианты размещения контейнеров в
два яруса. Основные варианты размещения контейнеров в
два яруса. Первый вариант — размещение в пределах высоты,
допускаемой габаритом погрузки (5300 мм). Первый ярус: высота строго 2438 мм: один контей-
нер типа 1А или два типа 1С . Второй ярус: а) высота 2438 мм — один контейнер
типа 1А, при высоте 2591 мм — один контейнер типа
1АА; б) высота 2438 мм — два контейнера типа 1С . Общая высота 5130 или 5283 мм с учетом высоты
площадки Z-образного профиля (254 мм). Второй вариант — размещение с превышением
высоты, допускаемой габаритом погрузки. Первый ярус: высота 2591 мм — один контейнер
типа 1АА или два типа 1СС. Второй ярус: высота 2591 мм — один контейнер
типа 1АА или два типа 1СС . Рис. 1. Колодцевая часть платформы:
1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме-
таллическая стенка колодца; 4 — направляющий металлический
элемент; УГР — уровень головки рельса; пунктирная
линия — внешний контур контейнера
Fig. 1. Well part of the platform:
1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well;
4 — guiding metal element; УГР — rail head level; dashed line — outer
contour of the container Рис. 1. Колодцевая часть платформы:
1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме-
таллическая стенка колодца; 4 — направляющий металлический
элемент; УГР — уровень головки рельса; пунктирная
линия — внешний контур контейнера
Fig. 1. Well part of the platform:
1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well;
4 — guiding metal element; УГР — rail head level; dashed line — outer
contour of the container Общая высота составляет 5436 мм. На железных дорогах еще имеются объекты ин-
фраструктуры, не отвечающие габариту приближения
строений С и высоте подвески контактного провода
(5750 мм). В связи с этим специалистами ВНИИЖТ и
железных дорог были проведены обследования указан-
ных объектов и сделана оценка, приведенная ниже. g. . p
p
:
1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well;
4 — guiding metal element; УГР — rail head level; dashed line — outer
contour of the container плекса было проведено натурное обследование факти-
ческих габаритов сооружений и устройств и прочности
пути на маршруте Москва — Владимир — Чепца — Оценка технических возможностей железных дорог по
пропуску вагонов с двухъярусной погрузкой контейнеров. В 2005 г. 22
© Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 По второму варианту погрузки
Наличие ограничений: • по осевой нагрузке — нет; • по габаритам сооружений — в двух тоннелях
верхний угол второго яруса будет задевать обделку:
Керакский тоннель Забайкальской железной дороги
(7344 км), Облученский тоннель Дальневосточной
железной дороги (8193 км); • по габаритам сооружений — в двух тоннелях
верхний угол второго яруса будет задевать обделку:
Керакский тоннель Забайкальской железной дороги
(7344 км), Облученский тоннель Дальневосточной
железной дороги (8193 км); Рис. 2. Продольный вид платформы:
1 — первый ярус; 2 — второй ярус
Fig. 2. Longitudinal view of the platform:
1 — first deck; 2 — second deck • по контактному проводу — на большинстве мо-
стов, тоннелей, путепроводов высота контактного про-
вода менее 5750 мм. Ориентировочные расходы в ценах
2005 г. на проведение работ по устранению ограниче-
ний по контактному проводу приведены в табл. 2. • по контактному проводу — на большинстве мо-
стов, тоннелей, путепроводов высота контактного про-
вода менее 5750 мм. Ориентировочные расходы в ценах
2005 г. на проведение работ по устранению ограниче-
ний по контактному проводу приведены в табл. 2. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124
Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров
1С или 1СС на колодцевую платформу модели 13-3124
Fig. 3. Double-deck loading of four 20-foot containers
1C or 1СС on a well platform model 13-3124
Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124 Испытания платформы. Колодцевая четырехосная
платформа модели 13-3124 успешно прошла прочност-
ные, тормозные и динамические испытания на Экс-
периментальном кольце ВНИИЖТ, после чего были
проведены ее комплексные динамические ходовые и
по воздействию на путь и стрелочные переводы испы-
тания на Скоростном испытательном полигоне (СП)
ВНИИЖТ Белореченская — Майкоп. Основанием для проведения испытаний платфор-
мы являлось указание МПС России от 16.10.2003 г. № П-107у. Испытания проводились со скоростями до
135 км/ч в прямых участках пути, до 120 км/ч — в кривой
радиусом 650 м, до 80 км/ч — в кривой радиусом 350 м и
до 50 км/ч — на боковое направление стрелочных пере-
водов марки 1/11. При движении по кривым участкам
пути реализовывались положительные поперечные не-
погашенные ускорения величиной до 0,7 – 0,8 м/с2. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1С
на колодцевую платформу модели 13-3124
Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров
1С или 1СС на колодцевую платформу модели 13-3124
Fig. 3. По второму варианту погрузки
Наличие ограничений: Double-deck loading of four 20-foot containers
1C or 1СС on a well platform model 13-3124
Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1С
на колодцевую платформу модели 13-3124 Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА
на колодцевую платформу модели 13-3124
Номинальное
габаритное
пространство
инфраструктуры
ис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА
на колодцевую платформу модели 13-3124
Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров
1А или 1АА на колодцевую платформу модели 13-3124
Fig. 4. Double-deck loading of two 40-foot containers
1A or 1AA on a well platform model 13-3124 В качестве ходовых частей платформы использова-
ны две двухосные тележки модели 18-100. Конструкция
верхнего строения пути на опытных участках СП: рель-
сы типа Р65, сваренные в плети, шпалы железобетонные
количеством 1840 – 2000 шт. на 1 км, балласт щебеноч-
ный. Фактическое состояние рельсовой колеи в период
проведения испытаний определялось по данным прохо-
да путеизмерительного вагона № 247 от 11.11.2003 г. На
всех опытных участках отступлений в содержании рель-
совой колеи выше 2-й степени обнаружено не было. В
прямом участке преобладали отступления по уровню
величиной от 9 до 12 мм и длиной от 2 до 17 м. с. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА
на колодцевую платформу модели 13-3124
минальное
габаритное
пространство
инфраструктур
4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА
на колодцевую платформу модели 13-3124
Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров
1А или 1АА на колодцевую платформу модели 13-3124
Fig. 4. Double-deck loading of two 40-foot containers
1A or 1AA on a well platform model 13-3124 По результатам испытаний были рекомендованы
следующие допускаемые в эксплуатации скорости дви-
жения: в прямых — до 90 км/ч, в кривых — скорости
при непревышении непогашенного ускорения 0,3 м/с2. Важным этапом в создании новой специализи-
рованной платформы и перспективной технологии
двухъярусной перевозки крупнотоннажных контей-
неров стало проведение эксплуатационных испыта-
ний — опытной перевозки погруженных в два яруса
20- и 40-футовых контейнеров с реальным грузом. По результатам испытаний были рекомендованы
следующие допускаемые в эксплуатации скорости дви-
жения: в прямых — до 90 км/ч, в кривых — скорости
при непревышении непогашенного ускорения 0,3 м/с2. Важным этапом в создании новой специализи-
рованной платформы и перспективной технологии
двухъярусной перевозки крупнотоннажных контей-
неров стало проведение эксплуатационных испыта-
ний — опытной перевозки погруженных в два яруса
20- и 40-футовых контейнеров с реальным грузом. Называевская — Мариинск — Юрты — Петровский
завод — Архара — Хабаровск — Находка — Москва. • грузоподъемность при применении тележки
модели 18-100 — 67 т; ВНИИЖТ с помощью диагностического ком- 225
© Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 I Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Рис. 2. Продольный вид платформы:
1 — первый ярус; 2 — второй ярус
Fig. 2. Longitudinal view of the platform:
1 — first deck; 2 — second deck
7
. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124
Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров
1С или 1СС на колодцевую платформу модели 13-3124
Fig. 3. Double-deck loading of four 20-foot containers
1C or 1СС on a well platform model 13-3124
7
Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124
2
1
12 500
1040-1080
14 950
17 950
19 170
254 Рис. 2. Продольный вид платформы:
1 — первый ярус; 2 — второй ярус
Fig. 2. Longitudinal view of the platform:
1 — first deck; 2 — second deck
7
3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124
Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров
1С или 1СС на колодцевую платформу модели 13-3124
Fig. 3. Double-deck loading of four 20-foot containers
1C or 1СС on a well platform model 13-3124
7
Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС
на колодцевую платформу модели 13-3124
По второму варианту пог
Наличие ограничений:
• по осевой нагрузке —
• по габаритам сооруж
верхний угол второго ярус
Керакский тоннель Забайк
(7344 км), Облученский т
железной дороги (8193 км);
• по контактному прово
стов, тоннелей, путепроводо
вода менее 5750 мм. Ориенти
2005 г. на проведение работ
ний по контактному проводу
Испытания платформы. платформа модели 13-3124 у
ные, тормозные и динамич
периментальном кольце ВН
проведены ее комплексные
по воздействию на путь и ст
тания на Скоростном испы
ВНИИЖТ Белореченская —
Основанием для проведе
мы являлось указание МП
№ П-107у. Испытания пров
135 км/ч в прямых участках п
радиусом 650 м, до 80 км/ч —
до 50 км/ч — на боковое нап
водов марки 1/11. При движ
2
1
12 500
1040-1080
14 950
17 950
19 170
254 По второму варианту погрузки
Наличие ограничений: © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
226 • производительность выше на 30 %; • производительность выше на 30 %; • себестоимость перевозок контейнеров ниже на
24 %; • среднегодовой дисконтированный доход на
одну платформу — 211,3 тыс. руб.; • повышение веса поезда на 800 – 1000 т в преде-
лах существующих длин станционных путей. ВНИИЖТ совместно с ЦЭ ОАО «РЖД» провел
анализ габаритных характеристик сооружений и вы-
соты подвески контактного провода на указанных на-
правлениях и установил, что для отработки практики
эксплуатации платформы 13-3124 при перевозке кон-
тейнеров в два яруса из всех указанных маршрутов
целесообразно принять два маршрута: Вместе с тем в 2006 г. при рассмотрении итогов опыт-
ной перевозки на одном из совещаний в ОАО «РЖД»,
несмотря на положительные результаты исследова-
ний и перспективность внедрения новой двухъярус-
ной технологии перевозок контейнеров, работы по
проекту были приостановлены, так как двухъярусная
перевозка не учитывала контейнеры типа 1ААА. первый: Койты — Микунь — Низовка — Коноша —
Вологда-2 — Кошта — Волховстрой-2 — Мга — Обу-
хово — Автово — Новый порт — Санкт-Петербург-
Варшавский; Перспективы внедрения технологии перевозок кон-
тейнеров с двухъярусной погрузкой, отмеченные в 2006 г. В связи с возникшей проблемой учета 40-футовых
контейнеров типа 1ААА для двухъярусной перевозки
и решением совещания у первого вице-президента
ОАО «РЖД» В. Н. Морозова от 29.09.2006 г. протокол
№ВМ-98 «О целесообразности завершения разработ-
ки и внедрения в эксплуатацию специализированной
платформы модели 13-3124 с двухъярусной погрузкой
контейнеров» ОАО «Трансконтейнер» определило
следующие направления для организации перевозок
контейнеров типа 1С, 1СС, 1А и 1АА с погрузкой в два
яруса на платформу модели 13-3124 [6, 7]: второй: Архангельск-город — Исакогорка — Коно-
ша — Вологда-2 — далее по первому маршруту. второй: Архангельск-город — Исакогорка — Коно-
ша — Вологда-2 — далее по первому маршруту. Наиболее подготовленным был первый маршрут,
на котором находились шесть сооружений, где вы-
сота подвески контактного провода ниже норм на
40 – 75 мм (эти отклонения могли быть устранены
регулировкой подвески контактного провода в не-
большие сроки при стоимости работ ориентировоч-
но 12 млн руб.). При этом для первого маршрута было
учтено, что по еще имеющемуся на нем одному пре-
пятствию (негабаритный мост на участке Мга — Обу-
хово) Октябрьская железная дорога уже ведет строи-
тельные работы, и оно будет устранено. • Москва — Екатеринбург — Новосибирск и обратно; • Койты — Низовка — Исакогорка — Архангельск-
город — Санкт-Петербург-Варшавский — Автово —
Новый порт. 227
© Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 По второму варианту погрузки
Наличие ограничений: Результаты обследования:
По первому варианту погрузки
Наличие ограничений:
• по осевой нагрузке 25 тс — нет;
• по габаритам сооружений — нет;
• по контактному проводу — нет. теризуется следующими нормативами:
р
р
р
фр
ру
ур
ризуется следующими нормативами: Называевская — Мариинск — Юрты — Петровский
завод — Архара — Хабаровск — Находка — Москва. Результаты обследования:
По первому варианту погрузки
Наличие ограничений:
• по осевой нагрузке 25 тс — нет;
• по габаритам сооружений — нет;
• по контактному проводу — нет. теризуется следующими нормативами:
р
р
р
фр
ру
ур
еризуется следующими нормативами: Московская, Юго-Восточная и Приволжская же-
лезные дороги для проведения эксплуатационных испы-
таний подготовили маршрут Лесок — Рязань — Ряжск — • по габаритам сооружений — нет; • по контактному проводу — нет. Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Железная дорога
Расходы, млн руб. Октябрьская
210
Московская
108
Горьковская
39
Северная
20
Юго-Восточная
30
Приволжская
80
Свердловская
15
Западно-Сибирская
24
Красноярская
30
Восточно-Сибирская
50
Забайкальская
259
Дальневосточная
385
Всего: 1250
Т а б л и ц а 2
Ориентировочные расходы на проведение работ по устранению
ограничений по контактному проводу для пропуска двухъярусной
погрузки с контейнерами 1АА и 1СС
T a b l e 2
Estimated costs of work to eliminate restrictions
on the overhead wire for passing double-decker loading with containers
1AA and 1СС Кочетовка — Анисовка — Саратов — Астрахань — Ку-
тум. Ученые и специалисты ВНИИЖТ и ВНИИАС
провели эксплуатационные испытания платформы
модели 13-3124 с двухъярусной погрузкой контейне-
ров типов 1АА и 1СС. Результаты — положительные. Успешная опытная перевозка контейнеров типа
1АА и 1СС, погруженных в два яруса, по маршруту
протяженностью около 3000 км и относительно невы-
сокие расходы на устранение ограничений по контакт-
ному проводу (1,25 млрд руб.) свидетельствовали о том,
что разработанная новая технология двухъярусной пе-
ревозки может быть рекомендована для сетевого вне-
дрения. Целесообразность такого решения подтверж-
далась высокой экономической эффективностью
двухъярусной перевозки, полученной в выполненных
ВНИИЖТ расчетах и характеризуемой следующими
данными по сравнению с одноярусной: • производительность выше на 30 %; Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Лельма — Шалакуша Северной железной дороги
(ориентировочная стоимость 30 млн руб.). бы стать одним из важнейших направлений техни-
ческого прогресса на железнодорожном транспорте. Это следует из того, что более половины перевозок
крупнотоннажных контейнеров включают перевозку
контейнеров типа 1А, 1С, 1АА и 1СС, возможность
двухъярусной перевозки которых уже доказана. Опытный образец платформы 13-3124 в то время
должен был пройти на Экспериментальном кольце
ВНИИЖТ ресурсные испытания. К сожалению, после
пробега 2000 км ресурсные испытания были прекра-
щены из-за разрушения сварных швов в скругляемых
местах перехода консольных площадок к несущей раме
колодца. Заключение. Проведенные учеными и специалиста-
ми ВНИИЖТ исследования по внедрению перевозок
крупнотоннажных контейнеров типа 1АА, 1А, 1СС и 1С
с погрузкой в два яруса на колодцевой платформе по-
зволяют сделать вывод, что для железных дорог Россий-
ской Федерации создана высокоэффективная техно-
логия перевозки крупнотоннажных контейнеров. Она
по-прежнему сохраняет свою актуальность и может
быть внедрена в настоящее время. Перечисленные в
статье мероприятия, подлежащие реализации для во
зобновления работ по внедрению данной технологии,
предлагается включить в программу внедрения такого
вида перевозок. Мероприятия, подлежащие реализации для возоб
новления работ по внедрению технологии перевозки
крупнотоннажных контейнеров типа 1А, 1С, 1АА и 1СС,
погруженных в два яруса 1. Разработка проекта модернизации колодцевой
платформы модели 13-3124 с целью улучшения сопря-
жения консольной части платформы и боковых стен ее
колодца и устранения других недостатков конструкции. 2. Актуализация данных по габаритной характери-
стике сооружений и высоте подвески контактного про-
вода на всех железных дорогах. Разработка программы
подготовки сети железных дорог к эксплуатации мо-
дернизированной колодцевой платформы, загружен-
ной в два яруса контейнерами типа 1А, 1С, 1АА и 1СС. СПИСОК ЛИТЕРАТУРЫ Как было сказано выше, не-
возможность применения данной технологии пере-
возки к контейнеру типа 1ААА стала одной из причин
отказа от ее внедрения. Другая причина заключается,
видимо, в том, что технология двухъярусной перевозки
более сложная по сравнению с одноярусной. Однако
с учетом высокой эффективности двухъярусной пере-
возки этот вопрос может найти решение при возобнов-
лении программы внедрения перевозок такого вида. 7. Ла з арен ко Ю. М.,
А рш и н цев Д. Н.,
Морозов Э. Н. О внедрении высокоэффективной технологии перевозки крупнотон-
нажных контейнеров в два яруса на железных дорогах Российской
Федерации // Промышленный транспорт XXI век. 2013. № 1. С. 21. СПИСОК ЛИТЕРАТУРЫ 1. Современные габаритные возможности железных дорог /
Ю. М. Лазаренко [и др.] // Железнодорожный транспорт. 1978. № 4. С. 61 – 66. 1. Современные габаритные возможности железных дорог /
Ю. М. Лазаренко [и др.] // Железнодорожный транспорт. 1978. № 4. С. 61 – 66. 3. Изготовление двух опытных образцов модерни-
зированной колодцевой платформы, межъярусных
замков. Проведение комплекса необходимых испыта-
ний и сертификации платформы. 2. Лазаренко Ю. М. Нестандартные решения для нестан-
дартных грузов // РЖД-Партнер. Спец. выпуск: Контрейлерные
перевозки. 2012. С. 31. 3. Богданов В. М. Использование габаритных возможностей
сети для повышения провозной способности // Увеличение габа-
ритов и повышение погонных нагрузок грузовых вагонов: сб. науч. тр. ВНИИЖТ. М.: Транспорт, 1983. Вып. 660. С. 4 – 17. 4. Разработка технических требований к испытаниям. 5. Изготовление партии (сто единиц) модернизи-
рованных колодцевых платформ и поставка их в вы-
бранные вагонные депо. тр. ВНИИЖТ. М.: Транспорт, 1983. Вып. 660. С. 4 – 17. 4. Лазаренко Ю. М. Лесным грузам — увеличенный габарит
погрузки // Железнодорожный транспорт. 1980. № 5. С. 20 – 23. 6. Разработка технологической инструкции по
двухъярусной погрузке и выгрузке крупнотоннажных
контейнеров и технических условий размещения и
крепления контейнеров 1А, 1С, 1АА и 1СС в два яруса
на модернизированной колодцевой платформе. 5. Лазаренко Ю. М., Богданов В. М. Совершенствование
габаритов на железных дорогах ОСЖД // Бюллетень ОСЖД. 1980. № 4. С. 9 – 13. 6. Лисицын А. Л., Лазаренко Ю. М., Вологин В. А. Пере-
возки крупнотоннажных контейнеров в два яруса // Железнодо-
рожный транспорт. 2002. № 8. С. 33 – 35. Приведенные мероприятия предусматривают ре-
шение технических вопросов, но в них не учтен еще
один важнейший аспект: необходимо положительное
отношение к двухъярусной перевозке крупных кон-
тейнерных операторов, транспортно-логистических
компаний, для которых важно обеспечить перевозку
контейнеров всех типов. Как было сказано выше, не-
возможность применения данной технологии пере-
возки к контейнеру типа 1ААА стала одной из причин
отказа от ее внедрения. Другая причина заключается,
видимо, в том, что технология двухъярусной перевозки
более сложная по сравнению с одноярусной. Однако
с учетом высокой эффективности двухъярусной пере-
возки этот вопрос может найти решение при возобнов-
лении программы внедрения перевозок такого вида. Приведенные мероприятия предусматривают ре-
шение технических вопросов, но в них не учтен еще
один важнейший аспект: необходимо положительное
отношение к двухъярусной перевозке крупных кон-
тейнерных операторов, транспортно-логистических
компаний, для которых важно обеспечить перевозку
контейнеров всех типов. © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
228 • производительность выше на 30 %; Дополнительно были указаны также направления
для организации кольцевых маршрутов: По второму рекомендуемому маршруту дополни-
тельно к указанным работам необходимо было произ-
вести регулировку подвески контактного провода на
двух мостах Северной железной дороги (866 и 856 км),
где ее высота ниже нормы на 75 мм (ориентировоч-
ная стоимость работ 5 млн руб.), и заменить пролетное
строение на мосту через реку Недзюга — 848 км участка Дополнительно были указаны также направления
для организации кольцевых маршрутов: • Санкт-Петербург-Варшавский — Сегежа —
Санкт-Петербург-Варшавский; • Санкт-Петербург-Варшавский — Автово — Новый
порт — Соликамск — Санкт-Петербург-Варшавский;
С
С Санкт-Петербург-Варшавский — Автово — Новый
порт — Соликамск — Санкт-Петербург-Варшавский;
• Соликамск — Новороссийск — Соликамск. порт — Соликамск — Санкт-Петербург-Варшавский;
• Соликамск — Новороссийск — Соликамск. • Соликамск — Новороссийск — Соликамск. 227
© Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 REFERENCES Valeriy V. SEMERKHANOV,
Senior Researcher, JSC “VNIIZhT” 1. Lazarenko Yu. M., Bogdanov V. M., Ostrov A. B., Vol'kovich Yu. N. Sovremennye gabaritnye vozmozhnosti zheleznykh dorog [Mo
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the transportation of large-capacity containers in two decks on the
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on the implementation of transportation of large-capacity containers
of the 1AA, 1A, 1CC and 1C types with loading in two decks on
a well platform have shown the high efficiency of the developed
transportation technology. It still retains its relevance and can be
implemented at the present time. The measures listed in the article
to be implemented to resume work on the implementation of this
technology are proposed to be included in the program for the in-
troduction of this type of transportation. Информация об авторАХ ЛАЗАРЕНКО Юрий Михайлович,
канд. техн. наук, консультант, АО «ВНИИЖТ» ЛАЗАРЕНКО Юрий Михайлович,
канд. техн. наук, консультант, АО «ВНИИЖТ» АРШИНЦЕВ Дмитрий Николаевич,
канд. техн. наук, руководитель группы, АО «ВНИИЖТ» СЕМЕРХАНОВ Валерий Викторович,
старший научный сотрудник, АО «ВНИИЖТ» СЕМЕРХАНОВ Валерий Викторович,
старший научный сотрудник, АО «ВНИИЖТ» МИТИНА Елена Алексеевна,
ведущий инженер, АО «ВНИИЖТ» МИТИНА Елена Алексеевна,
ведущий инженер, АО «ВНИИЖТ» КАПУСКИНА Елена Владимировна,
ведущий инженер, АО «ВНИИЖТ» КАПУСКИНА Елена Владимировна,
ведущий инженер, АО «ВНИИЖТ» Авторы данной статьи стремятся еще раз обратить
внимание на существование полностью разработан-
ной, но не внедренной высокоэффективной техно-
логии перевозок, которая и в настоящее время могла Статья поступила в редакцию 03.05.2020 г., актуализирована
17.07.2020 г., принята к публикации 22.07.2020 г. Статья поступила в редакцию 03.05.2020 г., актуализирована
17.07.2020 г., принята к публикации 22.07.2020 г. © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
228 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Для цитирования: О двухъярусной перевозке крупнотоннажных контейнеров: начало работ, приостановка программы,
мероприятия по ее пролонгации / Ю. М. Лазаренко [и др.] // Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229. DOI: https://
doi.org/10.21780/2223-9731-2020-79-4-224-229. Yuriy M. LAZARENKO, Yuriy M. LAZARENKO,
Cand. Sci. (Eng.), Consultant, JSC “VNIIZhT” Keywords: large-capacity container; well platform; double-
deck transportation; loading dimensions; transportation technology Cand. Sci. (Eng.), Consultant, JSC “VNIIZhT” Dmitriy N. ARSHINTSEV,
Cand. Sci. (Eng.), Head of the Group, JSC “VNIIZhT” On the double-deck transportation of large-tonnage containers: start of work, suspension
of the program, measures for its prolongation
Yu. M. LAZARENKO, D. N. ARSHINTSEV, V. V. SEMERKHANOV, E. A. MITINA, E. V. KAPUSKINA Joint Stock Company “Railway Research Institute” (JSC “VNIIZhT”), Moscow, 129626, Russia RZhD-Partner, Spets. vypusk: Kontreylernye perevozki [Specialist. issue: Piggyback transportation], 2012, p. 31. RZhD-Partner, Spets. vypusk: Kontreylernye perevozki [Specialist. issue: Piggyback transportation], 2012, p. 31. Abstract. At the beginning of the XXI century in order to in-
crease the competitiveness of container transportation on the
railways of Russia, comprehensive studies were carried out on the
possibility of transporting large-capacity containers loaded in two
decks. In contrast to the world experience in the development of
this method of transportation, where they are carried out on lines
with diesel traction, the possibility of transporting containers loaded
in two decks on electrified domestic mainlines is determined by the
presence of an overhead wire, which creates an additional restric-
tion for increasing the height of the freight. 3. Bogdanov V. M. Ispol'zovanie gabaritnykh vozmozhnostey
seti dlya povysheniya provoznoy sposobnosti [Using the overall
capacity of the network to increase the carrying capacity]. Uveli-
chenie gabaritov i povyshenie pogonnykh nagruzok gruzovykh
vagonov. Sb. nauch. tr. VNIIZhT [Increasing the dimensions and
increasing the running loads of freight cars. Proc. of articles of
scientific works of the VNIIZhT]. Moscow, Transport Publ., 1983,
no. 660, pp. 4 – 17. 4. Lazarenko Yu. M. Lesnym gruzam — uvelichennyy gaba
rit pogruzki [Increased loading gauge for the forest freights]. Zheleznodorozhnyy transport, 1980, no. 5, pp. 20 – 23. 4. Lazarenko Yu. M. Lesnym gruzam — uvelichennyy gaba
rit pogruzki [Increased loading gauge for the forest freights]. Zheleznodorozhnyy transport, 1980, no. 5, pp. 20 – 23. The article discusses the results of many years of comprehen-
sive research on the creation of a specialized well platform and
the development of a technology for transporting large-capacity
containers in it with loading in two decks, carried out by the
VNIIZhT in the early 2000s. The article provides the features of
the structure of the well platform, the layout of containers in it,
the types of tests carried out and data on the experimental trans-
portation of the platform loaded with containers in two decks. Information on the suspension of work on the introduction of
double-deck container transportation is provided and measures
are proposed that must be performed in case of resumption of
work on the introduction of this method of transportation on the
Russian railways network. yy
p
pp
5. Lazarenko Yu. M., Bogdanov V. M. E-mail: lazarenko_um@list.ru (Yu. M. Lazarenko) For citation: Lazarenko Yu. M., Arshintsev D. N., Semerkhanov V. V., Mitina E. A., Kapuskina E. V. On the double-deck
transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation // VNIIZhT
Scientific Journal. 2020. 79 (4): 224 – 229 (In Russ.). DOI: https://doi.org/10.21780/2223-9731-2020-79-4-224-229. 229
© Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 |
https://openalex.org/W4361924147 | https://figshare.com/articles/journal_contribution/Figure_S7_from_Inhibition_of_HER2_Increases_JAGGED1-dependent_Breast_Cancer_Stem_Cells_Role_for_Membrane_JAGGED1/22464423/1/files/39915747.pdf | English | null | Figure S3 from Inhibition of HER2 Increases JAGGED1-dependent Breast Cancer Stem Cells: Role for Membrane JAGGED1 | null | 2,023 | cc-by | 774 | CD24 - PE
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ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1
sion by flow cytometry. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468
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ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1
ssion by flow cytometry. CD24 - PE
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ementary Figure 7. Expression of CD44 and CD24 in response to lapatinib. A. HCC1954 cells were treated with DMSO (Vehicle) or 2M lapatinib
ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1
sion by flow cytometry. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468
were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468
erved as negative controls for CD44 high and CD24 low expressing cells.
C. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468
were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468
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https://openalex.org/W2606506418 | https://europepmc.org/articles/pmc5390353?pdf=render | English | null | Telomere shortening and accelerated aging in COPD: findings from the BODE cohort | Respiratory research | 2,017 | cc-by | 6,960 | Abstract Background: Chronic Obstructive Pulmonary Disease (COPD) may be associated with accelerated aging. Telomere
shortening is a biomarker of aging. Cross-sectional studies describe shorter telomeres in COPD compared with
matched controls. No studies have described telomere length trajectory and its relationship with COPD progression. We investigated telomere shortening over time and its relationship to clinical and lung function parameters in a
COPD cohort and smoker controls without COPD. Methods: At baseline leukocyte telomere length was measured by qPCR in 121 smokers with COPD and 121 without
COPD matched by age (T/S0). The measurements were repeated in 70 of those patients with COPD and 73 non-COPD
smokers after 3 years of follow up (T/S3). Results: At initial measurement, telomeres were shorter in COPD patients when compared to smoker controls (T/S = 0. 68 ± 0.25 vs. 0.88 ± 0.52, p = 0.003) independent from age and sex. During the follow-up period, we observed an
accelerated telomere shortening in individuals with COPD in contrast to smoker controls (T/S0 = 0.66 ± 0.21 vs. T/S3 = 0.46 ± 0.16, p < 0.001, for the patients with COPD and T/S0 = 0.83 ± 0.56 vs. T/S3 = 0.74 ± 0.52, p = 0.023
for controls; GLIM, p = 0.001). This shortening was inversely related to the baseline telomere length (r = −0.49,
p < 0.001). No significant relationship was found between the rate of change in telomere length and change in lung
function in the patients with COPD (p > 0.05). Conclusions: Compared with smokers, patients with COPD have accelerated telomere shortening and this rate of attrition
depends on baseline telomere length. Furthermore, the telomere length and its rate of shortening did not relate to clinical
and lung function parameters changes over 3 years of follow-up. Keywords: COPD, Telomeres, Aging It has been suggested that COPD is a disease of accel-
erated aging [4, 5] and telomere length has been pro-
posed as a biomarker of aging [6, 7]. Telomeres consist
of stretches of repetitive hexanucleotides (5´-TTAGGG-3´)
that protect the end of chromosomes from being recog-
nized as double-strand breaks and avoid truncation. Because the DNA cannot be duplicated at the end of the
chromosome, each duplication results in its shortening. Thus, telomeres get progressively shorter as cells divide, an
event that is known as the end-replication process. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Other
mechanisms may also account for the accelerated loss of
telomeres, such as the DNA damage induced by oxidative
stress [8]. Telomere shortening and accelerated aging
in COPD: findings from the BODE cohort Córdoba-Lanús Elizabeth1*
, Cazorla-Rivero Sara1, Espinoza-Jiménez Adriana1, Juan P. de-Torre
Pajares María-José4, Aguirre-Jaime Armando1, Celli Bartolomé5 and Casanova Ciro1,2 * Correspondence: elizabeth-cordoba@hotmail.com
1Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. del
Rosario 145, 38010 Santa Cruz de Tenerife, Spain
Full list of author information is available at the end of the article Elizabeth et al. Respiratory Research (2017) 18:59
DOI 10.1186/s12931-017-0547-4 Elizabeth et al. Respiratory Research (2017) 18:59
DOI 10.1186/s12931-017-0547-4 Open Access RESEARCH
Open Access
Telomere shortening and accelerated aging
in COPD: findings from the BODE cohort
Córdoba-Lanús Elizabeth1*
, Cazorla-Rivero Sara1, Espinoza-Jiménez Adriana1, Juan P. de-Torres3,
Pajares María-José4, Aguirre-Jaime Armando1, Celli Bartolomé5 and Casanova Ciro1,2 Telomere length measurement Venous blood was obtained at baseline and at the third-
year post enrollment. DNA was extracted from leuko-
cytes using the QIAamp DNA Mini Kit (GE Healthcare). Telomere length was measured using a qPCR based
protocol previously published [21, 22]. Briefly, DNA
samples were quantified using the Nanodrop lite spec-
trophotometer
(Thermo Scientific,
Wilmington,
DE,
USA). Telomere length measurement was performed in
triplicate using 20 ng of DNA. Intra-plate coefficients of
variance (CV) were calculated between the replicates
and samples with CV > 5% were excluded from further
analysis. As a reference DNA sample with shorter telo-
meres we used the DNA from MCF-7 cells. For longer
telomeres, we assayed a DNA from a young control indi-
vidual. These calibrator samples were assayed in tripli-
cate on each PCR plate to control for variation between
plates. Inter-assay variability was controlled by measur-
ing two control DNA samples per run as a normalizing
factor. Inter-plate CV for the calibrator sample was cal-
culated to be <9%. Standard curves were derived from
serially diluted reference DNA. Albumin, being a single
copy gene, was used as a reference gene. The primer
sequences and cycling conditions for the measurement
of telomere length were the same used by others [22]. qPCR reactions were performed in 20 μL reactions for
each individual: 10 μL SYBRGreen PCR Master Mix
(BioRad), 0.9 μM of Telg and Telc and 0.6 μM of Albu
and Albd. All the reactions were performed on tripli-
cates of the telomere and reference gene assays on the
iQ Cycler Real-Time PCR Instrument (BioRad). The aim of the present study was to investigate if telo-
mere shortening occurs over time in patients with
COPD and if this shortening is related to clinical and
lung function parameters. Background Chronic obstructive pulmonary disease (COPD), a major
cause of morbidity and mortality throughout the world,
is thought to result from the interaction of environmen-
tal agents such as tobacco smoking or exposure to
biomass fuel and inherited genetic factors [1]. COPD is
a multidimensional disease that frequently coexists with
other age-related co-morbidities such as osteoporosis,
cardiovascular disease, lung cancer, depression and dia-
betes [2, 3]. There is no uniform acceptance of the interaction be-
tween telomere length and COPD. However, some studies Page 2 of 8 Elizabeth et al. Respiratory Research (2017) 18:59 have shown that patients with COPD exhibit shorter telo-
meres in circulating leukocytes compared to age matched
smokers without COPD [9, 10]. Some authors have pro-
posed that telomere shortening might be accelerated in
patients with COPD and serve as a biomarker of disease
progression [11], a theory that has some clinical support
because the telomere length in peripheral leukocytes of
patients with COPD has been related to important health
outcomes such as all-cause and cancer mortality [12]. comparison (Fig. 1). From these subjects, 70 patients
with COPD age-matched with 73 control smokers
returned for all follow-up evaluations over 3-years
and were analyzed in the longitudinal study. The indi-
viduals included in the final analysis did not have any
relevant clinical difference with the ones that did not
complete the 3-year study (see Additional files 1 and 2). The study was approved by the institutional review board
at both hospitals. All participants provided written in-
formed consent. The unanswered question fueling the debate about the
meaning of telomere shortening in patients with COPD
is that all of the studies performed have been cross-
sectional in design, not informing whether there are
changes in length over time and whether there is any re-
lationship between those changes and outcomes. That
this is possible in COPD is highlighted by a recent study
that analyzed leukocyte telomere trajectory in a cohort
of individuals with coronary artery disease and found
that this is powerfully influenced by baseline telomere
length in a pattern suggestive of negative feedback regu-
lation [13]. Baseline findings The clinical characteristics and lung function data of
the 121 COPD patients and 121 controls at baseline,
are summarized in Table 1. The range of airflow ob-
struction distributed by GOLD stages in COPD was
as follows: 1 (19.8%), 2 (43%), 3 (28.9%) and 4 (8.3%). As expected, patients with COPD had worse lung
function and a higher BODE index than controls. However, the two groups were similar in age, sex,
BMI and Charlson co-morbidity score. Although the
total pack years smoking was higher in COPD pa-
tients, there were more current smokers in the con-
trol group. Telomere length measured by the T/S
ratio inversely correlated with age in COPD (r =
−0.21; p = 0.02) and in smoker controls (r = −0.19; p =
0.02). Given this relationship, all subsequent analyses
were adjusted by age. For
the
longitudinal
analysis,
telomere
length
changes were calculated as the difference between
baseline (T/S0) and the third year (T/S3) of the telo-
mere length measure. Individuals analyzed for follow-
up were categorized as follows: subjects showing a
steeper rate of telomere shortening in contrast to
subjects with a lower telomere shortening rate, main-
tenance or lengthen of their telomeres (defined by the
median telomere length change). g
g
A t-Student, ANOVA, Chi2 and Paired Sample T
test were used to test differences in means and pro-
portions
of
baseline
and
follow-up
characteristics
between
groups. The
association
between
baseline
telomere length (T/S) or telomere length change with
clinical and/or pulmonary function variables was ex-
plored using Pearson’s correlation coefficients. A mul-
tiple logistic regression was performed to test the
association of telomere length with COPD susceptibil-
ity adjusting for age, sex and pack years. By using a
general linear modelling for repeated measures (GLIM)
we tested the telomere dynamics difference between
patients with COPD and smokers without COPD, or
within these groups between current and former
smokers. We also conducted a longitudinal analysis
to evaluate the progression of the disease of clinical
and pulmonary function variables using change in
telomere length as comparative factor (GLIM). SPSS
20.0 IBM Co software was used for all statistical
analyses and two-tailed p-values < 0.05 were consid-
ered significant. COPD patients had significant shorter telomeres
than smokers without COPD (T/S = 0.68 ± 0.25 vs. Methods
Subjects j
A total of 422 subjects were screened for this study at
the Hospital Universitario La Candelaria, Tenerife and
the Clinica Universitaria de Navarra, Pamplona, Spain. From these, the control group of 165 smokers without
COPD had a smoking history of > 15 pack-years and
normal lung function (FEV1 > 80%; FEV1/FVC ≥0.70). There were 257 smokers with COPD followed annually
as part of the BODE study [14]. Inclusion criteria: age >
40 years, smoking history >15 pack-years and post-
bronchodilator FEV1/FVC ratio < 0.70 measured 20 min
after administration of 400 mg of albuterol. Pulmonary
function test, spirometry lung volumes and exercise cap-
acity were measured according to ATS-ERS guidelines
[15–17] using the European Community for Steel and
Coal as reference values [18]. Dyspnea was evaluated by
mMRC scale [19]. The BODE Index was calculated as
previously described [14]. Co-morbidity was quantified
using the Charlson index [20]. Patients were clinically
stable (no exacerbation for at least 6 weeks) at the time
of evaluation. Repeated determinations of the complete
blood count revealed similar values at all visits. Exclu-
sion criteria: uncontrolled co-morbidities such as malig-
nancy at baseline, asthma or other pulmonary conditions
than COPD. From the screened group, 121 patients with
COPD were matched with 121 smokers without COPD
and were included in the present study for baseline Telomere length was calculated as a ratio of telomere
to albumin as previously described [22]. The T/S ratio
for an experimental DNA sample is T, the number of
nanograms of the Standard DNA that matches the ex-
perimental sample for copy number of the telomere
template, divided by S, the number of nanograms of the
standard DNA that matches the experimental sample for
copy number of the albumin single copy gene. The telo-
mere length standardized to the reference single copy
gene (T/S) was calculated using the “ΔΔCp with effi-
ciency correction” calculation method [23]. Elizabeth et al. Respiratory Research (2017) 18:59 Page 3 of 8 Fig. 1 Consort diagram illustrating the selection and assessment of patients and control smokers included in the study Fig. 1 Consort diagram illustrating the selection and assessment of patients and control smokers included in the study Results For the cross-sectional analysis, patients with COPD
were categorized in three groups by telomere length
ratio (T/S) tertiles at baseline: shorter, medium or
longer telomeres. Baseline findings 0.88 ± 0.52, p < 0.0001) even after adjusting for age,
sex and pack-years (95% CI: 0.11–0.64, p = 0.003),
(Table 1 and Fig. 2). There were no significant differ-
ences between males (0.68 ± 0.28) and females (0.66 ±
0.20) within the COPD group or in the smokers
(0.82 ± 0.53
vs. 0.96 ± 0.49
for
males
and
females,
respectively). There was no relationship between telomere length
and the clinical and lung function parameters (Table 2)
or between patients with less and more severe COPD
(GOLD 1–2 vs. GOLD 3–4 or BODE ≤2 vs. BODE > 2)
(p > 0.05). In addition, no significant associations were
found between comorbidities such as cardiovascular
events, diabetes, hypertension or cancer and relative
telomere length in patients with COPD. Elizabeth et al. Respiratory Research (2017) 18:59 Page 4 of 8 Page 4 of 8 Table 1 Baseline characteristics of COPD patients and smokers
without COPD included in the study
Variable
COPD cases
(N = 121)
Smokers
(N = 121)
p-value
Sex (male%)
66
62
N.S. Age (years)a
57 ± 8
57 ± 8
N.S. BMI (Kg/m2)a
27 ± 5
28 ± 4
N.S. Smoking habitc
(pack-yrs)ac
60 ± 25
44 ± 22
<0.0001
Active smoking (%)
50
64
0.027
T/S ratioa
0.68 ± 0.25
0.88 ± 0.52
<0.0001
FEV1 (L)a
1.66 ± 0.7
2.9 ± 0.7
<0.0001
FEV1 (% pred)a
59 ± 21
101 ± 14
<0.0001
FVC (% pred)a
89 ± 22
108 ± 15
<0.0001
FEV1 / FVC (%)a
53 ± 12
76 ± 5
<0.0001
PaO2 (mmHg)a
72.3 ± 14.3
78.7 ± 10
<0.001
KCO (%)
79.6 ± 25.1
97.3 ± 21.3
0.001
IC/TLC (%)
36 ± 9
45 ± 8
<0.001
6MWD (m)a
523 ± 89
551 ± 76
0.03
mMRC dyspneab
1 (0–2)
0 (0–0)
0.006
BODE indexb
1 (0–3)
0 (0–1)
<0.001
Charlson indexb
0 (0–1)
0 (0–0)
N.S. Data are presented as amean ± SD and bmedian (25th-75thpc) and compared
by Student’s t-test or Chi2 test. cNumber of packs of cigarettes smoked per day
x number of years smoking. Percentage BMI body mass index, T/S ratio relative
telomere length, FEV1 forced expiratory volume in one second, FVC forced vital
capacity, % pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion
capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio,
6MWD six-min walk distance test. Baseline findings N.S non-significant Table 1 Baseline characteristics of COPD patients and smokers
without COPD included in the study Telomere length dynamics This difference in telomere length remained significant
after 3 years between the 70 patients with COPD age
matched with 73 smoker controls that presented the
follow-up (T/S3 = 0.46 ± 0.16 vs. 0.74 ± 0.52, p < 0.001);
even after adjusting for age, sex and smoking habit in a
logistic regression analysis (95% CI: 0.12–0.90), p = 0.03). The telomere length ratio in the control group of
smokers without COPD, decreased significantly (T/S0 =
0.83 ± 0.56 vs. T/S3 = 0.74 ± 0.52, p = 0.002) after the
follow-up period. The same occurred in the group of pa-
tients with COPD (T/S0 = 0.66 ± 0.21 vs. T/S3 = 0.46 ±
0.16, p < 0.001). However, when we compared the telo-
mere trajectory between these groups over the follow-up
period, we observed an accelerated telomere shortening
in individuals with COPD in contrast to the control
group (GLIM, general lineal model for repetitive mea-
sures, p = 0.001) (Fig. 3). Relation of telomere length change and clinical variables
We found a strong relationship between baseline telo-
mere length and change in telomere length (r = −0.49,
p < 0.001; adjusted by age) (Fig. 4). Compared with COPD patients that did not change,
lengthened or had a low rate of telomere shortening,
those patients with a more rapid shortening of their telo-
meres had similar lung function characteristics (Table 3). By using correlation matrices, we were not able to find
any significant relationship between the rate of change
in telomere length and change in lung function in the
patients with COPD (see Additional file 3). This lack of
association was seen whether we compared current vs. former smokers, number of comorbidities or mortality
(Chi2, p > 0.05). Compared with COPD patients that did not change,
lengthened or had a low rate of telomere shortening,
those patients with a more rapid shortening of their telo-
meres had similar lung function characteristics (Table 3). Data are presented as amean ± SD and bmedian (25th-75thpc) and compared
by Student’s t-test or Chi2 test. cNumber of packs of cigarettes smoked per day
x number of years smoking. Percentage BMI body mass index, T/S ratio relative
telomere length, FEV1 forced expiratory volume in one second, FVC forced vital
capacity, % pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion
capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio,
6MWD six-min walk distance test. Telomere length dynamics N.S non-significant By using correlation matrices, we were not able to find
any significant relationship between the rate of change
in telomere length and change in lung function in the
patients with COPD (see Additional file 3). This lack of
association was seen whether we compared current vs. former smokers, number of comorbidities or mortality
(Chi2, p > 0.05). Fig. 2 Average telomere length and SE relative telomere length (T/S) in COPD patients (n = 121) vs. age-matched smokers without COPD (n = 121) Elizabeth et al. Respiratory Research (2017) 18:59 Page 5 of 8 Page 5 of 8 Table 2 Pulmonary function characteristics of the three groups
of patients with COPD defined by their baseline telomere length
Variable
Short T/Sa
(n = 40)
Medium T/Sa
(n = 41)
Long T/Sa
(n = 40)
p-value
T/S ratiob
0.44 ± 0.09
0.66 ± 0.07
1.09 ± 0.21
<0.001
Sex (male%)
65
66
67
N.S. Age (years)b
59 ± 7
58 ± 8
55 ± 9
N.S. BMI (Kg/m2)b
28 ± 6
27 ± 5
27 ± 5
N.S. Smoking habitd
(pack-yrs)bd
62 ± 28
63 ± 24
57 ± 23
N.S. Active smoking (%)
42
56
52
N.S. FEV1 (L)b
1.70 ± 0.71
1.64 ± 0.67
1.66 ± 0.74
N.S. FEV1 (% pred)b
61 ± 23
59 ± 21
58 ± 21
N.S. FVC (% pred)b
89 ± 24
92 ± 22
87 ± 21
N.S. FEV1 / FVC (%)b
55 ± 12
51 ± 13
53 ± 12
N.S. PaO2 (mmHg)b
71.1 ± 15.7
71.9 ± 15.8
73.5 ± 11.5
N.S. Kco (%)
74.1 ± 25.6
75.5 ± 24.1
75.2 ± 21.1
N.S. IC/TLC (%)
37 ± 6
36 ± 8
35 ± 10
N.S. 6MWD (m)b
517 ± 77
537 ± 95
513 ± 92
N.S. mMRC dyspneac
1 (0–2)
1 (0–2)
1 (0–2)
N.S. BODE indexc
1 (0–2)
1 (0–3)
1 (0–3)
N.S. Charlson indexc
0 (0–1)
0 (0–1)
0 (0–1)
N.S. aGroups defined by telomere length (T/S) tertiles: <0.54, 0.54–0.73 and >0.73. Data are presented as bmean ± SD and cmedian (25th-75thpc) and compared
by ANOVA test or Chi2 test. dNumber of packs of cigarettes smoked per day x
number of years smoking. BMI body mass index, T/S ratio relative telomere
length, FEV1 forced expiratory volume in one second, FVC forced vital capacity,
% pred per cent predicted. Telomere length and change over time Telomere length and change over time
In our study, at baseline, telomere length was shorter
with older age, both in the COPD patients and the
smokers without COPD. However, COPD patients pre-
sented shorter telomeres than the control group inde-
pendent of age and sex. Other studies evaluating the
relation between telomere length and COPD have shown
discordant results. Morla et al. [24] failed to find a differ-
ence in telomere length between COPD patients and
smokers, whereas some other studies have reported
shorter telomeres in subjects with COPD compared to
smokers and healthy individuals [8, 10]. These discord-
ant results may have been due to differences in sample
size in the studies or by technical bias or defects in study
design, some of which lacked of appropriate controls. We found no relationship between telomere length and
clinical or lung function parameters in our COPD co-
hort in the cross-sectional analysis. This is in agreement
with the results of Savale et al. [9] who described a bor-
derline correlation between PaO2 and PaCO2 and telo-
mere
length
but
strangely
not
to
lung
function
parameters. However, Rode et al. [25] in a study of more
than 45.000 individuals in a Danish population reported
a modest correlation between telomere length and the
lung function expressed by the FEV1. More recently,
Rutten et al. studying several markers of aging in pa-
tients with COPD, found telomere length to be the only
one associated with lung function [26]. All these studies aGroups defined by telomere length (T/S) tertiles: <0.54, 0.54–0.73 and >0.73. Data are presented as bmean ± SD and cmedian (25th-75thpc) and compared
by ANOVA test or Chi2 test. dNumber of packs of cigarettes smoked per day x
number of years smoking. BMI body mass index, T/S ratio relative telomere
length, FEV1 forced expiratory volume in one second, FVC forced vital capacity,
% pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion capacity
of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min
walk distance test. N.S non-significant Telomere length dynamics PaO2 partial oxygen tension, KCO diffusion capacity
of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min
walk distance test. N.S non-significant Table 2 Pulmonary function characteristics of the three groups
of patients with COPD defined by their baseline telomere length with COPD have shorter telomeres than smokers who
do not have COPD. However, there were no associations
between telomere length and clinical and lung function
parameters at baseline or between changes in telomere
length and change in those parameters overtime. To our
knowledge, this is the first study reporting the course of
telomere length change in a well-characterized cohort of
patients with COPD and smoker controls. Telomere length and clinical variables were cross-sectional in design and in consequence not
adequate to evaluate the possible relationship between
telomere length and COPD progression. In addition, the
only lung function parameter evaluated was FEV1 and
patients with comorbidities were excluded. Previous cross-sectional studies have concentrated pri-
marily on the relationship between telomere length and
the FEV1. We expanded on those studies relating not
only FEV1, but also lung hyperinflation (IC/TLC), diffu-
sion capacity (KCO) and gas exchange to telomere length. Disappointingly, we were unable to document any asso-
ciation between telomere length in COPD patients with
any clinical or functional expression of the disease or
presence of any comorbidities at baseline. This is in gen-
eral agreement with most of the published studies that
have reported poor associations, if any, between the ac-
tual telomere length and the FEV1. Of interest, the stud-
ies that have described an association between telomere
shortening and lower FEV1 have included larger sample
size, thus facilitating a statistical significance to those The current report is the first one to document that
COPD patients have an accelerated rate of telomere
shortening in contrast to smoker controls, and this dif-
ference was more marked in those individuals with lon-
ger baseline telomeres. In our study, 85% of the COPD
patients showed telomere length shortening after 3 years
of follow-up, a proportion that is similar to that ob-
served in general population studies [27–29], however,
the rate of decline is significantly lower in those normal
individuals. It is important to compare our findings with
that of other populations including different pathologies. Discussion This longitudinal study shows that COPD patients
experience an accelerated telomere shortening process
compared
with
smokers
without
COPD
and
this
telomere attrition occurs in close relation to baseline
telomere length. The study also confirms that patients Fig. 3 Telomere length (relative T/S ratio) dynamics in COPD patients (n = 70) vs. age-matched smokers without COPD (n = 73) after 3 years’ follow-up
(p = 0.001, using GLIM - general lineal model for repetitive measures; T/S differences between groups p(T/Sxgroups)=0.002) Elizabeth et al. Respiratory Research (2017) 18:59 Page 6 of 8 Page 6 of 8 Fig. 4 Correlation between baseline telomere length and the rate of
change in telomere shortening in COPD patients after 3 years’ follow-up
(r = −0.49, p = 0.001, adjusted by age) Fazarneh et al. [13] analyzed leukocyte telomere trajec-
tory over 5 years in a cohort of individuals with coronary
artery disease and found, as we have, that telomere
shortening rate is powerfully influenced by baseline telo-
mere length. Our results support a pattern suggestive of
negative feedback regulation in the telomere shortening
dynamics, as has been proposed by others [29]. It may
be that once a critical telomere length has been reached,
activation of certain mechanisms in the cells occur to
prevent telomere shortening over years accounting for
less attrition per replication or maintenance of viable
telomere lengths in subjects with shorter telomeres. The exact reason why telomeres shorten faster in pa-
tients with COPD was beyond the scope of this study. However, oxidative stress and inflammation are the most
important factors thought to be responsible for the loss
of telomeric DNA [8], which in turn may favor the de-
velopment of structural tissue damage [30]. Studies on
mouse models of accelerated aging and lung dysfunc-
tion, suggested that this process might enhance suscepti-
bility to COPD [5]. Fig. 4 Correlation between baseline telomere length and the rate of
change in telomere shortening in COPD patients after 3 years’ follow-up
(r = −0.49, p = 0.001, adjusted by age) Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per
cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in
each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Additional files Additional file 1: Baseline characteristics of COPD patients with and without
three-year follow-up included in the study. (DOCX 14 kb)
Additional file 2: Baseline characteristics of smokers without COPD with
and without three-year follow-up included in the study. (DOCX 75 kb)
Additional file 3: Correlations between the rate of change in telomere
length and the change in pulmonary function variables in patients with
COPD after three years of follow-up. (DOCX 68 kb) Additional file 1: Baseline characteristics of COPD patients with and without
three-year follow-up included in the study. (DOCX 14 kb)
Additional file 2: Baseline characteristics of smokers without COPD with
and without three-year follow-up included in the study. (DOCX 75 kb)
Additional file 3: Correlations between the rate of change in telomere
length and the change in pulmonary function variables in patients with
COPD after three years of follow-up. (DOCX 68 kb) Additional file 1: Baseline characteristics of COPD patients with and without
three-year follow-up included in the study. (DOCX 14 kb) Additional file 1: Baseline characteristics of COPD patients with and without
three-year follow-up included in the study. (DOCX 14 kb) Additional file 2: Baseline characteristics of smokers without COPD with
and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 2: Baseline characteristics of smokers without COPD with
and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 3: Correlations between the rate of change in telomere
length and the change in pulmonary function variables in patients with
COPD after three years of follow-up. (DOCX 68 kb) This study has several limitations. Telomere length
was measured on circulating leukocytes and therefore
our findings may not reflect the process occurring in the
whole lung. Interestingly, telomere length in blood cor-
relates well with telomere length in lung tissue of COPD
[31] and rates of telomere shortening are similar in dif-
ferent tissues [32]. We used qPCR relative telomere
length measures rather than absolute ones which may
result in a loss of precision, however qPCR results were
reported to be strongly correlated those obtained with
southern blot technique [22]. Leukocyte telomere length
is also considered a marker of oxidative stress and in-
flammation, and both contribute to COPD development. Telomere length is determined by environmental as well
as genetic factors. There is a large inter-individual vari-
ability in telomere length in humans of the same age
that makes difficult any cross-sectional comparisons. Conclusions In summary, in this longitudinal observational study we
found that compared with smoker controls, an acceler-
ated telomere shortening occurs in patients with COPD,
even if they had shorter telomeres at baseline. Interest-
ingly, the speed of shortening relates inversely to base-
line telomere length. However, the telomere length and
its rate of shortening did not relate to clinical and lung
function parameters and their change over time, making
telomere length change an unlikely useful biomarker of
COPD progression. Because the value of a biomarker resides primarily in
its capacity to reflect association to prognosis or to
change in disease progression, we followed patients and
controls over 3 years. We observed no correlation be-
tween the rate of shortening of telomeres and the
change in lung function, or for that matter with any
other clinical variable, rendering those findings difficult
to interpret of to apply clinically. Perhaps, a longer
period of observation or a larger sample may be neces-
sary to evaluate these clinical and physiological variables
or other patient related outcomes such as exacerbations,
cardiovascular events and all-cause mortality. On the
other hand, these findings suggest that the rate of telo-
mere shortening may not be a viable surrogate marker
of disease progression of major clinical utility. Funding
Th
d The study was supported by the Instituto de Salud Carlos III (PI 12/00355);
European Regional Development Funds, ERDF, and Spanish Respiratory Society,
SEPAR (PI 13/007). Acknowledgments We will like to thank Angela Montejo-de-Garcini, Hilaria González Acosta and
Delia Mayato for their excellent technical assistance. We are also thankful to
Antonio Gonzalez Biorganic Institute (Tenerife, Spain) for their kindly donation
of the MCF-7 cells line. Telomere length and clinical variables Table 3 Pulmonary function variables over time and telomere length rate of change in COPD patients
Variable
High rate of shorteningb
(n = 35)
Low rate of shortening maintenance or lengtheningc
(n = 35)
Baseline
3-years
p-value
Baseline
3-years
p-value
FEV1 (L)
1.66 ± 0.72
1.59 ± 0.68
0.04
1.60 ± 0.5
1.52 ± 0.5
0.15
FEV1(%pred)
59 ± 20
58 ± 20
0.63
59 ± 19
58 ± 19
0.54
FVC (L)
3.01 ± 0.99
2.95 ± 0.98
0.35
3.15 ± 0.94
3.01 ± 0.97
0.12
FEV1/FVC
54 ± 10
53 ± 11
0.21
52 ± 12
52 ± 13
0.77
PaO2 (mmHg)
73.5 ± 7.9
70.9 ± 9.6
0.04
72.1 ± 12.9
68.8 ± 11.6
0.09
KCO (%)a
77.3 ± 23.7
74.9 ± 23.4
0.21
74.4 ± 19.1
70.6 ± 20.4
0.16
IC/TLC (%)
35 ± 9
31 ± 10
0.03
36 ± 8
32 ± 8
0.02
Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per
cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in
each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per
cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in
each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Elizabeth et al. Respiratory Research (2017) 18:59 Page 7 of 8 Page 7 of 8 findings. This is important when attempting to relate
statistical associations to practical the clinical application
of those findings. Availability of data and materials Any requests for data and material should be directed to the corresponding
author. Competing interests p
g
The authors declare that they have no competing interests. Additional files Our control smokers presented a shorter tobacco
exposure history than the cohort of patients with
COPD. However, analysis between current vs. former
smokers in both cohorts did not show significantly
differences. Another limitation is that the sample size
or duration of observation (3 years) may not have
been large or long enough to find significant associa-
tions between telomere shortening and lung function
parameters. In this context, we cannot discard that
our findings may be affected by regression towards
the mean. Further studies with a larger follow-up
period with many time points of measurements are
needed to validate these findings. However, for imple-
mentation of precision medicine, biomarkers need to
have clinical applicability in small numbers, if not in
individuals. Lastly,
we
did
not
investigate
other
markers of aging; however, other authors who have
done so, and have found telomere length to be the
most relevant of all [26]. Abbreviations 6MWD: 6-min walk distance; BMI: Body mass index; COPD: Chronic
obstructive pulmonary disease; FEV1: Forced expiratory volume in one
second; FVC: Forced vital capacity; GLIM: General linear modelling for
repeated measures test; GOLD: Global initiative for chronic obstructive lung
disease; IC/TLC: Inspiratory to total lung capacity ratio; KCO: Diffusion capacity
of carbon monoxide; N.S.: Non-significant; PaO2: Partial oxygen tension;
pPCR: Quantitative real time polymerase chain reaction; SD: Standard deviation;
T/S: Relative telomere length ratio; T/S0: Relative telomere length ratio at
baseline; T/S3: Relative telomere length ratio at the third year of follow-up Authors´ contributions E.C.L. and C.C. participated in conception and design; analysis and interpretation
and drafting the manuscript for important intellectual content. S.C.R., A.E.J. and
A.A.J. participated in analysis and interpretation. B.C. participated in the
interpretation of the results and helped draft the manuscript for important
intellectual content. All authors read and approved the final manuscript. Ethics approval and consent to participate Ethical approval was obtained from Hospital Universitario La Candelaria,
Tenerife and the Clinica Universitaria de Navarra, Pamplona, Spain. Written
informed consent was obtained from all participants. Page 8 of 8 Page 8 of 8 Page 8 of 8 Page 8 of 8 Elizabeth et al. Respiratory Research (2017) 18:59 Author details
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https://openalex.org/W3011499678 | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0229990&type=printable | English | null | Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3-methyl-5-pyrazolone derivatization | PloS one | 2,020 | cc-by | 6,348 | PLOS ONE PLOS ONE RESEARCH ARTICLE Development of a RP-HPLC method for
determination of glucose in Shewanella
oneidensis cultures utilizing 1-phenyl-3-
methyl-5-pyrazolone derivatization Norberto M. GonzalezID1*, Alanah Fitch1, John Al-Bazi2 1 Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of
America, 2 Department of Chemistry, Northeastern Illinois University, Chicago, IL, United States of America * ngonzalez7@luc.edu * ngonzalez7@luc.edu OPEN ACCESS Citation: Gonzalez NM, Fitch A, Al-Bazi J (2020)
Development of a RP-HPLC method for
determination of glucose in Shewanella oneidensis
cultures utilizing 1-phenyl-3-methyl-5-pyrazolone
derivatization. PLoS ONE 15(3): e0229990. https://
doi.org/10.1371/journal.pone.0229990 Editor: Tommaso Lomonaco, University of Pisa,
ITALY Received: November 12, 2019
Accepted: February 18, 2020
Published: March 12, 2020
Copyright: © 2020 Gonzalez et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Copyright: © 2020 Gonzalez et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Abstract A method was developed and validated for low-level detection of glucose. The method
involves quantitation of glucose though derivitization with 1-phenyl-3-methyl-5-pyrazolone
(PMP) and HPLC-DAD analysis. The developed method was found to be accurate and
robust achieving detection limits as low as 0.09 nM. The applicability of the method was
tested against microbial samples with glucose acting as a carbon fuel source. The method
was shown to be able to accurately discriminate and quantify PMP-glucose derivatives
within Shewanella oneidensis MR-1 samples. The method proved capable at examining glu-
cose usage during the early hours of microbial growth, with detectable usage occurring as
early as two hours. S. oneidensis cultures were found to grow more effectively in the pres-
ence of oxygen which coincided with more efficient glucose usage. Glucose usage further
increased in the presence of competing electron acceptors. The rate at which S. oneidensis
reached exponential growth was affected by the presence of ferric iron under microaerobic
conditions. Such samples reached exponential growth approximately two hours sooner than
aerobic samples. Introduction Microorganisms can utilize organic material to facilitate culture growth, which can include
simple organic carbons such as acetate, lactate, fumarate and, to a lesser extent, carbohydrates
such as glucose [1–3]. Understanding the relative use of these substances may be important in
a wide range of fields, one example of which is the use of a carbon source by bacteria for micro-
bial fuel cell development. Data Availability Statement: https://doi.org/ Data Availability Statement: https://doi.org/10. 6084/m9.figshare.10062095.v1; https://doi.org/10. 6084/m9.figshare.11741700.v1; https://doi.org/10. 6084/m9.figshare.11741703.v1. Most methods are individual to the carbon source and may involve a wide number of strat-
egies. In the case of glucose common methods include glucose assays [4], copper-iodometric
methods [5], mass spectrometry [6], and chromatographic methods to include gas chromatog-
raphy and high-performance liquid chromatography (HPLC) [7–9]. Glucose assays are among
the fastest and simplest forms of analysis. They suffer, however, from high cost with numerous Funding: The authors received no specific funding
for this work. Competing interests: The authors have declared
that no competing interests exist. 1 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures samples and are limited to one or only a few reducing sugars. Furthermore, a survey of glu-
coses assays available from leading manufacturers showed method sensitivities as low as 1 μM
limiting their use for biological detections [10–13]. HPLC methods allow for a decrease in cost when testing numerous samples and for quanti-
tation of various reducing sugars either individually or simultaneously. An increasing popular
LC method involves the use of derivatizing reducing sugars like glucose with 1-phenyl-
3-methyl-5-pyrazolone (PMP) (Fig 1). First proposed by Honda et al. [14] the method involves
directly reacting PMP with a reducing sugar under basic conditions to form a PMP-reducing
sugar derivative that can be used for observing multiple reducing sugars simultaneously in the
ultraviolet spectrum. While the method has been refined by various research groups [15–17]
to include unicellular algae [18], the usefulness of the method for analysis of bacterial cultures
has not been examined. Many current methods of PMP derivatization suffer from long reten-
tion times exceeding 25 minutes and inconsistent reaction times ranging from 30–120 min-
utes. Further, many methods suffer from a lack of full validation for LC methods set by such
governing agency as the International Council on Harmonisation of Technical Requirements
for Pharmaceuticals for Human Use (ICH) [19,20]. Proper method validation would improve
method robustness and repeatability. In this study, a modified PMP method was developed for examining glucose. The method
focuses on achieving decreased run times, improved method robustness through method vali-
dation, and achieving lower detection limits not previously seen in similar works. The applica-
bility of the method was tested using the microorganism Shewanella oneidensis MR-1 and
examines the rate of glucose consumption by the microbe over time. Data Availability Statement: https://doi.org/ Several publications
attempted to address the ability of Shewanella to utilize glucose utilizing different instrumental Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose
under basic conditions. Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose
under basic conditions. Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose
under basic conditions. n of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose https://doi.org/10.1371/journal.pone.0229990.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 2 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures determinations of glucose. Work conducted by Nakagawa et al. [21] utilized a genetically
altered Shewanella strain and enzymatic assays for glucose measurements. Howard et al. [22]
also utilized a mutated Shewanella strain, however, the group incorporated LC method with
refractive index (RI) detection for glucose detection. Likewise, Choi et al. [23] also incorpo-
rated the use of LC and RI detection of glucose used by a mutated Shewanella strain. Rosen-
baum et al. [24] used a wild type from of Shewanella and HPLC with pulsed amperometric
detection (PAD) for quantifying glucose in growth cultures. Although these works have dem-
onstrated that refractive index detectors can detect glucose in growth media, RI detectors suf-
fer from limited sensitivity and gradient incompatibilities that reduces their ability to achieve
low detection limits. S. oneidensis was chosen as the model for three reasons. Firstly, the organism, in general, is
of intense interest due to its utilization in microbial fuel cells [25–29]. S. oneidensis is a faculta-
tive anaerobe used in microbial fuel cells (MFC), and has been shown to be well adapted at
using small carbon compounds as a fuel source [30,31]. The microbe has shown difficulty uti-
lizing larger carbon compounds like glucose primarily due to a lack of key enzymes required
for glycolysis [22,32–36]. However, some research has suggested Shewanella can utilize glucose
when the microbe is allowed to condition in a glucose containing solution, or when the
microbe has adapted it metabolism to an oxygenated environment prior to growth [37]. Instrumentation The method development and validation experiments were performed using an Agilent Tech-
nologies 1100 Series HPLC system equipped with a quaternary pump, auto sampler, and a
diode array detector. The chromatographic data were obtained using Agilent Technologies
ChemStation for LC Rev.A10.02[1757] software. The column used was a YMC-Pack ODS-AQ
with a column length of 150 mm, an inside diameter of 4.6 mm and a particle size of 3 microns. Standards and reagents The mobile phase organic solvent acetonitrile was purchased from Fisher Chemical and was of
HPLC grade. Potassium phosphate dibasic was purchased from Sigma-Aldrich and was of
ACS grade. The glucose standard was purchased from Fisher Chemical and was of ACS grade. The derivatizing reagent 1-phenyl-3-methyl-5-pyrazolone (PMP) was purchased from Sigma-
Aldrich and was of ACS grade. The tryptic soy broth (TSB) growth medium was purchased
from Sigma-Aldrich and was of microbiology grade. Iron oxide and iron chloride were pur-
chased from Fisher Chemical and were of reagent grade. The Shewanella oneidensis MR-1
microbe were purchased from ATCC as a frozen culture. Data Availability Statement: https://doi.org/ Sec-
ondly, the use of PMP derivatization and HPLC analysis has not been previously seen for
tracking carbohydrate utilization by S. oneidensis. Finally, current literature has focused on the
utilization of glucose over an extended growth window. Few publications have focused on
examining the use of glucose during early (0–15 hours) microbial growth and at which point
glucose utilization begins. Preparation of standard solutions and samples Stock solutions. Solutions of PMP were prepared by dissolving 87 mg of PMP in 1 mL of
methanol to yield a 0.5 M stock solution of PMP-methanol. Glucose stock solutions were pre-
pared by dissolving 0.125 g of glucose in 50 mL of deionized water to yield a 0.0139 M stock
solution of glucose. The appropriate aliquot of 0.0139 M glucose stock was used for all other PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 3 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures stock solution preparations. Solutions of TSB were prepared by dissolving 30 g of TSB in 1 L of
deionized water. All TSB solutions were autoclaved after preparation. For TSB containing fer-
ric iron, both soluble and insoluble iron was first dissolved in the TSB prior to incubation. Standard solutions. Standards of PMP-glucose were prepared by combining 800 μL of a
0.0139 M solution of glucose with 800 μL each of 0.5 M NaOH and 0.5 M solution of PMP in
methanol to yield a solution at a pH of 13. The reaction was carried out at 70˚C with agitation
every 30 minutes. After derivatization, the solution was neutralized at 4˚C with 800 μL 0.5 M
HCl. Reaction impurities were extracted using 2 mL of dichloromethane. The solution was
mixed vigorously for 30 seconds and centrifuged at 4˚C and 5000 rpm for 5 mins. The dichlor-
omethane extraction was repeated twice more for a total of 3 extractions. The upper aqueous
layer containing the PMP-glucose was removed for analysis. Sample solutions. The TSB was prepared by autoclaving 80 mL of the growth media. Media designated as microaerobic was purged with nitrogen gas as the media cooled to room
temperature. Media designed as aerobic was saturated with oxygen gas for 10 minutes. The
samples were prepared by adding 1 mL of a S. Oneidensis MR-1 containing solution to the 80
mL of autoclaved TSB. The microaerobic flasks were sealed with a septa cap to prevent addi-
tional oxygen exposure while aerobic flasks were covered with foil. Samples were placed in an
incubator set at a temperature of 30˚C and a shake speed of 150 rmp. The samples were set to
grow for 15 hours with sampling occurring throughout the growth period. S. oneidensis samples. The analysis of glucose occurred utilizing a single growth culture. Preparation of standard solutions and samples Samples extracted from a single culture over a 15-hour incubation period exhibited greater
reproducibility when compared to sampling a new culture for every hour of analysis. Addi-
tionally, utilizing a single growth culture allowed for samples to be collected every 15–30 min-
utes when samples exhibited exponential growth. All results were replicated with a second
growth culture. Microbial growth was normalized, and the glucose utilization was averaged. Samples extracted from a single culture over a 15-hour incubation period exhibited greater
reproducibility when compared to sampling a new culture for every hour of analysis. Addi-
tionally, utilizing a single growth culture allowed for samples to be collected every 15–30 min-
utes when samples exhibited exponential growth. All results were replicated with a second
growth culture. Microbial growth was normalized, and the glucose utilization was averaged. Microbial samples were inoculated in 80 mL of TSB and allowed to incubate under microaero-
bic and aerobic conditions for 15 hours at 30˚C. At various intervals over the growth period, the
growth of the microbe was determined by examining its turbidity at 650 nm, and 1 mL of growth
media was collected for analysis by HPLC. Growth media samples were derivatized and examined
by HPLC in the same manner as the method development and validation samples. Preparation
steps included centrifugation of the samples and extraction of the sample supernatant. Microbial samples were inoculated in 80 mL of TSB and allowed to incubate under microaero-
bic and aerobic conditions for 15 hours at 30˚C. At various intervals over the growth period, the
growth of the microbe was determined by examining its turbidity at 650 nm, and 1 mL of growth
media was collected for analysis by HPLC. Growth media samples were derivatized and examined
by HPLC in the same manner as the method development and validation samples. Preparation
steps included centrifugation of the samples and extraction of the sample supernatant. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 Optimization of chromatographic parameters Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains
that the reaction has reached completion. https://doi.org/10.1371/journal.pone.0229990.g002 https://doi.org/10.1371/journal.pone.0229990.g002 3 μm) column was selected which provided a uniform peak with adequate resolution. A 3 μm
YMC guard column with a 4.0 mm inside diameter was used to prolong the life of the column. Gradient selection. The separation of PMP-glucose from the corresponding matrix was
of interest. This was achieved utilizing a segmented gradient which consisted of 15 mM potas-
sium phosphate dibasic buffer at a pH of 7.2 (Eluent A) and ACN (Eluent B) (Table 1). This
gradient provided a reasonable retention time of 16.7 min with significant resolution between
the peak of interest and the sample matrix (Fig 3A and 3B). Optimization of chromatographic parameters Wavelength selection. The wavelength used for the detection of PMP-glucose was selected
by the analysis of glucose, PMP, and PMP-glucose on an offline UV detector. The λmax for
PMP- glucose was selected to be 245 nm. The UV spectrum of PMP-glucose using a DAD was
used as further evidence for the location of the PMP-glucose peak in sample chromatograms. g
g
g
by the analysis of glucose, PMP, and PMP-glucose on an offline UV detector. The λmax for
PMP- glucose was selected to be 245 nm. The UV spectrum of PMP-glucose using a DAD was
used as further evidence for the location of the PMP-glucose peak in sample chromatograms. Reaction optimization. The optimal reaction time for the derivatization was performed
by multiple reactions ranging from 30 to 150 min. Reaction mixtures were injected and the
peak areas were determined and plotted against the reaction time (Fig 2). The optimal reaction
time was determined to be 90 minutes, when an increase in the PMP-glucose peak area was no
longer observed, indicating that the reaction was complete. Reaction optimization. The optimal reaction time for the derivatization was performed
by multiple reactions ranging from 30 to 150 min. Reaction mixtures were injected and the
peak areas were determined and plotted against the reaction time (Fig 2). The optimal reaction
time was determined to be 90 minutes, when an increase in the PMP-glucose peak area was no
longer observed, indicating that the reaction was complete. Column selection. Both reversed-phase and normal-phase columns were tested for
method development using a mobile phase consisting of 15 mM potassium phosphate dibasic
pH 7.2 and ACN. Selection of the appropriate column was determined by injecting a sample of
PMP-glucose and observing the overall separation and peak characteristics. Based on the anal-
ysis of six C18, two amino, and two phenyl columns, a YMC-Pack ODS-AQ (150 x 4.6 mm, 4 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Fig 2. Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains constant after 90 minutes indicating
that the reaction has reached completion. Fig 2. Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains constant after 90 minutes indicating
that the reaction has reached completion. Fig 2. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 Method validation System suitability. To ensure reliability of the developed method, five injections of an
8.33 mM PMP-glucose sample were performed. The separation parameters were evaluated for
each injection to ensure the resolution and reproducibility of the system was adequate
(Table 3). Based on the acceptance criteria for each parameter, it was determined that the
selected method parameters were acceptable. Specificity. Specificity studies were performed to ensure no co-eluting impurities with the
peak of PMP-glucose. Forced degradation was performed as part of the peak purity studies
[19,20,38]. Samples of 1 mL PMP-glucose were subjected to acid and base degradation using 1
mL of various concentrations of HCl and NaOH. The degraded solutions were neutralized
with the appropriate acid or base. Oxidation degradation was assessed using l mL of various
percentages of hydrogen peroxide. Additionally, l mL of PMP-glucose was subjected to heat
and UV degradation. The percent degradation for PMP-glucose was assessed utilizing HPLC. The results showed the greatest degradation occurring under both 3 M NaOH and HCl as well
as 0.001% hydrogen peroxide. The determination of peak purity was conducted by combining 100 μL of the samples sub-
jected to 0.001% H2O2, 3 M NaOH, and 3 M HCl degradation and injecting this mixture into
the HPLC system. Successive scans of the PMP-glucose peak were conducted and overlaid to
determine the purity. From these scans, PMP-glucose peak was determined to have a purity of
99.9%. This value is well within the acceptance criteria of 99%. These results indicate that
impurities within the reaction mixture will not interfere with the PMP-glucose peak. Robustness. The robustness of the method was tested to measure its capacity to remain
unaffected by small variations in the method parameters. Robustness was particularly focused
on the resolution of PMP-glucose from adjacent peaks. Small variations in the method param-
eters were studied by deliberately changing the wavelength, flow rate, buffer pH and ionic
strength, and the temperature of the column. Acceptance criteria for method robustness have
not been set by the ICH, therefore a lower specification limit (LSL) of 1.5 (baseline resolution) Table 3. System suitability study. Method development 6 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Table 2. Summery of method parameters. Column
YMC Pack ODS-AQ (150 x 4.6 mm, 3 μm)
Injection Volume
5 μL
Mobile Phase
Eluent A: 15 mM Potassium Phosphate Dibasic pH 7.2 Eluent B: 100% ACN
Flow Rate
1 mL/min
Column Temperature
29.5˚C
Wavelength
245 nm
Run Time
35 min
Equilibration Time
10 min
https://doi.org/10.1371/journal.pone.0229990.t002 Method development Development of the method focused on maximizing the peak area and theoretical plates while
achieving adequate resolution. Optimization of the method parameters examined the effect of
varying injection volume, flow rate, temperature, and buffer pH and ionic strength. Based on
these studies, the optimal method parameters were selected (Table 2). The method showed a
substantial decrease of 10–15 minutes in run time when compared to many other PMP
methods. Table 1. Segmented gradient profile. Percent composition
Time (Min)
Eluent A
Eluent B
0
90
10
9
86
14
30
36
64
35
36
64
https://doi.org/10.1371/journal.pone.0229990.t001 Table 1. Segmented gradient profile. 5 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures The decrease in retention time can be attributed to two factors. The column used was 100
h
t
d h d
ll
ti l
i
th
th
d b
th
k [15 18] M
Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. https://doi.org/10.1371/journal.pone.0229990.g003
LOS ONE
Determination of glucose in Shewanella oneidensis cultures Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. https://doi.org/10.1371/journal.pone.0229990.g003 The decrease in retention time can be attributed to two factors. The column used was 100
mm shorter and had a smaller particle size than those used by other works [15–18]. More
importantly, the mobile phase was changed to a phosphate buffer as opposed to the commonly
seen acetate buffer. The result is a weaker interaction between PMP-glucose with the stationary
phase due to an increase in mobile phase pH. Increasing the mobile phase pH consequently
decreased the retention time of PMP-glucose. The decrease in retention time can be attributed to two factors. The column used was 100
mm shorter and had a smaller particle size than those used by other works [15–18]. More
importantly, the mobile phase was changed to a phosphate buffer as opposed to the commonly
seen acetate buffer. The result is a weaker interaction between PMP-glucose with the stationary
phase due to an increase in mobile phase pH. Increasing the mobile phase pH consequently
decreased the retention time of PMP-glucose. Method validation Parameter
Acceptance Criteria
Mean Values (n = 5)
Plate Number
2000
399586 ± 39.7
Tailing Factor (Tf)
0.9 Tf 2
1.242 ± 0.00242
Resolution
1.5
7.213 ± 0.0004
% RSD Retention Time
2%
0.0299 ± 0.0005
% RSD Peak Area
2%
1.97 ± 0.0835
% Drift Peak Area
2%
1.09 ± 0.0604
https://doi.org/10.1371/journal.pone.0229990.t003 7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020
7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures was established as the acceptance criteria. After testing each condition in triplicates, the study
showed the method was unaffected by small variations in method parameters and therefore is
considered robust (S1 Table). Limit of quantitation and detection. The limit of quantitation (LOQ) and the limit of
detection (LOD) for the method were determined by measuring the magnitude of the PMP-
glucose peak height to the magnitude of the baseline noise (S/N). A S/N ratio of 10 is accept-
able for the LOQ and 3 for the LOD. The LOQ was found to be 0.2 nM with a S/N ratio of 9.8,
and the LOD was found to be 0.09 nM with a S/N ratio of 3.7. The values for LOQ and LOD
were performed in triplicates. The limit of detection of was found to be an order of magnitude
lower than the lowest known LOD for glucose utilizing similar instrumentation [39]. The
lower detection limit can be attributed to the use of a column with a particle size of 3 microns
when compared to the 5 microns used for other works. Reducing the particle size resulted in
an increase in theoretical plates and sharper PMP-glucose peak. Linearity and range. Linearity studies were conducted to measure how well a calibration
plot of peak area versus concentration approximates a straight line. Several glucose concentra-
tions covering the range of 16.65 mM to 0.2 nM (the LOQ) were tested. The expected maxi-
mum glucose concentration within a sample was 13.87 mM (2.5 g/L). The upper range
corresponds to 120% of the maximum glucose concentration within TSB while the lower limit
was set to the limit of quantitation, 0.2 nM. A linear regression equation was then processed
along with a correlation coefficient (S1 Fig). The correlation coefficient of 0.999 meets the
acceptance criteria of 0.999. Method validation The calculated percent bias was determined to be 0.65% meet-
ing the ICH guideline of NMT ± 3% indicating the results are not forced though the origin. Accuracy. The accuracy of the method was determined by investigating how closely the
test results reflect the true value. The accuracy was conducted by preparing 3 samples of PMP-
glucose in the range of 0.5 to 2.5 g/L. All 3 samples were performed in triplicates. Based on the
linear regression equation, the recovered concentrations were calculated. The percent recovery
fell within the acceptance range of 98–102% (S2 Table). Precision. The injection precision for the method was tested to measure how similar the
results are with repeated injections. A 2.5 g/L sample of PMP-glucose was prepared and
injected six times. After averaging the peak areas, a percent RSD of 0.093% was calculated. This value is within the acceptance criteria range of a %RSD 1.5% (S3 Table). The method precision was conducted to measure how similar the results are among sepa-
rate stock solutions. Six samples of PMP-glucose were prepared from separate stock solutions
at a concentration of 2.5 g/L and diluted to 1.5 g/L. After injecting each sample, the peak areas
were average together and a percent relative standard deviation of 0.16% was calculated (S3
Table). This value meets the acceptance criteria of a percent RSD 1.5%. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 Method application The applicability of the method was investigated through the quantitation of glucose con-
sumed by S. oneidensis during early growth development. Cell cultures were grown for 15
hours. The turbidity of the cultures was measured at 30 to 60 minute intervals. The optical
density achieved was dependent on the growth conditions (Fig 4A). The maximum growth
was highest under aerobic compared to microaerobic conditions with oxygen rich cultures
exhibiting 5 times the turbidity achieved by their oxygen deficient counterparts. The optical
density disparity between the microaerobic and aerobic cultures correlates to the use of glucose
by S. oneidensis (Fig 4B). Aerobic cultures utilized the most glucose after 15 hours. The addi-
tion of oxygen in the growth media resulted in a 2-fold increase in glucose utilization com-
pared to microaerobic cultures. Microaerobic cultures containing Fe(III) as the predominate 8 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures E | https://doi.org/10.1371/journal.pone.0229990
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9 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
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March 12, 2020 9 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Fig 4. A comparison of a) S. oneidensis growth to b) the microbe’s utilization of glucose after 15 hours and c) after 2 hours of initial growth. Glucose usage
increases with increasing oxygen concentration and upon the addition of ferric iron. Fig 4. A comparison of a) S. oneidensis growth to b) the microbe’s utilization of glucose after 15 hours and c) after 2 hours of initial growth. Glucose usage
increases with increasing oxygen concentration and upon the addition of ferric iron. electron acceptor exhibited a more rapid onset of exponential growth compared to all other
growth conditions (Fig 5A). These results agree with S. oneidensis’s ability to use various termi-
nal electron acceptors to sustain growth [39–41]. Additionally, this early onset correlates to the
time at which glucose begins to be utilized (Fig 5B). The strength of the method is apparent when examining culture samples grown for two
hours. Of the six culture types, the method could detect glucose across all but the microaerobic
culture (Fig 4C). Measured glucose usage after five hours ranges between 9 to 40 mg/L. Comparable utilization times have not been reported in previous glucose studies [21–23]. Fig 5. Conclusions An accurate and robust method was developed for analysis of glucose by derivatization with
1-phenyl-3-methyl-5-pyrazolone (PMP). The developed method focused on achieving low
detection limits and reduced run times when compared to similar works. The applicability of
the method was tested on microbial samples and was shown to be capable in determining the
levels of glucose throughout the growth of Shewanella oneidensis MR-1. The developed method
was sensitive and capable quantify glucose usage in microbial cultures after only two hours. Supporting information S1 Fig. Linearity of PMP-glucose with increasing
the LOQ (0.2 nM) while the upper limit correspond
(3 g/L). (TIF)
S1 Table. Robustness study. (DOCX)
S2 Table. Accuracy study. (DOCX)
S3 Table. Precision studies. (DOCX) S1 Fig. Linearity of PMP-glucose with increasing concentration. The lower limit represe
the LOQ (0.2 nM) while the upper limit corresponds to 120% of the expected glucose in T
(3 g/L). (TIF)
S1 Table. Robustness study. (DOCX)
S2 Table. Accuracy study. (DOCX)
S3 Table. Precision studies. (DOCX) S1 Fig. Linearity of PMP-glucose with increasing concentration. The lower limit represents
the LOQ (0.2 nM) while the upper limit corresponds to 120% of the expected glucose in TSB
(3 g/L). S1 Fig. Linearity of PMP-gluco
the LOQ (0.2 nM) while the upp
(3 g/L). (TIF)
S1 Table. Robustness study. (DOCX)
S2 Table. Accuracy study. (DOCX)
S3 Table. Precision studies. (DOCX) Method application Normalized results for a) optical density and b) glucose usage. The onset of exponential growth appears sooner for microaerobic samples containing ferric iron in
the growth media, which also correlates to the time at which glucose utilization becomes more rapid. https://doi.org/10.1371/journal.pone.0229990.g005 Fig 5. Normalized results for a) optical density and b) glucose usage. The onset of exponential growth appears sooner for microaerobic samples containing ferric iron in
the growth media, which also correlates to the time at which glucose utilization becomes more rapid. https://doi.org/10.1371/journal.pone.0229990.g005 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990
March 12, 2020 10 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Interestingly, the method revealed an ability of S. oneidensis to utilize a combination of elec-
tron acceptors to facilitate both microbial growth and consumption of glucose. These results
agree with those proposed by Choi et al. [23] and Serres and Riley [32] indicating that S. onei-
densis can grow in the presence of glucose only once oxygen is present within the media envi-
ronment. When oxygen is limited, S. oneidensis exhibited stunted growth regardless of the
presence of ferric iron. Further evidence for stunted growth comes when examining the two-
hour growth cultures. Microaerobic cultures, except for those cultures containing iron chlo-
ride, did not register glucose usage suggesting the microbe has difficulty using glucose under
these conditions. These results may indicate that oxygen is the preferred electron acceptor,
and that the use of glucose when iron chloride is present may occur though a separate
metabolism. Acknowledgments We are grateful to the Department of Chemistry at Northeastern Illinois University for provid-
ing resources critical to sample analysis. We are grateful to the Department of Chemistry at Northeastern Illinois University for provid-
ing resources critical to sample analysis. References 1. Lovley DR, Phillips EJP. Novel Mode of Microbial Energy Matabolism: Organic Carbon Oxidation Cou-
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March 12, 2020 |
https://openalex.org/W4281484139 | https://www.researchsquare.com/article/rs-1589885/latest.pdf | English | null | Solving Steady-State Wave Responses of One-Dimensional Multi-Degree-of-Freedom Lattices with Strong Nonlinearities Based on an Improved Incremental Harmonic Balance Method | Research Square (Research Square) | 2,022 | cc-by | 15,902 | Solving Steady-State Wave Responses of One-
Dimensional Multi-Degree-of-Freedom Lattices with
Strong Nonlinearities Based on an Improved
Incremental Harmonic Balance Method Hongyu Wang
Dalian University of Technology
Xuefeng Wang ( xwang201@eng.ua.edu )
Peking University https://orcid.org/0000-0002-9071-6322
Jian Zhao
Dalian University of Technology
Jian Zhang
Dalian University of Technology
Yu Huang
Dalian Ocean University Hongyu Wang
Dalian University of Technology
Xuefeng Wang ( xwang201@eng.ua.edu )
Peking University https://orcid.org/0000-0002-9071-6322
Jian Zhao
Dalian University of Technology
Jian Zhang
Dalian University of Technology
Yu Huang
Dalian Ocean University Research Article Keywords: strong nonlinearity, incremental harmonic balance method, wave problem, delay differential
equation Posted Date: May 25th, 2022 DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 * Jian Zhao, Email: jzhao@dlut.edu.cn * Xuefeng Wang, Email: wang_xf@pku.edu.cn * Jian Zhao, Email: jzhao@dlut.edu.cn
* Xuefeng Wang, Email: wang_xf@pku.edu.cn DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Abstract The nonlinearity plays an important role in modulation of wave propagation characteristics, such as the
adjustment of band structures by media nonlinearities. When strong nonlinearities are involved in a
multi-degree-of-freedom (multi-DoF) wave propagation problem, traditional methods have difficulties
to solve it accurately and efficiently due to the growth of dimensions. An algorithm based on an improved
incremental harmonic balance (IHB) method is developed in this work to obtain steady-state solutions
of a general wave problem with complex nonlinearities. A multi-DoF wave problem is firstly transformed
to a delay differential equation (DDE), and Jacobian matrices of a harmonic balanced residual of the
DDE can be directly constructed by conducting fast Fourier transform of the residual without any
numerical integration. The algorithm decouples wave vectors from basis functions to significantly reduce
the number of the functions, and it is more efficient than that based on a traditional IHB method of
solving a wave problem, especially for the case that high-order basis functions are involved to handle
strong nonlinearities. Moreover, the nonlinear wave problem can be solved when frequencies are given
and wave vectors unknown, which is a challenge of a traditional IHB method. In this work, one-
dimensional diatomic lattices with Hertz contact law and cubic spring models are studied as examples,
where dispersion curves and bandgap properties are generated. Results show that it is necessary to use
high-order Fourier functions to obtain accurate steady-state responses when strong nonlinearities exist. Results also show that the convergence rate of the method with use of a fixed frequency is faster than
that of a fixed wave vector. Keywords: strong nonlinearity, incremental harmonic balance method, wave problem,
delay differential equation Keywords: strong nonlinearity, incremental harmonic balance method, wave problem,
delay differential equation Solving Steady-State Wave Responses of One-
Dimensional Multi-Degree-of-Freedom Lattices
with Strong Nonlinearities Based on an Improved
Incremental Harmonic Balance Method1
Hongyu Wang a, Xuefeng Wang b, *, Jian Zhao a, *, Jian Zhang a, Yu Huang c
a State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian
University of Technology, Dalian, China.
b Department of Advanced Manufacturing and Robotics, College of Engineering,
Peking University, Beijing, China.
c College of Ocean and Civil Engineering, Dalian Ocean University, Dalian, China. c College of Ocean and Civil Engineering, Dalian Ocean University, Dalian, China. 1. Introduction Dispersion is an important characteristic of wave propagation, which attracts attentions of many
researchers. Interesting phenomena of dispersion were found in previous studies, such as stop-bands,
pass-bands, adjustable band gaps, etc., and these phenomena can be influenced by materials and media
structures [1], e.g., band structures can be significantly varied by changing media nonlinearities [2, 3]. Many devices were implemented in different applications with use of dispersion characteristics, such as
vibration/noise reductions and acoustic modulators [4-6]. Wave propagation problems are usually modeled as linear systems when media are weakly excited,
where wave properties, such as dispersion, can be analytically studied [7]. The linear assumption is an
appropriate approach to describe wave motions under small excitations, but it is inaccurate to calculate
general wave motions under strong excitations that generate strong nonlinearities. To understand wave
propagation in general cases and develop effective methods to control wave characteristics, many
researchers paid attentions to obtain dynamic responses of nonlinear wave problems. The nonlinearity of a wave propagation system can be caused by medium structures (e.g. the cubic
spring [8]), contact models (e.g. Hertz contact law [9]), external excitations (e.g. electrostatic [10] and
electromagnetic forces [11]), etc. Periodic responses of wave problems with nonlinearities can be solved
by linearization methods, numerical and experimental methods, perturbation methods, and incremental
harmonic balance (IHB) methods. For the case of complex wave propagation problems with strong
nonlinearities, it is usually difficult to calculate steady-state solutions accurately and effectively. In some studies, propagation characteristics were obtained by linear approximation, where effects
of nonlinear interactions were ignored [12]. Numerical methods, such as Runge-Kutta methods and
numerical simulations [13-18], were used to verify dispersion properties. Perturbation and incremental
harmonic balance (IHB) methods are semi-analytical methods to study nonlinear differential equations. Perturbation methods were used in solving weakly nonlinear wave problems [19-23]. Vakakis et al. [8,
24] used a multi-scale perturbation method to study a nonlinear periodic system with external excitations. In the work, a spatial multi-scale method was used to study a single-coupled periodic system with cubic
nonlinearities, and amplitude-dependent nonlinear wave propagation characteristics were obtained [8]. An asymptotic method was developed to study nonlinear standing waves, which is suitable for problems
with weak nonlinearities under small vibrations [24]. Sreelatha et al. [25] used the perturbation method
to study propagations of nonlinear waves in a two-dimensional heterogeneous lattice. 1. Introduction In this work, three
cases of quadratic, cubic, and quadratic-cubic-combined nonlinearities were involved, and solutions with
weak nonlinearities were obtained. Narisetti et al. [26, 27] used a perturbation method to study wave
propagations in discrete nonlinear structures, where amplitude-dependent characteristics were obtained. This method was extended to wave propagation problems in a two-dimensional periodic lattice with
weak nonlinearities. However, the perturbation method will be inaccurate when complex and strong
nonlinearities are introduced [28]. At this time, the IHB method can be employed to solve such strong
nonlinear problems. The IHB method was first proposed by Lau and Cheung, which is a combination of Newton's
method and Galerkin process [29, 30]. The IHB method was mainly used to obtain steady-state solutions
of vibrations in past works [31-33]. Since dispersion is the characteristic of steady-state waves, the IHB
method was used to study the nonlinear filtering characteristics of a 1D atomic chain in a low-frequency
range [34]. It was found that the movements of the band-gap depends on the degree of nonlinearities. A
general IHB method was proposed in [9] to study propagations of plane waves in periodic media with
strong nonlinearities, and the method was verified by comparing dispersion curves with a numerical
method. In the work [35], the IHB method was used in the study of nonlinear elastic waves, and diode
effects were observed through experiments. In the above IHB methods, wave responses are obtained only if wave vectors are given, which
cannot hold for many cases. When wave responses are expected to be controlled at a certain external
excitation frequency, the wave vector is unknown and has to be calculated as a variable. On the other
hand, the number of basis functions used in the above IHB methods for wave problems is much larger
than that of harmonic terms of wave responses, since the basis functions are made of many sets of
harmonic functions with different phases that are multiples of wave vectors. Practically, to avoid complex
and time-consuming Galerkin integration calculations, low-order trigonometric functions were usually
used as basis functions in a traditional IHB method, which will reduce the accuracy when strong
nonlinearities are involved. Based on the original IHB method, Wang [36] developed a new IHB method to solve wave problems
of 1D nonlinear single-degree-of-freedom (single-DoF) systems. 1. Introduction The key of this method is to transform
the governing equation of a nonlinear wave problem into a delayed differential equation (DDE) with
multiple delays and advances [37], and then the DDE can be solved by an improved IHB method [28]. It
was proved that steady-state solutions of the original wave problem are the same as those of the
transformed DDE. The advantage of this transformation approach is that the wave vector will be
decoupled from basis functions and it can be served as a variable in the DDE. Thus, this method
significantly reduces the number of basis functions, as well as the dimension of general coordinates, in a
IHB method, and is capable to solve wave responses at a given excitation frequency. The method was
used to calculate wave responses of 1D single-DoF systems [36]. Multi-degree-of-freedom (multi-DoF)
systems are more general and complicated due to coupling of DoFs. The expression of the Jacobian
matrix is more complicated and cannot be obtained directly by the above method. Thus, a method for solving multi-DoF wave problems will be derived here. The method will be extended to solve steady-
state responses of wave propagations at a fixed frequency, and its performance will be studied. There are three main contributions in this paper. First, a general method to obtain steady-state
solutions of multi-DoF wave propagation problems is developed. The method can be more efficient than
traditional IHB methods of solving wave problems when high-order basis functions are involved to
handle strong nonlinearities. Second, results of this work show that it is necessary to use high-order
Fourier functions to obtain accurate steady-state wave responses when strong nonlinearities exist, which
was not been explicitly recognized in past works since only low-order Fourier functions were used to
solve wave problems. Third, the method can be used to calculate steady-state wave responses and wave
vectors simultaneously when excitation frequencies are given, and results also show that the convergence
rate of solving steady-state responses at a fixed frequency is faster than that at a fixed wave vector. This article consists of four sections. In the next section, the IHB method is developed by
transforming multi-DoF wave propagation problems into multi-DoF DDEs when frequencies or wave
vectors are given. 1. Introduction In the third section, two examples, including a 1D diatomic lattice model with a Hertz
contact law and a cubic-stiffness spring, are used to show the results and performance of the proposed
IHB method. The fourth section summarizes outcomes of this work. 2.1 Transformation of Multi-DoF Wave Problems to DDEs (1), the number i can be set to zero to simplify the expression: (
(
)
)
(
,
,
,
,
, )
0
n
n
L
R
F U
U
U
U
t
−
+
=
(3) (
(
)
)
(
,
,
,
,
, )
0
n
n
L
R
F U
U
U
U
t
−
+
=
(3) (
(
)
)
(
,
,
,
,
, )
0
n
n
L
R
F U
U
U
U
t
−
+
= (3) and the steady-state solution of the j-th unit can be written as and the steady-state solution of the j-th unit can be written as and the steady-state solution of the j-th unit can be written as ( )
(
)
j
j
U
U
t
T
=
−
(4) ( )
(
)
j
j
U
U
t
T
=
−
(4) ( )
(
)
j
j
U
U
t
T
=
− (4) where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term ,
,
,
j
L
R
T
j
j
n
n
=
= −
+
(5) (5) n which μ represents the value of the wave vector in the 1D medium. Thus, the DDE can be written as (
(
)
)
(
,
,
,
,
, , )
0
n
n
L
R
F U
U
U
U
t
−
+
=
(6) (
(
)
)
(
,
,
,
,
, , )
0
n
n
L
R
F U
U
U
U
t
−
+
= (6) It is noted that in Eq. (6), both time-lag and time-advance terms are included. It is noted that in Eq. (6), both time-lag and time-advance terms are included. 2.1 Transformation of Multi-DoF Wave Problems to DDEs Suppose that when a traveling wave reaches a steady state in an infinite periodic medium, each particle
vibrates with a specific phase difference from adjacent particles, and motions of all particles are periodic
in space. Therefore, steady-state solutions of a 1D multi-DoF wave problem can be obtained by solving
periodic solutions of a multi-DoF DDE. First, the construction of the DDE is shown as follows. The governing equation of the 1D multi-DoF wave problem with a general nonlinearity can be
written as (
)
(
)
( )
( )
(
,
,
,
,
, )
0
i n
i n
i
i
L
R
F U
U
U
U
t
−
+
=
(1) (1) where
( )
F is a nonlinear function to describe the wave propagation, t is the time variable, the prime represents the time derivative,
( )i
U
represents motions of particles in the i-th period unit in the medium,
and nL and nR represent numbers of units on the left and right, respectively, which have effects on the
unit i. For a 1D medium with n particles appearing periodically, the number of particles in a period unit
of the wave shape is n, and
( )i
U
is an n-dimensional vector: represents the time derivative,
( )i
U
represents motions of particles in the i-th period unit in the medium,
and nL and nR represent numbers of units on the left and right, respectively, which have effects on the
unit i. For a 1D medium with n particles appearing periodically, the number of particles in a period unit
of the wave shape is n, and
( )i
U
is an n-dimensional vector: ( )
( )
( )
( )
1
2
,
,
,
i
T
i
i
i
n
U
u
u
u
=
(2) (2) where
( )
i
k
u
is the motion of the k-th particle in the i-th period unit with k=1, …, n. Thus, function
( )
F
has n components
1
[
,
,
]T
n
F
F
F
=
. has n components
1
[
,
,
]T
n
F
F
F
=
. In Eq. (1), the number i can be set to zero to simplify the expression: In Eq. 2.2 Construction of Multi-DoF Delayed Variables The steady-state solution of the DDE in Eq. (6) can be derived by modifying the method in [37]. First, a
dimensionless time variable can be defined as imensionless time variable can be defined as t
=
(7) t
=
(7) t
= (7) The first and second derivative of U can be expressed as The first and second derivative of U can be expressed as dU
dU d
U
dt
d
dt
=
=
(8) dU
dU d
U
dt
d
dt
=
=
(8)
2
2
2
(
)
(
)
d U
d
d
d
U
U
U
dt
d
dt
dt
=
=
=
(9) (8) 2
2
2
(
)
(
)
d U
d
d
d
U
U
U
dt
d
dt
dt
=
=
=
(9) (9) respectively, where the over-dot represents the derivative with respect to τ. The time-delay variable is
expressed as ( )
(
)
j
j
U
U
T
=
−
(10) (10) Substituting Eq. (7) to Eq. (10) into Eq. 2.2 Construction of Multi-DoF Delayed Variables (6) yields (
(
)
)
( ,
,
,
,
, , , )
0
n
n
R
L
F U U U
U
+
−
=
(11) (11) The steady-state periodic solution U(τ) can be approximated by the Fourier series: 1
,
T
T
T
S
S
n
U
C q
C q
=
,
(12) 1
,
T
T
T
S
S
n
U
C q
C q
=
,
(12 (12) where the superscript T represents the transposition of the vector, CS is a set of truncated Fourier basis
functions where the superscript T represents the transposition of the vector, CS is a set of truncated Fourier basis
functions
1, cos ,
, cos
, sin ,
, sin
T
S
C
M
M
=
(13) (13) in which M is the truncated order, and qk with k=1, …, n are coefficient vectors of CS for the k-th particle in a unit, which can be expressed as particle in a unit, which can be expressed as 1
1
1
1
1
1
0
1
1
0
1
1
[
,
,
,
,
,
,
]
[
,
,
,
,
,
,
]
T
M
M
n
n
n
n
n
T
n
M
M
q
a
a
a
b
b
q
a
a
a
b
b
=
=
(14) (14) m
U
C Q
=
(15) m
U
C Q
=
(15) (15) where Cm is a n × n(2M+1) matrix (2
1) 1
(2
1) 1
(2
1) 1
(2
1) 1
(2
1) 1
(2
1) 1
0
0
0
0
0
0
T
S
M
M
T
m
M
S
M
T
M
M
S
C
C
C
C
+
+
+
+
+
+
=
(16) (16) and Q is a n(2M+1) ×1 vector nd Q is a n(2M+1) ×1 vector 1
2
[
,
,
,
]
T
T
T
T
n
Q
q
q
q
=
(17) 1
2
[
,
,
,
]
T
T
T
T
n
Q
q
q
q
=
(17) (17) The first and second derivatives of the steady-state solution U can be expressed as The first and second derivatives of the steady-state solution U can be expressed as 1
2
m
m
U
CG Q
U
CG Q
=
=
(18) 1
2
m
m
U
CG Q
U
CG Q
=
= (18) where Gm1 and Gm2 are both n(2M+1)-dimensional square matrices: where Gm1 and Gm2 are both n(2M+1)-dimensional square matrices: 1
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
1
(2
1) (2
1)
1
(2
1) (2
1)
(2
1) (2
1)
1
0
0
0
0
0
0
M
M
M
M
M
M
M
M
m
M
M
M
M
H
H
G
H
+
+
+
+
+
+
+
+
+
+
+
+
=
(19) (19) 2
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
2
(2
1) (2
1)
2
(2
1) (2
1)
(2
1) (2
1)
2
0
0
0
0
0
0
M
M
M
M
M
M
M
M
m
M
M
M
M
H
H
G
H
+
+
+
+
+
+
+
+
+
+
+
+
=
(20) (2
1) (2
1)
2
(2
1) (2
1)
2
(2
1) (2
1)
(2
1) (2
1)
2
0
0
0
0
M
M
M
M
m
M
M
M
M
H
G
H
+
+
+
+
+
+
+
+
=
(20) (20) in which H1 and H2 are the first-order and second-order derivative operator matrices, respectively: 1
0
0
0
0
0
0
0
T
T
M
M
M
M M
M
M M
H
S
S
=
−
,
2
2
2
0
0
0
0
0
0
0
T
T
M
M
M
M M
M
M M
H
S
S
=
−
−
with
1
0
0
S
M
=
(21) (21) where 0M is an M-dimensional zero vector and 0M×M is an M-dimensional zero matrix. 2.2 Construction of Multi-DoF Delayed Variables In Eq. (11), the time-delay variable can be expressed as: In Eq. (11), the time-delay variable can be expressed as: ( )
1
j
m
U
C Q
=
(22) (22) where Cm1 is a n × n(2M+1) matrix: where Cm1 is a n × n(2M+1) matrix: (2
1) 1
(2
1) 1
1
(2
1) 1
(2
1) 1
(2
1) 1
(2
1) 1
0
0
0
0
0
0
T
ST
M
M
T
m
M
ST
M
T
M
M
ST
C
C
C
C
+
+
+
+
+
+
=
(23) (23) in which CST is a set of basis functions with a phase difference Tj, i.e., the value of the wave vector of
the j-th unit: [1, cos(
),
,cos
(
), sin(
),
, sin
(
)]
T
ST
j
j
j
j
C
T
M
T
T
M
T
=
−
−
−
−
(24) (24) In previous IHB methods for solving multi-DoF wave problems, CST were directly used as basis
functions, so that the number of the basis functions is 1 2(
)
R
L
n
n
M
+
+
, which is much larger than M, the
order of harmonic functions of the response. The basis functions were also directly integrated in the
harmonic balance procedure and information of Tj was lost. Thus, it is necessary to decouple Tj and
the basis functions: the trigonometric functions in Eq. (24) can be transformed as cos
(
)
cos
cos
sin
sin
,
1 ,
,
sin
(
)
cos
sin
sin
cos
,
1,
,
j
j
j
j
j
j
M
T
M
MT
M
MT
M
M
M
T
M
MT
M
MT
M
M
−
=
+
=
−
= −
+
=
(25) (25) and Eq. (22) can be written as and Eq. (22) can be written as and Eq. 2.2 Construction of Multi-DoF Delayed Variables (22) can be written as
( )
( )
j
j
m
m
U
C D Q
=
(26) ( )
( )
j
j
m
m
U
C D Q
=
(26) ( )
( )
j
j
m
m
U
C D Q
=
(26) (26) where
( )
j
m
D
is n(2M+1) square matrix: where
( )
j
m
D
is n(2M+1) square matrix: where
( )
j
m
D
is n(2M+1) square matrix: re
( )
j
m
D
is n(2M+1) square matrix: where
( )
j
m
D
is n(2M+1) square matrix: (2
1) (2
1)
(2
1) (2
1)
( )
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
0
0
0
0
0
0
j
M
M
M
M
j
M
M
j
M
M
m
M
M
M
M
j
D
D
D
D
+
+
+
+
+
+
+
+
+
+
+
+
=
(27) (27) in which Dj, the delay matrix operator, is in which Dj, the delay matrix operator, is in which Dj, the delay matrix operator, is 0
0
1
0
0
0
cos
sin
cos
sin
0
0
sin
cos
sin
cos
0
j
j
j
j
j
j
j
j
j
T
T
MT
MT
D
T
T
MT
MT
−
−
=
(28) (28) Therefore, the basis functions are still CS and information of Tj is in Dj. Substituting Eq. (15), Eq. (18),
and Eq. (26) into Eq. (11) yields Therefore, the basis functions are still CS and information of Tj is in Dj. Substituting Eq. (15), Eq. (18),
and Eq. (26) into Eq. (11) yields 2
1
(
,
,
,
,
, , , )
0
L
R
n
n
m
m
m
m
m
m
m
m
F C G Q
C G Q
C D
Q
C D
Q
−
+
=
(
)
(
)
(29) (29) 2.3 Newton Method to Solve Steady-State Responses If a guess of the solution U is not equal to the steady-state solution, there is a nonzero residual r that If a guess of the solution U is not equal to the steady-state solution, there is a nonzero residual r that
can be written as 2
1
( , , , )
(
,
,
,
,
, , , )
L
R
n
n
m
m
m
m
m
m
m
m
r
Q
F C G Q
C G Q
C D
Q
C D
Q
−
+
=
(
)
(
)
(30) (30) which is an n-dimensional vector for a multi-DoF wave problem. Its harmonic balanced residual R is 2
2
0
1
( ,
,
)
( ,
,
,
)
m
R Q
C
r
Q
d
=
(31) (31) where Cm2 is a n × n(2M+1) matrix: 1
(2
1) 1
(2
1) 1
2
(2
1) 1
1
(2
1) 1
(2
1) 1
(2
1) 1
1
0
0
0
0
0
0
S
M
M
m
M
S
M
M
M
S
C
C
C
C
+
+
+
+
+
+
=
(32) (32) in which Cs1 is a set of basis functions orthogonal to Cs: in which Cs1 is a set of basis functions orthogonal to Cs: 1
1 , cos ,
, cos
, sin ,
, sin
2
T
S
C
M
M
=
(33) (33) Newton's method is used to solve Q to make R in Eq. (31) vanish. Newton’s iterative formula is Q
J
Q
J
J
R
+
+
= − Q
J
Q
J
J
R
+
+
= −
(34) (34) where R represents the harmonic balanced residual, JQ, Jω, and Jμ represent Jacobian matrices of
variables Q, ω, and μ, respectively, and
Q ,
, and
are increments of the variables. The
numerical integration method to obtain R from Eq. (31) is usually time-consuming. The following
method can be used to improve the efficiency. 2.3 Newton Method to Solve Steady-State Responses Let the residual r be where R represents the harmonic balanced residual, JQ, Jω, and Jμ represent Jacobian matrices of
variables Q, ω, and μ, respectively, and
Q ,
, and
are increments of the variables. The
numerical integration method to obtain R from Eq. (31) is usually time-consuming. The following
method can be used to improve the efficiency. Let the residual r be 1
[ ,
, ]T
n
r
r
r
=
(35) (35) where
,
1,
,
kr
k
n
=
are residuals of n particles in a unit. The harmonic balanced residual 1
2
[
,
,
,
]
T
T
T T
n
R
R
R
R
=
(36) 1
2
[
,
,
,
]
T
T
T T
n
R
R
R
R
=
(36) (36) can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …,
n, is the FFT of rk: can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …,
n, is the FFT of rk: can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …,
i
h FFT f can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …, n, is the FFT of rk: 1
1
1
1
1
1
0
1
1
2
2
2
2
2
2
0
1
1
0
1
1
[
,
,
, ,
,
]
[
,
,
,
,
,
]
[
,
,
,
,
,
]
T
M
M
T
M
M
n
n
n
n
n
T
n
M
M
R
p
p
p
l
l
R
p
p
p
l
l
R
p
p
p
l
l
=
=
=
(37) (37) in which
k
m
p and
k
ml denote the values of the real and imaginary parts of the m-th order Fourier
function of the k-th particle, respectively. in which
k
m
p and
k
ml denote the values of the real and imaginary parts of the m-th order Fourier
function of the k-th particle, respectively. Jacobian matrices in Eq. 2.3 Newton Method to Solve Steady-State Responses (34) can be calculated by exchanging the sequence of partial derivative
and integral: 2
2
0
1
Q
m
R
r
J
C
d
Q
Q
=
=
(38)
2
2
0
1
m
R
r
J
C
d
=
=
(39)
2
2
0
1
m
R
r
J
C
d
=
=
(40) (38) (39) (40) In this work, the method proposed in [35] is extended to construct a semi-analytical formula of JQ: 1
1
1
( )
2
1
R
L
n
j
Q
m
DD
m
m
m
D
m
m
m
j
m
m
j
n
J
L f
L
G
L f L
G
L f L
D
−
−
−
=−
=
+
+
(41) (41) where
m
L and
1
m
L− are n(2M+1) square matrices: where
m
L and
1
m
L− are n(2M+1) square matrices: where
m
L and
1
m
L− are n(2M+1) square matrices: 1
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
1
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
1
0
0
0
0
0
0
M
M
M
M
M
M
M
M
m
M
M
M
M
L
L
L
L
+
+
+
+
+
+
+
+
+
+
+
+
=
(42)
2
(2
1) (2
1)
(2
1) (2
1)
1
(2
1) (2
1)
2
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
2
0
0
0
0
0
0
M
M
M
M
M
M
M
M
m
M
M
M
M
L
L
L
L
+
+
+
+
−
+
+
+
+
+
+
+
+
=
(43) (42) (43) in which L1 and L2 are 2M+1 square matrices: in which L1 and L2 are 2M+1 square matrices: 1
0
0
1
0
0
1
0
1
1
0
1
0
0
L
j
j
j
j
=
−
−
−
(44) 1
0
0
1
0
0
1
0
1
1
0
1
0
0
L
j
j
j
j
=
−
−
−
(44) 2
0
1
0
1
1
2
0
0
0
0
2
0
1
0
1
j
j
L
j
j
=
−
−
(45)
fDD is
1
(2
1) (2
1)
0
dd
M
M
f
f
+
+
(46) 2
0
1
0
1
1
2
0
0
0
0
2
0
1
0
1
j
j
L
j
j
=
−
−
(45) 2
0
1
1
2
0
0
0
0
2
0
1
0
1
j
L
j
j
=
−
−
(45) 2
0
1
1
2
0
0
0
0
2
0
1
0
1
j
L
j
j
=
−
−
(45) (45) 0
1
j
−
fDD is
1
(2
1) (2
1)
(2
1) (2
1)
0
0
dd
M
M
DD
n
M
M
dd
f
f
f
+
+
+
+
=
(46) 1
(2
1) (2
1)
(2
1) (2
1)
0
0
dd
M
M
DD
n
M
M
dd
f
f
f
+
+
+
+
=
(46) 1
(2
1) (2
1)
(2
1) (2
1)
0
0
dd
M
M
DD
n
M
M
dd
f
f
f
+
+
+
+
=
(46) (46) in which
k
dd
f
, k=1, …, n is Toeplitz form of
0
[
]
k
k
k
M
M
f
f
f
−
that is a coefficient vector of M-order in which
k
dd
f
, k=1, …, n is Toeplitz form of
0
[
]
k
k
k
M
M
f
f
f
−
that is a coefficient vector of M-order Fourier functions of
kF
U
, which can be simply calculated by FFT of
kF
U
: Fourier functions of
kF
U
, which can be simply calculated by FFT of
kF
U
: Fourier functions of
kF
U
, which can be simply calculated by FFT of
kF
U
: 0
0
0
0
0
k
k
M
k
k
k
k
dd
M
M
k
k
M
f
f
f
f
f
f
f
f
−
−
=
(47) (47) fD and fj are 1
(2
1) (2
1)
(2
1) (2
1)
0
0
d
M
M
D
n
M
M
d
f
f
f
+
+
+
+
=
and
1,1
1,
,1
,
n
j
n
n n
f
f
f
f
f
=
(48) (48) respectively, in which
k
df , k=1, …, n and
1
2
,
k k
jf
, k1, 2=1, …, n are Toeplitz forms of coefficient vectors of
kF
U
and
( )
k
j
F
U
with
,
,
L
R
j
n
n
= −
, respectively, which can be obtained by FFT of
kF
U
and
( )
k
j
F
U
. 2.3 Newton Method to Solve Steady-State Responses The Jacobian matrices with respect to the frequency ω and wave vector μ can be obtained by FFTs of
r
and
r
, where FFTs of
r
and
r
, where 2
(
, , )
m
m
r
F C G Q
=
(49) 2
(
, , )
m
m
r
F C G Q
=
(49) (49) and
( )
( )
(
,
,
, , )
j
j
m
m
m
m
m
m
r
F C Q C D
Q C D
D Q
=
(50) and ( )
( )
(
,
,
, , )
j
j
m
m
m
m
m
m
r
F C Q C D
Q C D
D Q
=
(50) ( )
( )
(
,
,
, , )
j
j
m
m
m
m
m
m
r
F C Q C D
Q C D
D Q
=
(50) (50) respectively, in which
m
D is an n(2M+1) square matrix: respectively, in which
m
D is an n(2M+1) square matrix: respectively, in which
m
D is an n(2M+1) square matrix: (2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
(2
1) (2
1)
0
0
0
0
0
0
M
M
M
M
M
M
M
M
m
M
M
M
M
D
D
D
D
+
+
+
+
+
+
+
+
+
+
+
+
=
(51) (51) and D is a partial derivative matrix operator of the wave vector: and D is a partial derivative matrix operator of the wave vector: and D is a partial derivative matrix operator of the wave vector: 0
0
0
0
0
0
0
0
0
0
0
0
0
j
D
jM
j
jM
−
=
−
(52) 0
0
0
0
0
0
0
0
0
0
0
0
0
j
D
jM
j
jM
−
=
−
(52) 0
0
0
0
0
0
0
0
0
0
0
0
0
j
D
jM
j
jM
−
=
−
(52) (52) There are two cases when solving Eq. 2.3 Newton Method to Solve Steady-State Responses of
kF
U
and
( )
k
j
F
U
with
,
,
L
R
j
n
n
= −
, respectively, which can be obtained by FFT of
kF
U
and
( )
k
j
F
U
. 3.1.1 Model Description and Calculation In this work, the proposed method is used to study a 1D diatomic lattice model under the Hertz contact
law [9]. A unit of the diatomic chain model consists of two different masses, m1 and m2, as shown in
Fig. 2. Both ends of the chain are subjected to an initial compression force of F0, and the initial
compression displacement of two adjacent particles is δ0, which is given by F0 and the particle stiffness. The nonlinearity of the 2-DoF system is strong when the compression force is large. The nonlinearity of the 2-DoF system is strong when the compression force is large. Figure. 2 Schematic diagram of a 1D diatomic lattice under Hertz contact law Figure. 2 Schematic diagram of a 1D diatomic lattice under Hertz contact law As shown in Fig. 2, u1 and u2 denote dynamic displacements of the two particles with masses of
m1 and m2, respectively. These displacements are relative to their static positions under the initial
compression F0. 2.3 Newton Method to Solve Steady-State Responses (34). One is that when the wave vector μ is fixed, Eq. (34)
can be written as Q
J
Q
J
R
+
= −
(53) (53) and Newton method can be used to solve Q and ω iteratively. In the other case, when the frequency ω
is given, Eq. (34) can be written as and Newton method can be used to solve Q and ω iteratively. In the other case, when the frequency ω
is given, Eq. (34) can be written as Q
J
Q
J
R
+
= −
(54) (54) In the same way, Q and μ can be iteratively solved by the Newton method. In the same way, Q and μ can be iteratively solved by the Newton method. The procedure to calculate steady-state wave solutions used in this work is summarized in Fig. 1. The procedure can be automatically implemented by a computer program and the only manual work
is to give partial differentiations of the DDE, which is a much easier task than derivation of Jacobian
matrices in traditional IHB methods. Figure. 1 The procedure of solving wave propagation problems with strong nonlinearities Figure. 1 The procedure of solving wave propagation problems with strong nonlinearities 3.1.1 Model Description and Calculation (56) can be expressed as 2
3
3
1
2
2
1
2
2
3
3
2
2
2
2
1
2
(
)
(
)
(
)
(
)
d u
m
dt
d u
m
dt
+
+
+
+
=
−
=
−
(62) (62) where 0
0
0
+
=
,
0
0
0
+
=
and
1
1
1
1
0
0
0
+
=
(63) (63) in which 1
0
1
2
(
)
u
u
−
=
−
−
,
0
2
1
(
)
u
u
=
−
−
and
1
1
0
1
2
(
)
u
u
=
−
−
(64) (64) The diatomic chain is composed of aluminum balls and stainless steel balls in this example, where the
parameters are E1=68.9 GPa, E2=193 Gpa, R1=R2=9.5025 mm, v1=0.35, v2=0.3, m1=9.73 g, m2=29.10
g, and F0=20 N. The diatomic chain is composed of aluminum balls and stainless steel balls in this example, where the
parameters are E1=68.9 GPa, E2=193 Gpa, R1=R2=9.5025 mm, v1=0.35, v2=0.3, m1=9.73 g, m2=29.10
g, and F0=20 N. 3.1.1 Model Description and Calculation The system displacement vector of the i-th unit can be represented as ( )
( )
( )
1
2
,
i
T
i
i
U
u
u
=
(55) (55) The governing equation of the 1D diatomic lattice under the Hertz contact law can be written as The governing equation of the 1D diatomic lattice under the Hertz contact law can be written as 2
3
3
1
2
2
1
2
2
3
3
2
2
2
2
1
2
(
)
(
)
(
)
(
)
i
i
i
i
i
i
d u
m dt
d u
m
dt
+
+
+
+
+
=
−
=
−
(56) (56) where where 0
0
0
i
i
i
i
+
=
,
0
0
0
i
i
i
i
+
=
and
1
1
1
1
0
0
0
i
i
i
i
+
+
+
+
+
=
(57) (57) i
i
1
i+
in which in which 1
0
1
2
(
)
i
i
i
u
u
−
=
−
−
,
0
2
1
(
)
i
i
i
u
u
=
−
−
and
1
1
0
1
2
(
)
i
i
i
u
u
+
+ =
−
−
(58) 1
0
1
2
(
)
i
i
i
u
u
−
=
−
−
,
0
2
1
(
)
i
i
i
u
u
=
−
−
and
1
1
0
1
2
(
)
i
i
i
u
u
+
+ =
−
−
(58) (58) Γ denotes the coefficient of nonlinear recovering forces: nd Γ denotes the coefficient of nonlinear recovering forces: 1
2
1
2
1
2
2
2
2
1
1
2
1
1
4
(
)
3[
(1
)
(1
)]
E E
R
R
E
E
−
+
=
−
+
−
(59) 1
2
1
2
1
2
2
2
2
1
1
2
1
1
4
(
)
3[
(1
)
(1
)]
E E
R
R
E
E
−
+
=
−
+
−
(59) (59) in which E1, E2, ν1, and ν2 denote the elastic modulus and Poisson's ratio of masses m1 and m2,
respectively, and R1 and R2 denote radii of the particles, respectively. 3.1.1 Model Description and Calculation The initial compression
displacement can be expressed as in which E1, E2, ν1, and ν2 denote the elastic modulus and Poisson's ratio of masses m1 and m2,
respectively, and R1 and R2 denote radii of the particles, respectively. The initial compression
displacement can be expressed as 1
2
2
2
0
1
2
1
2
3
0
1
2
9
(
) (
)
16
F
k
k
R
R
R R
+
+
=(
) (60) 1
2
2
2
0
1
2
1
2
3
0
1
2
9
(
) (
)
16
F
k
k
R
R
R R
+
+
=(
) (60) (60) where
2
1
1
1
1
k
E
−
=
and
2
2
2
2
1
k
E
−
=
(61) where
2
1
1
k
−
=
and
2
2
1
k
−
=
(61) where 2
1
1
1
1
k
E
−
=
and
2
2
2
2
1
k
E
−
=
(61) (61) Without loss of generality, i can be set to 0, and Eq. (56) can be expressed as Without loss of generality, i can be set to 0, and Eq. 3.1.1 Model Description and Calculation Thus, the residual r can be expressed as 3
3
2
+
+
2
2
1
1
2
1
3
3
2
+
+
2
2
2
2
2
2
1
( ,
,
,
)
(
)
(
( ,
,
,
)
(
)
T
g
S
g
T
g
S
g
r
Q
m C G q
r
Q
m C G q
=
−
+
=
−
+
)
(
)
(68) (68) where 0
2
1
(
)
T
T
S
g
S
g
C q
C q
=
−
−
and
1
0
1
1
2
(
)
T
T
S
g
S
g
C D q
C q
=
−
−
(69) 0
1
1
2
(
)
T
T
S
g
S
g
C q
C D q
−
=
−
−
,
0
2
1
(
)
T
T
S
g
S
g
C q
C q
=
−
−
and
1
0
1
1
2
(
)
T
T
S
g
S
g
C D q
C q
=
−
−
(69) (69) Based on the procedure in Fig. 1, harmonic balance residuals R1 and R2 can be calculated by FFTs of r1
and r2, respectively. The Jacobian matrix JQ, Jω, and Jμ can be calculated by following the procedure
given in Eq. (38) to Eq. (41), as shown in Appendix A. 3.1.1 Model Description and Calculation The initial guess of the solution Ug can be expressed as g
m
g
U
C Q
=
(65) g
m
g
U
C Q
=
(65)
where (65) g
m
g
U
C Q
=
(65)
where
1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
(66) where 1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
(66) 1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
(66) (66) is a guess of
1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
, in which is a guess of
1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
, in which s a guess of
1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
, in which 1
1
1
1
1
2
1
2
2
2
2
2
2
1
2
1
[0 , ,
,
,
,
,
]
[0 ,
,
,
,
,
,
]
T
g
M
M
T
g
M
M
q
A
a
a
b
b
q
a
a
a
b
b
=
=
(67) 1
1
1
1
1
2
1
2
2
2
2
2
2
1
2
1
[0 , ,
,
,
,
,
]
[0 ,
,
,
,
,
,
]
T
g
M
M
T
g
M
M
q
A
a
a
b
b
q
a
a
a
b
b
=
=
(67) (67) and A represents a presetting amplitude of the first-order cosine function of u1, which controls the
nonlinearity strength. Vibrations of the two particles make the constant components of qg1 and qg2
equal to zero, which are dropped in the following calculation. Thus, the residual r can be expressed as and A represents a presetting amplitude of the first-order cosine function of u1, which controls the
nonlinearity strength. Vibrations of the two particles make the constant components of qg1 and qg2
equal to zero, which are dropped in the following calculation. 3.1.2 Steady-State Responses with Given Wave Vectors When the wave vector of a wave problem is given, Newton’s iterative formula shown in Eq. (53) can be used to find solutions of q1, q2, and ω. Since the coefficient of the 1st-order cosine function of u1,
i e the first element of Q is given as A and the frequency is unknown the formula is converted to be used to find solutions of q1, q2, and ω. Since the coefficient of the 1st-order cosine function of u1,
i.e. the first element of Q, is given as A and the frequency is unknown, the formula is converted to (70) xJ
x
R
= −
(70) where x are variables consisting of the frequency and coefficients of the rest of the basis functions: sisting of the frequency and coefficients of the rest of the basis functions: 1
1
1
2
2
2
2
1
1
1
[ ,
, ,
,
,
,
,
,
,
]
T
M
M
M
M
x
a
b
b
a
a
b
b
=
(71) (71) in which the first element of the coefficient vector Q, is replaced by the frequency ω, Jx is the Jacobian
matrix of x, in which the first column vector of JQ is replaced by Jω, and an increment of x is denoted
by Δx. Convergence analysis of basis functions is carried out for the proposed IHB method at different
strengths of nonlinearities. Frequencies of steady-state wave responses with different wave vectors
and A=0.99δ0 are calculated by different orders of basis functions, as shown in Table 1. The amplitude
A is used to control nonlinearity strength, and A=0.99δ0 yields a strong nonlinearity. Results show that
frequencies calculated with low orders of basis functions (M less than seven) cannot converge in some
cases. When M is higher (M = 7 and 9), frequencies of all cases will converge and the resultant
responses can be accurate. Convergence rates are different with wave vectors. For example, the
difference between frequencies with M=5 and M=7 is 3.8 Hz when μ=0.3, and the value is 0.1 Hz
when μ=0.6. To secure convergence for all wave vectors, it is necessary to use high-order basis
functions. Table 1. Frequencies (kHz) of steady-state waves with different orders M when A=0.99δ0. Table 1. Frequencies (kHz) of steady-state waves with different orders M when A=0.99δ0. 3.1.2 Steady-State Responses with Given Wave Vectors μ
0.3
0.6
0.9
1.2
1.5
2.1
M=1
0.6002
1.1932
1.7706
2.3245
2.8259
3.5886
M=3
0.6127
1.2231
1.8160
2.3721
2.8852
3.5776
M=5
0.6192
1.2265
1.8162
2.3732
2.8898
3.5994
M=7,9
0.6230
1.2266
1.8163
2.3733
2.8899
3.6047 Computing efficiency of the improved IHB method is compared with that of traditional IHB
methods. At the same condition (A=0.99δ0 and μ=0.9), values of calculation time in MATLAB with
use of different orders as M=1, 3, 5, 7 are shown in Table 2. Results show that calculation time of a
traditional IHB method and that of the improved IHB method are close when a low order of basis
functions (M =1) is used. With the order increasing, calculation time of the improved IHB method is
almost unchanged and still short (less than 0.4s). However, calculation time of the traditional IHB
method increases exponentially, since the number of integration increases exponentially with the order
of basis functions. For example, calculation time of the improved IHB method with M =7 is 0.35s, and
that of the traditional IHB method is 66.81s. A nonlinear multi-DoF wave problem requires high-order
truncated Fourier series to obtain converged steady-state responses. Thus, the method shown in the
work has the advantage of dealing with the complex multi-DoF wave problems. Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9
M
1
3
5
7
Improve IHB
0.366949
0.343543
0.302675
0.357626
Traditional IHB
0.752322
3.917901
8.157872
66.81462 Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9 Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9 Dispersion curves are shown in Fig. 3 when different truncated orders of Fourier series are used
for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A= 0.99δ0) cases. When A= 0.1δ0, dispersion
curves with M=5 and M=9 are overlapped but are different from the curve with M=1. Moreover, when
the wave vector is large (μ>2.7), no solution can be calculated with use of low-order basis functions
with M=1 and M=5, since the calculation does not converge. For the strong nonlinearity case, the
region where solutions cannot be calculated with low-order basis functions is even larger (μ>2.1). Thus, it is also important to use high-order basis functions to ensure existence of solutions. Dispersion
curves with weak and strong nonlinearities are different. 3.1.2 Steady-State Responses with Given Wave Vectors When the value of the wave vector is small (lower than 1.5), frequencies at different nonlinearities are very close. When the value is large,
dispersion curves are separated, where the frequency decreases as the nonlinearity increases. Figure 3. The dispersion curves with different orders M when A=0.1δ0 and A=0.99δ0 Figure 3. The dispersion curves with different orders M when A=0.1δ0 and A=0.99δ0 Dispersion curves of optical (higher) and acoustic (lower) waves together constitute the bandgap
of the system, which are shown in Fig. 4 for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A=
0.99δ0) cases. The shaded part is the stopband, where waves cannot travel when their frequencies are
those in the region. Red dashed lines form the stopband for the strong nonlinearity case and blue
dashed lines form that for the weak nonlinearity case. As the nonlinearity increases, the stopband will
move to the lower-frequency region. Meanwhile, the stronger the nonlinearity is, the larger the region
of the stopband is. Figure 4. Bandgap properties of 1D diatomic lattice in the Hertz contact model Figure 4. Bandgap properties of 1D diatomic lattice in the Hertz contact model 3.1.3 Steady-state Responses with Given Frequencies When the frequency of a wave problem is fixed, Eq. (54) is used as Newton's iterative formula. Similarly, with A given as the first element of Q, the formula is changed to xJ
x
R
= −
(72) (72) where 1
1
1
2
2
2
2
1
1
1
[ ,
, ,
,
,
,
,
,
,
]
T
M
M
M
M
x
a
b
b
a
a
b
b
=
(73) (73) in which the first element of the coefficient vector Q, is replaced by the wave vector 𝜇, and Jx is the
Jacobian matrix of x, in which the first column vector of JQ is replaced by Jμ. At different frequencies, wave vectors of steady-state responses of acoustic waves with a strong
nonlinearity (A=0.99δ0) are calculated with use of different orders of basis functions, which are shown
in Table 3. Results show that wave vectors can converge when the order of basis functions is larger
than or equal to 3, which means that steady-state wave responses solved with fixed frequencies can
converge faster (M ≥3) than those solved with fixed wave vectors (M ≥7). Table 3. Wave vectors of steady-state waves with the different orders as M=1,3,5,7 when A=0.99δ0
f (kHz)
0.5
1
1.5
2
2.5
3
3.5
4
M=1
0.25
0.50
0.76
1.02
1.30
1.61
2.02
2.45
M=3
0.24
0.49
0.74
1.00
1.27
1.57
1.96
2.76
M=5,7
0.24
0.49
0.74
1.00
1.27
1.57
1.96
2.76 Table 3. Wave vectors of steady-state waves with the different orders as M=1,3,5,7 when A=0.99δ0 Dispersion curves of acoustic waves obtained by fixed wave vectors and fixed frequencies are
compared in Fig. 5 for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A= 0.99δ0) cases. Results
from the two methods are the same, which verifies the accuracy of the new method that solves the
wave problem with fixed frequencies, and the new method has a faster convergence rate. Figure 5. Comparison between dispersion curves of acoustic waves solved with fixed wave vectors Figure 5. Comparison between dispersion curves of acoustic waves solved with fixed wave vectors and fixed frequencies 3.2.1 Model Description and Calculation In this work, the proposed method is used to study a 1D diatomic lattice model with a cubic spring
[38]. A unit of the diatomic chain model consists of two different masses, m1 and m2 (Fig. 6). The
nonlinearity of the 2-DoF system gets stronger as displacements of particles get larger. Figure 6. Schematic diagram of a 1D diatomic lattice with cubic spring. Figure 6. Schematic diagram of a 1D diatomic lattice with cubic spring. In Fig. 6, k1 and k2 denote stiffness coefficients of two types of linear springs in the diatomic
chain, and Γ1 and Γ2 denote coefficients of third-order polynomials of two nonlinear springs. The
system displacement can be written as ( )
( )
( )
1
2
,
i
T
i
i
j
U
u
u
=
(74) ( )
( )
( )
1
2
,
i
T
i
i
j
U
u
u
=
(74 (74) where i denotes the location of the unit. When i=0, the governing equation of the system can be expressed
as where i denotes the location of the unit. When i=0, the governing equation of the system can be expressed
as where i denotes the location of the unit. 3.2.1 Model Description and Calculation When i=0, the governing equation of the system can be expressed
as as 1
1
1
1
(
,
)
(
,
,
)
0
L
NL
j
j
j
j
j
j
j
j
j
mu
Ku
f
u
u
f
u
u
u
−
−
+
+
+
=
(75) (75) where 1
2
0
0
m
m
m
=
,
1
2
1
2
1
2
k
k
k
K
k
k
k
+
−
=
−
+
,
1
2
( )
( )
j
u
t
u
u
t
=
,
1
1
1
1
2
1
2
( )
(
,
)
( )
L
j
j
j
u t
f
u
u
k
u
t
−
−
= −
and
3
1 3
1
1
1
1
2
2
1
2
3
1 3
1
2
1
2
2
1
(
)
(
)
(
,
,
)
(
)
(
)
NL
j
j
j
j
u
u
u
u
f
u u
u
u
u
u
u
−
−
−
+
−
=
−
+
−
(76) 1
2
0
0
m
m
m
=
,
1
2
1
2
1
2
k
k
k
K
k
k
k
+
−
=
−
+
,
1
2
( )
( )
j
u
t
u
u
t
=
, 1
1
1
1
2
1
2
( )
(
,
)
( )
L
j
j
j
u t
f
u
u
k
u
t
−
−
= −
and
3
1 3
1
1
1
1
2
2
1
2
3
1 3
1
2
1
2
2
1
(
)
(
)
(
,
,
)
(
)
(
)
NL
j
j
j
j
u
u
u
u
f
u u
u
u
u
u
u
−
−
−
+
−
=
−
+
−
(76) (76) With an initial guess
1
2
[
,
]
T
T
T
g
g
g
Q
q
q
=
, the residual of the governing equation can be expressed as 2
3
3
1
1
2
1
1
2
1
1
2
2
1
2
1
1
2
2
1
1
2
2
3
3
2
2
2
2
1
2
2
1
1
2
1
1
1
2
1
2
2
1
1
(
)
(
)
(
)
(
)
(
)
(
)
T
T
T
T
T
T
T
T
S
g
S
g
S
g
S
g
S
g
S
g
S
g
S
g
T
T
T
T
T
T
T
T
S
g
S
g
S
g
S
g
S
g
S
g
S
g
S
g
r
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
r
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
−
−
=
+
+
−
−
+
−
+
−
=
+
+
−
−
+
−
+
−
2
3
3
1
1
2
1
1
2
1
1
2
2
1
2
1
1
2
2
1
1
2
2
3
3
2
2
2
2
1
2
2
1
1
2
1
1
1
2
1
2
2
1
1
(
)
(
)
(
)
(
)
(
)
(
)
T
T
T
T
T
T
T
T
S
g
S
g
S
g
S
g
S
g
S
g
S
g
S
g
T
T
T
T
T
T
T
T
S
g
S
g
S
g
S
g
S
g
S
g
S
g
S
g
r
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
r
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
−
−
=
+
+
−
−
+
−
+
−
=
+
+
−
−
+
−
+
−
(77) Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFT Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs of r1 and r2, respectively. frequencies Bandgap properties of hardened spring (Γ=0.05), softened spring (Γ=-0.05), and linear spring
(Γ=0) cases are shown in Fig. 8. Three curves at a low-frequency region are dispersion curves of
acoustic waves, and the other three are those of optical waves. A part formed by two lines with the
same color is a stopband region of a type of springs. Compared with a linear spring, the stopband
region of the hardened spring is higher, and that of the softened spring is lower. Figure 8. Bandgap properties of different spring models Figure 8. Bandgap properties of different spring models 3.2.1 Model Description and Calculation Jacobian matrices JQ, Jω, and Jμ can be calculated by following the procedure
given in Eq. (38)- Eq. (41), as shown in Appendix B. A set of the model parameters are given in Table 4, which will be used in the calculation and
analysis of the diatomic chain system. The frequency ωn is a reference frequency that is given in [36],
and the ratio of the system frequency to the reference frequency
n
=
is used as a dimensionless
frequency in this problem. Table 4. Cubic spring model parameters [38]
m1
m2
k1
k2
Γ1
Γ2
ωn
1
2
1
5
±0.05
±0.05
2.45 Table 4. Cubic spring model parameters [38] Table 4. Cubic spring model parameters [38] Steady-state responses of given wave vectors and frequencies with Γ1,2=0.05 are calculated with
use of different orders of basis functions, which are shown in Table 5 and Table 6, respectively. Results
show that the convergence rate of given frequencies is faster (M ≥3) than that of given wave vectors
(M ≥5), which is consistent with that of the wave problem in Section 3.1. Table 5. of steady-state waves with different orders M and different wave vectors μ when Γ=0.05
μ
0.3
0.6
0.9
1.2
1.5
1.8
2.1
M=1
0.0646
0.1299
0.1969
0.2675
0.3430
0.4837
0.6464
M=3
0.0646
0.1301
0.1967
0.2657
0.3397
0.4250
0.5638
M=5,7
0.0647
0.1302
0.1965
0.2640
0.3326
0.4040
0.4653
Table 6. Wave vectors of steady-state waves with different orders M and different when Γ=0.05
0.1
0.3
0.5
0.7
0.9
1.1
1.3
1.5
M=1
0.19
0.56
0.83
1.30
1.67
2.03
2.41
2.79
M=3,5
0.19
0.56
0.83
1.30
1.67
2.03
2.41
2.79 Table 5. of steady-state waves with different orders M and different wave vectors μ when Γ=0.05 Dispersion curves solved with fixed wave vectors and fixed frequencies are shown in Fig. 7 for
hardened spring (Γ=0.05), softened spring (Γ=-0.05), and linear spring (Γ=0) cases. Results show that
dispersion curves obtained by the two methods are the same. As wave vectors increase, frequencies of
hardened and softened nonlinear springs are higher and lower than those of linear springs, respectively. Figure 7. Comparison between dispersion curves solved with fixed wave vectors and
f
i Figure 7. Comparison between dispersion curves solved with fixed wave vectors and
frequencies Figure 7. Comparison between dispersion curves solved with fixed wave vectors and 4. Conclusion An algorithm based on an improved IHB method is developed to obtain steady-state solutions of general
multi-DoF wave propagation problems with strong nonlinearities. In this algorithm, no numerical
integration is needed to obtain residuals and Jacobian matrices, which are most time-consuming procedures in traditional IHB methods. Meanwhile, use of a delay matrix operator enables to decouple
wave vectors from basis functions, which significantly reduces the number of basis functions, and high-
order basis functions are able to be employed in this method to handle strong nonlinearities. Meanwhile,
the method can solve a nonlinear wave problem when either the frequency or wave vector is given, which
makes the method more adaptive to different applications. Results of examples show advantages of the
method in calculation efficiency and accuracy when a wave problem with strong nonlinearities is solved. It is able to use the method to obtain dispersion curves for weak and strong nonlinearity cases, and results
show that strong nonlinearities can significantly change bandgaps. Acknowledgments We gratefully acknowledge support from the National Natural Science Foundation of China (No. U1930206). Author Contributions All authors contributed to the concept development and manuscript editing. Hongyu Wang, Xuefeng
Wang and Jian Zhao contributed to the development of the method, Jian Zhang contributed to method
validation, and Yu Huang contributed to analysis of wave characteristics. Competing Interests The authors declare that they have no conflict of interest. Funding This work was supported by the National Natural Science Foundation of China (No. U1930206). under Hertz contact law Substituting the dimensionless time variable
t
=
into Eq. (62) yields 2
3
3
2
1
2
2
1
2
2
3
3
2
2
2
2
2
1
2
(
)
(
)
(
)
(
)
d u
m
d
d u
m
d
+
+
+
+
=
−
=
−
(A1) (A1) The vectors u1 and u2 and their first-derivative, second-derivative, and time-delay terms can be
approximated by M-order Fourier functions: 1
1
2
2
( )
( )
T
S
T
S
u
C q
u
C q
=
=
,
1
1 1
2
1
2
( )
( )
T
S
T
S
u
C G q
u
C G q
=
=
,
1
2
1
2
2
2
( )
( )
T
S
T
S
u
C G q
u
C G q
=
=
and
1
1
1 1
1
2
1
2
( )
( )
T
S
T
S
u
C D q
u
C D q
−
−
=
=
(A2) (A2) respectively, where CS, q1, and q2 are (2M+1) ×1 vectors, G1, G2, D-1, and D1 are 2M+1 square matrices. espectively, where CS, q1, and q2 are (2M+1) ×1 vectors, G1, G2, D-1, and D1 are 2M+1 square matrices. Substituting Eq. (A2) into Eq. (A1), the governing equation can be expressed as 3
3
2
+
+
2
2
1
2
1
3
3
2
+
+
2
2
2
2
2
1
(
)
(
0
(
)
0
T
S
T
S
m C G q
m C G q
−
+
=
−
+
=
)
(
)
(A3) (A3) and ξ, η, and ξ1 in Eq. under Hertz contact law (A3) can be expressed as 0
1
1 2
(
)
T
T
S
S
C q
C D q
−
=
−
−
,
0
2
1
(
)
T
T
S
S
C q
C q
=
−
−
and
1
0
1 1
2
(
)
T
T
S
S
C D q
C q
=
−
−
(A4) (A4) The Jacobian matrix JQ can be calculated by following the procedure of Eq. (41). To obtain JQ in
this example, intermediate variables fDD, fD, and fj, j =-1, 0, 1 will be calculated first. For the second
derivative of U: 1
(2
1) (2
1)
2
(2
1) (2
1)
0
0
dd
M
M
DD
M
M
dd
f
f
f
+
+
+
+
=
(A5) (A5) the FFT of
F
U
is calculated first, where the FFT of
F
U
is calculated first, where the FFT of
F
U
is calculated first, where 2
1
2
2
0
0
m
F
U
m
=
(A6 2
1
2
2
0
0
m
F
U
m
=
(A6) (A6) Since every term in the matrix is a constant,
1
dd
f and
2
dd
f can be directly represented as 2
1
1
2
1
0
0
dd
m
f
m
=
and
2
2
2
2
2
0
0
dd
m
f
m
=
(A7) (A7) respectively. Since there is no first derivative of U, fD is a zero matrix. Data Availability The datasets generated during the current study are available from the corresponding author on
reasonable request. under Hertz contact law (40): 2
1
1
1
0
2
2
2
1
0
1
1
s
s
r
J
C
d
r
J
C
d
=
=
(A14)
where
1
1
2
1
2
1
2
2
1
1
1
3 ( )
(
)
2
3 ( )
(
)
2
T
S
g
T
S
g
r
C D Dq
r
C D Dq
−
= −
= −
(A15) 2
1
1
1
0
2
2
2
1
0
1
1
s
s
r
J
C
d
r
J
C
d
=
=
(A14) 2
1
1
1
0
2
2
2
1
0
1
1
s
s
r
J
C
d
r
J
C
d
=
=
(A14) (A14) where where 1
1
2
1
2
1
2
2
1
1
1
3 ( )
(
)
2
3 ( )
(
)
2
T
S
g
T
S
g
r
C D Dq
r
C D Dq
−
= −
= −
(A15) 1
1
2
1
2
1
2
2
1
1
1
3 ( )
(
)
2
3 ( )
(
)
2
T
S
g
T
S
g
r
C D Dq
r
C D Dq
−
= −
= −
(A15) (A15) nd Jμ can be obtained by FFT of Eq. (A15). and Jμ can be obtained by FFT of Eq. (A15). and Jμ can be obtained by FFT of Eq. (A15). under Hertz contact law (39): 2
1
1
1
0
2
2
2
1
0
1
1
s
s
r
J
C
d
r
J
C
d
=
=
(A12) (A12) where where where
1
1
2
1
2
T
S
g
r
m C G q
= 1
1
2
1
2
2
2
2
2
2
T
S
g
T
S
g
r
m C G q
r
m C G q
=
=
(A13) 1
1
2
1
2
2
2
2
2
2
T
S
g
T
S
g
r
m C G q
r
m C G q
=
=
(A13) (A13) and Jω can be simply calculated by FFT of Eq. (A13). The Jacobian matrix
1
2
[
,
]
T
T
T
J
J
J
=
can be
calculated by the procedure in Eq. (40): and Jω can be simply calculated by FFT of Eq. (A13). The Jacobian matrix
1
2
[
,
]
T
T
T
J
J
J
=
can be
calculated by the procedure in Eq. under Hertz contact law Time delay terms fj, j= -1,0,1 are 1
(2
1) (2
1)
1
(2
1) (2
1)
(2
1) (2
1)
0
0
0
M
M
T
M
M
M
M
f
f
−
+
+
−
+
+
+
+
=
,
0
0
1
2
0
0
0
3
4
T
T
T
T
f
f
f
f
f
=
and
(2
1) (2
1)
(2
1) (2
1)
1
1
(2
1) (2
1)
0
0
0
M
M
M
M
T
M
M
f
f
+
+
+
+
+
+
=
(A8) (A8) According to Section 2.3,
1
Tf −,
0
f and
1
Tf are Toplitz forms of coefficient vectors that are obtained by According to Section 2.3,
1
Tf −,
0
f and
1
Tf are Toplitz forms of coefficient vectors that are obtained by
FFT of
1
F
,
F
and
1
F
, respectively, where According to Section 2.3,
1
Tf −,
0
f and
1
Tf are Toplitz forms of coefficient vectors that are obtained by
FFT of
1
F
U
−
,
F
U
and
1
F
U
, respectively, where According to Section 2.3,
1
Tf −,
0
f and
1
Tf are Toplitz forms of coefficient vectors that are obtained by
F
F
F
FFT of
1
F
U
−
,
F
U
and
1
F
U
, respectively, where 1
2
1
3
0
( )
2
0
0
F
U
−
−
=
(A9) 1
2
1
3
0
( )
2
0
0
F
U
−
−
=
(A9)
1
1
1
2
2
2
1
1
1
2
2
2
1
3
3
3
( )
( )
( )
2
2
2
3
3
3
( )
( )
(
)
2
2
2
F
U
+
−
=
−
+
(A10)
1
1
2
0
0
3
( )
0
2
F
U
=
−
(A11) 1
2
1
3
0
( )
2
0
0
F
U
−
−
=
(A9)
1
1
1
2
2
2
1
1
1
2
2
2
1
3
3
3
( )
( )
( )
2
2
2
3
3
3
( )
( )
(
)
2
2
2
F
U
+
−
=
−
+
(A10)
1
1
2
0
0
3
( )
0
2
F
U
=
−
(A11) (A9) 1
1
1
2
2
2
1
1
1
2
2
2
1
3
3
3
( )
( )
( )
2
2
2
3
3
3
( )
( )
(
)
2
2
2
F
U
+
−
=
−
+
(A10)
1
1
2
0
0
3
( )
0
2
F
U
=
−
(A11) (A10) (A11) The Jacobian matrix
1
2
[
,
]
T
T
T
J
J
J
=
can be calculated by the procedure in Eq. Appendix B: Jacobian matrices of 1D diatomic lattice with
cubic springs Incorporating the dimensionless time variable
t
=
into Eq. (75) yields 2
2
1
3
1 3
1
1
1
2
1
1
2
2
2
1
1
2
2
1
2
2
2
2
1
3
1 3
2
2
1
2
2
1 1
2
1
1
2
1
2
2
1
2
(
)
(
)
(
)
0
(
)
(
)
(
)
0
d u
m
k
k u
k u
k u
u
u
u
u
d
d u
m
k
k u
k u
k u
u
u
u
u
d
−
−
+
+
−
−
+
−
+
−
=
+
+
−
−
+
−
+
−
=
(B1) (B1) Substituting Eq. (A2) into Eq. (B1), the governing equation can be expressed as Substituting Eq. (A2) into Eq. (B1), the governing equation can be expressed as 2
3
3
1
2
1
1
2
1
1
2
2
1
2
1
1
2
2
1
1
2
2
3
3
2
2
2
1
2
2
1
1
2
1
1
1
2
1
2
2
1
1
(
)
(
)
(
)
0
(
)
(
)
(
)
0
T
T
T
T
T
T
T
T
S
S
S
S
S
S
S
S
T
T
T
T
T
T
T
T
S
S
S
S
S
S
S
S
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
m
C G q
k
k C q
k C q
k C D q
C q
C q
C q
C D q
−
−
+
+
−
−
+
−
+
−
=
+
+
−
−
+
−
+
−
=
(B2) (B2) The Jacobian matrix of Q, JQ, can be calculated by the procedure in Eq. (41). Appendix B: Jacobian matrices of 1D diatomic lattice with
cubic springs (39), where The Jacobian matrix of ω, Jω, can be calculated by the procedure in Eq. (39), where 1
1
2
1
2
2
2
2
2
2
T
S
g
T
S
g
r
m C G q
r
m C G q
=
=
(B4) (B4) According to Section 2, the Jacobian matrix of ω can be calculated by the FFT of Eq. (B4). According to Section 2, the Jacobian matrix of ω can be calculated by the FFT of Eq. (B4). The Jacobian matrix of μ, Jμ, can be calculated by the procedure in Eq. (40), where 2
1
2
1
2
2
1
1
2
1
2
2
2
2
1
1
2
2
1
1
1
1
3
(
) (
)
3
(
) (
)
T
T
T
T
S
g
S
g
S
g
S
g
T
T
T
T
S
g
S
g
S
g
S
g
r
k C D Dq
C q
C D q
C D Dq
r
k C D Dq
C q
C D q
C D Dq
−
−
−
= −
−
−
= −
−
−
(B5) (B5) According to Section 2, the Jacobian matrix of μ can be calculated by the FFT of Eq. (B5). Appendix B: Jacobian matrices of 1D diatomic lattice with
cubic springs The parameters can
be expressed as 2
1
2
2
0
0
m
F
U
m
=
,
1 2
2
2
1
2
1
0
3
(
)
0
0
k
u
u
F
U
−
−
−
−
−
=
,
1 2
1
2
2
2
1
0
0
3
(
)
0
F
k
u
u
U
=
−
−
−
and
1
1
2
1 2
2
1
2
1
2
1
1
2
2
1
2
1
1
1
2
2
2
1 2
2
2
1
1
2
1
1
2
1
2
1
2
2
1
1
2
3
(
)
3
(
)
3
(
)
3
(
)
3
(
)
3
(
)
F
F
u
u
k
k
u
u
u
u
k
u
u
F
F
F
u
k
u
u
k
k
u
u
u
u
u
u
−
+
+
−
+
−
−
−
−
=
=
−
−
−
+
+
−
+
−
(B3) 2
1
2
2
0
0
m
F
U
m
=
,
1 2
2
2
1
2
1
0
3
(
)
0
0
k
u
u
F
U
−
−
−
−
−
=
,
1 2
1
2
2
2
1
0
0
3
(
)
0
F
k
u
u
U
=
−
−
−
F
F
and
1
1
2
1 2
2
1
2
1
2
1
1
2
2
1
2
1
1
1
2
2
2
1 2
2
2
1
1
2
1
1
2
1
2
1
2
2
1
1
2
3
(
)
3
(
)
3
(
)
3
(
)
3
(
)
3
(
)
F
F
u
u
k
k
u
u
u
u
k
u
u
F
F
F
u
k
u
u
k
k
u
u
u
u
u
u
−
+
+
−
+
−
−
−
−
=
=
−
−
−
+
+
−
+
−
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https://openalex.org/W3139004221 | https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/265087/1/978-3-030-66262-2_6.pdf | English | null | MOVING: A User-Centric Platform for Online Literacy Training and Learning | Progress in IS | 2,021 | cc-by | 75,397 | Claudia Koschtial
Thomas Köhler
Carsten Felden Editors e-Science e-Science Open, Social and Virtual Technology for
Research Collaboration Progress in IS Progress in IS More information about this series at http://www.springer.com/series/10440 Progress in IS “PROGRESS in IS” encompasses the various areas of Information Systems in theory
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Claudia Koschtial
TU Bergakademie Freiberg
Freiberg, Germany
Carsten Felden
TU Bergakademie Freiberg
Freiberg, Germany Thomas Köhler
Media Center
TU Dresden
Dresden, Germany ISSN 2196-8705
ISSN 2196-8713 (electronic)
Progress in IS
ISBN 978-3-030-66261-5
ISBN 978-3-030-66262-2 (eBook)
https://doi.org/10.1007/978-3-030-66262-2 © The Editor(s) (if applicable) and The Author(s) 2021. This book is an open access publication. Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International
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The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland This Springer imprint is published by the registered company Springer Nature Switzerland A The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Introduction This publication, e-science: The enhanced science, is a collection of conference
papers, reviewed and selected in a double-blind review process by a distinguished
reviewer committee. From the very beginning when John Taylor introduced the term,
e-science did not only comprise infrastructure as an enabler of scientific discovery,
but also “global collaboration in key areas of science” (Taylor 1999). As computer
technologies and digital tools pervade the academic world, it is time to ask what
changes are implied when an “e” is added to science. What is primarily discussed in
Germany and Great Britain under the term e-science corresponds in the USA to the
concept of cyber infrastructures and in Australia to the concept of e-research. More recently the discourse about e-science has been dealing with collaborative
research that is based on a comprehensive digital infrastructure. This infrastructure
both ultimately integrates all relevant resources for a research domain in a digital
format and provides tools for processing such data. In computing-intensive research
scenarios, e-science includes distribution of computing capacities, supporting collab-
orative processes of a rather inter-institutional character, such as (inter)national
networks. The open innovation approach creates new platforms for developing and
publishing research results. For example the MOVING platform (http://moving-
project.eu/moving-platform/ cf. Vagliano et al. 2018) supports new collaborative
research practices and has become a resource for further research. In this sense and in addition to the technological aspect (virtualization of hard-
ware),e-sciencealsohasasocialandpolitics-of-scienceaspect(cooperativeresearch,
reusability of data and interoperability of digital tools). Although there is the will
to expand e-science methods into the wider economy and society, this development
is occurring slowly. New skill sets are being acquired in the e-humanities, virtual
engineering or visual analytics (Redecker and Punie 2017; Köhler 2018). Yet e-
science also comprises open access, e-learning and grid computing; these changes
are enabled by state funding and public interest. As a result, the concept of e-science
continues to generate new concepts for particular disciplines such as e-geography,
e-humanities, e-medicine or e-engineering. The 2014 International Conference on Infrastructures and Cooperation in e-
Science and e-Humanities reflected the broad ongoing discussion concerning the
changesaffectingresearchandteachinginuniversitiesnowadays.Itaddressedcurrent v vi
Introduction
Section 3:
IT
perspectives
Section 2:
Organizational &
sociotechnical
perspectives
Section 4:
Cases &
experiences
Section 1: Definition and terms
Section 5: Future prospects
Fig. 1 Structure of “e-science: the enhanced science” Introduction vi Fig. 1 Structure of “e-science: the enhanced science” questionsandsolutionsrelatedtotechnologiesorapplicationsaswellastheirimplica-
tionsfortheconductofscience.Itinvestigateddigitallyenhancedacademicinitiatives
from technological and socio-scientific perspectives. Introduction This volume is subdivided into five sections representing different perspectives
on e-science, as seen in the figure below. The first section introduces the book and
reviews the literature concerning the definition of e-science. Section 2 provides orga-
nizational and socio-technical perspectives, especially the use of web 2.0 tools from
an individual viewpoint and the successful implementation of such tools from an
organizational viewpoint. As e-science of course relates to information technology,
Section 3 covers IT perspectives, and Section 4 presents domain-specific cases and
experiences. Finally, the proceedings close with future prospects (Fig. 1). The introductory section of the proceedings Digital research infrastructure: an
overview starts out with C. Koschtial’s contribution, an analysis of the terms covered
by the field of digital research, that is, e-science itself, and related terms like cyber-
science or science 2.0. As e-science is a socio-technical system, it can be approached
from the perspective of the human user, the task or the technology, as identified by
Heinrich (1993, pp. 8). The aim is to identify the dominant approach to e-science, to
distinguish between the different terms and identify how the terms reflect changes
in the prevailing research streams. Section 2 deals with individual usage of tools and organizational enablement of
this. The first paper of the second section, authored by T. Köhler, C. Lattemann
and J. Neumann, is entitled Organizing Academia Online: Organization models in
e-learning Versus e-science Collaboration, identifies forms of organizational gover-
nance enabling effective e-collaboration for scientists. Organizational governance Introduction vii captures (social, output or behavioural) controls that are suitable for effective e-
collaborationinscientificcommunities.Basedonthreecasestudies,theauthoridenti-
fies IT as a key factor in successful virtualization and concludes that there is a need for
virtualized organization models which refer to processes and structure. The second
contributionfrominthissectionbyB.MohamedandT.Köhlerinvestigatesindividual
researchers and their will to use web 2.0 tools. In the third paper, focus on concep-
tualizing and validating digital research collaboration between novice researchers. Based on the FISH model, an online survey of 140 novice researchers was carried out
and analysed using Partial Least Squares for the analysis of the data. One main result
is that successful usage of online tools enhances the belief in web 2.0 as a useful
instrument. The second main result is that benefits experienced by sharing enhance
motivation for collaboration. Introduction One of the most important elements in search content is metadata, which is
shown to be useful for finding data and algorithms. Section 4 presents cases and experiences in the field of e-science. In the first
paper, M. Heidari and O. Arnold show that fully digitalized scholarly activities such
as online examinations can have a high variability, which presents a manageability
challenge. The authors analyse the variability of legally analogue exam processes and
prove the necessity for establishing management models. The authors of the second
paper, Designing External Knowledge Communication in a Research Network: The
Case of Sustainable Land Management, examine factors influencing the knowl-
edge communication process. The aim is to find factors in successful communi-
cation between researchers and stakeholders as a representation of collaboration. The authors describe steps that need to be taken to enable successful communica-
tion: formulate the problem, analyse the situation, define communication objectives,
identify target groups, formulate the message and develop a communication strategy
and activities. S. Münster’s paper, Researching Scientific Structures Via Joint Author-
ships: The Case of Virtual 3D Modelling in Humanities is the last in Section 4. This
case study of scientific structures is an analysis of co-authoring for a defined set
of conferences. The topics are interdisciplinarity, number of publications and co-
authoring, and multipliers. The author identifies multipliers for knowledge in the
field of 3D modelling. Finally, in Section 5, A. Skulimowski presents a Delphi study trying to shed
some light on future developments in e-science, especially in selected IT technolo-
gies. He focuses on two emerging systems, brain-computer interfaces and global
expert systems that process databases, communication and unstructured formats like
videos. These systems may lead to collective rather than collaborative research, as
one researcher cannot manage the volume of information alone anymore. Another
scenario based on the automated data analyses is that papers can be produced almost
completely with minimal human intervention. In any case, Skulimowski paints an
interesting picture of the future of science. We hope that you will find this an interesting collection of a wide range of
perspectives, which contributes to your ideas and visions of e-science. Introduction Based on an online study comparing Germany as a
whole with the federal state of Saxony, the final contribution of the second section
authored by S. Albrecht, C. Minet, S. Herbst, D. Pscheida and T. Köhler presents
research into the extent to which digital tools are adopted. One finding is that certain
tools are now used by more than the half of the scientists in their daily professional
life, but web 2.0 tools like microblogs and social networking sites are used far less
often. In Section 3, the focus is on digital tools or information infrastructures, which
have not been considered yet. The first paper contributed by O. Schonefeld, M. Stührenberg and A. Witt in this section discusses important guidelines for research
infrastructures, which are used to support teaching, research and young researchers. Regarding IT, research infrastructures should be maintained in collaboration between
organizations. To reduce costs, energy efficient or green, technologies should be
considered, and secure networks are needed enabling to minimize risks. Concerning
the aspect of information infrastructure, the authors stress the relevance of data
repositories and publication servers in a format that allows the stored documents or
data to be used in the long term. Further important considerations regarding research
infrastructures include copyright laws with specific national regulations and personal
data protection. Accordingly, the authors identify a need for an IT strategy and
corresponding roles such as that of data protection officer in organizations providing
a research infrastructure. The second paper authored by A. Apaolaza, T. Backes, S. Barthold, I. Bienia, T. Blume, C. Collyda, A. Fessl, S. Gottfried, P. Grunewald, F. Günther, T. Köhler, R. Lorenz, M. Heinz, S. Herbst, V. Mezaris, C. Nishioka, A. Pournaras, V. Sabol, A. Saleh, A. Scherp, U. Simic, A.M.J. Skulimowski, I. Vagliano, M. Vigo, M. Wiese
and T. Zdolšek Draksler introduces MOVING: A User-Centric Platform for Online
Literacy Training and Learning. The platform enables the usage of machine learning
for searching, organizing and managing unstructured data sources. The data sources
comprise but are not limited to publications, videos or social media. The contribution
presentsthewebplatformfromauser-centredperspectiveinordertogiveanoverview
of the functionalities. The final paper of Section 3 from G. Heyer and V. Boehlke presents a research
infrastructure called CLARIN-D. This is a web-based platform for the e-humanities,
used to collect and provide digital content, with the services needed to store the viii Introduction content. Acknowledgements First of all, the conference was part of the e-science Network of the Technische
Universität Bergakademie Freiberg, Technische Universität Dresden and Leipzig
University of Applied Sciences. This conference and the resulting publication have
been enabled and financially supported by the European Social Fund ESF and the
Saxon State Ministry of Science and Culture, whom we want to thank herewith. Additionally, we want to thank Dean Prof. Dr. Andreas Horsch for his financial
support in order to make the book available as open access publication. The editors especially want to thank all the authors whose contributions give
this volume its special quality, and for their patient support throughout the process ix Introduction of publication. Furthermore, we want to thank all reviewers for their helpful and
progress enabling comments, enhancing the quality of all contributions. We want to
thank Dominik Wuttke as well as Ilia Vershinin for their exact transfer of all the papers
to LNCS. For the language correction, we want to thank Dr. Kate Sotejeff-Wilson
for her support and quality assurance. We wish you, the readers, inspiring reading! We wish you, the readers, inspiring reading! Claudia Koschtial
Thomas Köhler
Carsten Felden Freiberg/Dresden, Germany
Spring 2020 Freiberg/Dresden, Germany
Spring 2020 Contents Understanding e-Science—What Is It About? . . . . . . . . . . . . . . . . . . . . . . . . 1
Claudia Koschtial
Organising Academia Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Thomas Köhler, Christoph Lattemann, and Jörg Neumann
The Fish Model: When Do Researchers Collaborate Online? . . . . . . . . . . 29
Bahaaeldin Mohamed and Thomas Köhler
The Use of Digital Tools in Scholarly Activities. Empirical Findings
on the State of Digitization of Science in Germany, Focusing
on Saxony . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida,
and Thomas Köhler
Digital Research Infrastructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Maik Stührenberg, Oliver Schonefeld, and Andreas Witt
MOVING: A User-Centric Platform for Online Literacy Training
and Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Aitor Apaolaza, Tobias Backes, Sabine Barthold, Irina Bienia,
Till Blume, Chrysa Collyda, Angela Fessl, Sebastian Gottfried,
Paul Grunewald, Franziska Günther, Thomas Köhler, Robert Lorenz,
Matthias Heinz, Sabrina Herbst, Vasileios Mezaris, Chifumi Nishioka,
Alexandros Pournaras, Vedran Sabol, Ahmed Saleh, Ansgar Scherp,
Ilija Simic, Andrzej M.J. Skulimowski, Iacopo Vagliano, Markel Vigo,
Michael Wiese, and Tanja Zdolšek Draksler
CLARIN-D: An IT-Based Research Infrastructure
for the Humanities and Social Sciences . . . . . . . . . . . . . . . . . . . . . . . . . . References Heinrich, L.J.: Wirtschaftsinformatik. Oldenbourg Verlag, München (1993) Köhler, T.: Research training for doctoral candidates in the field of education and technology. In:
Drummer, J., Hakimov, G., Joldoshov, M., Köhler, T., Udartseva, S. (eds.) Vocational Teacher
Education in Central Asia. Developing Skills and Facilitating Success. Springer, Berlin (2018)
Redecker, C., Punie, Y.: European framework for the digital competence of educators DigCompEdu. Publications Office of the European Union Luxembourg (2017) Köhler, T.: Research training for doctoral candidates in the field of education and technology. In:
Drummer, J., Hakimov, G., Joldoshov, M., Köhler, T., Udartseva, S. (eds.) Vocational Teacher
Education in Central Asia. Developing Skills and Facilitating Success. Springer, Berlin (2018) Redecker, C., Punie, Y.: European framework for the digital competence of educators DigCompEdu. Publications Office of the European Union, Luxembourg (2017) Taylor, J.: e-Science. http://www.e-science.clrc.ac.uk, https://web.archive.org/web/200102222
31418/, http://www.e-science.clrc.ac.uk/ (1999). Last Accessed 18 Feb 2020 Taylor, J.: e-Science. http://www.e-science.clrc.ac.uk, https://web.archive.org/we
31418/, http://www.e-science.clrc.ac.uk/ (1999). Last Accessed 18 Feb 2020 Vagliano, I., Guenther, F., Heinz, M., Apaolaza, A., Bienia, I., Breitfuss, G., Blume, T., Collyda, C.,
Fessl, A., Gottfried, S., Hasitschka, P., Kellermann, J., Köhler, T., Maas, A., Mezaris, V., Saleh,
A., Skulimowski, A.M.J., Thalmann, S., Vigo, M., Wertner, A., Wiese, M. & Scherp, A.: Open
innovation in the big data era with the MOVING platform: An integrated working and training
approach for data-savvy information professionals. IEEE MultiMedia 25, 3, 8–21, July–Sept. 2018 (2018) Contents . . . . 99
Gerhard Heyer and Volker Böhlke
Toward Process Variability Management in Online Examination
Process in German Universities: A State of the Art . . . . . . . . . . . . . . . . . . . 111
Maryam Heidari and Oliver Arnold xi Contents xii Designing External Knowledge Communication in a Research
Network The Case of Sustainable Land Management . . . . . . . . . . . . . . . . . 131
Thomas Köhler, Thomas Weith, Sabrina Herbst, and Nadin Gaasch
Researching Scientific Structures via Joint Authorships—The
Case of Virtual 3D Modelling in the Humanities . . . . . . . . . . . . . . . . . . . . . . 151
Sander Münster
Visions of a Future Research Workplace Arising from Recent
Foresight Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Andrzej M. J. Skulimowski Understanding e-Science—What Is It
About? Claudia Koschtial Abstract Our daily life has experienced significant changes in the Internet age. The emergence of e-science is regarded as a dramatic one for science. Wikis, blogs,
virtual social networks, grid computing and open access are just a brief selection
of related new technologies. In order to understand the changes, it is necessary to
define these aspects of e-science precisely. Right now, no generally used term or
common definition of e-science exists, which limits the understanding of the true
potential of the concept. Based on a well-known approach to science in terms of
three dimensions—human, task and technology—the author provides a framework
for understanding the concept which enables a distinctive view of its development. The concept of e-science emerged in coherence with the technological development
of web 2.0 and infrastructure and has reached maturity. This is impacting on the
task and human dimensions as in this context, the letter “e” means more than just
electronic. Keywords e-Science · Open access · Grid computing · Science 2.0 Keywords e-Science · Open access · Grid computing · Science 2.0 1
Introduction The “e” in combination with a number of well-known terms implies a transfor-
mation into online networks and the usage of information technologies, which has
evolved in both private and professional life. Science, in its most general meaning as
scholarship comprising all disciplines, has also been subject to this transformation. This development is being referred to as electronic/enhanced science, or e-science. The transformation may enable changes going beyond technology itself. According
to Luskin, the big e means more than just electronic (Luskin 2012). Fausto et al. (2012) stated this more precisely: “Increasing public interest in science information
in a digital and Science 2.0 era promotes a dramatically, rapid, and deep change
in science itself”. The goal of this paper is to review research as work in progress. C. Koschtial (B)
Technische Universität Bergakademie Freiberg, Freiberg, Germany
e-mail: claudia.koschtial@web.de 1 1 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_1 2 2 C. Koschtial The resulting literature analysis shows what and how science is changing due to the
impact of using online networks and information technology. The change in science can be traced back to the 1990s, when the concept of
collaborative laboratories (collaboratories) evolved (Bly et al. 1997, p. 1). In 1996,
the term cyberscience was sharpened by Nentwich (1999) who refers cyberscience
to research activity which scientists were increasingly carrying out in the developing
information and communication space. Taylor (1999) produced a definition close to
this one: “e-science is about global collaboration in key areas of science, and the
next generation of infrastructure that will enable it” and “e-science will change the
dynamic of the way science is undertaken”. The definitions mark just the beginning
of an ongoing transformation. Most recent aspects of e-science contain open access
or science 2.0, referring to the usage of web 2.0 technologies like social networks,
blogs or wikis. The cited definitions share some elements: activity of research, scien-
tists, infrastructure, collaboration, information and communication. Nevertheless, a
common definition does not yet exist, and more diverse terms have emerged since
the first occurrence of this concept. Understanding the potential and extent of the
change requires an analysis of the concept itself. The present research is an initial step
towards this, which can be used as a basis for designing a comprehensive framework
of the concept of e-science in order to support the work of scientists. 1
Introduction The remainder of the paper is as follows: the second section presents related work
and the research gap. The third section explains how the research has been carried
out and how the concept is going to be analysed in order to derive a definition. In
Sect. 4, the results of the analyses are presented, leading to a discussion in Sect. 5. 2
Related Work Science defines one possible way to make reality understandable. Leaving behind
myth and religion, the ancient Greek philosophy represented an early systematic
examination of the world. It dates from 2500 years ago, when the society transformed
in the search for education and elucidation. Schools evolved, so science was (and
still is) closely connected to teaching (Schülein and Reitze 2012, 31 p.) Nowadays, there is no common perception or description of the change comprised
by the term e-science (Yahyapour 2018, p. 369). The literature often deals with
open access or particular problems related to data availability. Shneiderman (2012,
p. 1349) stresses the potential for understanding and rethinking how a phenomenon
is analysed. He promotes methodologies that move away from laboratory to real-
world conditions, especially to analyse areas like “secure voting, global environ-
mental protection, energy sustainability, and international development” (Shnei-
derman 2012, p. 1349). Eastman approaches the underlying process of e-science
in terms of data analysis. He formulates an observational-inductive model in order
to reflect on Knowledge Discovery in Databases and Data Sensor High-Performance
Computing Models without a theoretical basis. His idea sounds promising, but he Understanding e-Science—What Is It About? 3 provides few arguments for it (Eastman et al. 2005, 67 p.). Work and related organisa-
tional aspects of science like group learning and cooperative processes are addressed
by Pennington (2011, 55 p.). The mentioned literature is exemplary of a search in three literature databases
(see Sect. 3.1). No general analysis of this area of discourse exists yet, so the usage
and definitions of the terms have not been analysed before. Scientific understanding
dependsheavilyonthesepapers,however.Inordertosharpentheconceptandidentify
discussed characteristics of e-science, the present authors performed the following
literature analysis. 3
Research Approach This section introduces the area of discourse and describes the applied methodology
in Sect. 3.1. The applied research framework is then proposed in Sect. 3.2. 3.1
Research Field and Methodology The research follows the method proposed by Fettke (2006, 257 p.). The research
process itself demands that researchers have increasingly complex knowledge, which
is usually beyond the borders of their own fields (Reinefeld 2005, p. 4). Two research
challenges can be identified: • The Internet can be used to search for and communicate information, but success
in identifying information is not guaranteed. • The vast amount of data is challenging to process in order to identify relevant
content. The mentioned challenges appear as well for the field of e-science. A couple of
terms being used in e-science comprise some or all the elements mentioned above. The ones which have been mentioned so far are: The mentioned challenges appear as well for the field of e-science. A couple of
terms being used in e-science comprise some or all the elements mentioned above. The ones which have been mentioned so far are: • e-science itself meaning electronic or digitally enhanced science (Hiller 2005,
p.5); • cyber infrastructure (Hey 2006); • e-research (University of Technology Sydney 2013); • cyberscience (Atkins 2005, 1 p.); and • science 2.0 (Leibnitz 2012). As these terms appear at different points in time, the meaning has to be reflected
on and trends need to be considered in order to understand the circumstances in
which they arose. Relevant literature was identified by searching the title, abstract
and keywords for the terms “e-science”, “eScience”, “e-research”, “eResearch”,
“science 2.0”, “cyberscience”, “cyberinfrasructure”, “grid computing” and “grid” 4
C. Koschtial
Fig. 1 Heirich’s human—task—technology framework (Heinrich 1993, p. 8) and its adaption to
the field of e-science 4 4 C. Koschtial Fig. 1 Heirich’s human—task—technology framework (Heinrich 1993, p. 8) and its adaption to
the field of e-science togetherwith“e-science”inthreedatabases:EBSCOAcademicSearch,ACMDigital
Library and IEEE XPlore. To increase the amount of results, Google Scholar was
also searched for titles in the period from 1994 to 2005. Digital humanities were
excluded as it refers solely to e-science in the field of humanities. 3.2
Research Framework A research framework is needed in order to identify the essence of the concept of
e-science and differences between the terms being used. Science 2.0 includes a range of topics. Shneiderman (2012, p. 1349) identified
research on sociotechnical systems as the basis for an increasing collaboration. Hein-
rich (1993, p. 8) regards sociotechnical information systems as composed of human,
task and technical dimensions; he sees such systems as open, complex and sophis-
ticated. Figure 1 shows the general framework created by Heinrich (left-hand side)
and its adaption to the context of e-science (right-hand side). Regarding the given definitions, some initial characteristics can be extracted:
scientists, information and communication, infrastructure, collaboration and
research. In order to reflect all aspects of e-science, collaboration is added to the
framework, as this was inherent in all definitions. Figure 2 shows the framework
used. 4
Results The literature search led to 148 definitions of the selected terms related to e-
science. The most frequent definition was “e-science” (43%), followed by “grid” 5 5 Understanding e-Science—What Is It About? Fig. 2 E-science framework including collaboration Fig. 2 E-science framework including collaboration (32%), “science 2.0” (9%), “cyberinfrastructure” (8%), “e-research” (7%) and
“cyberscience” (3%). Table 1 shows the number of definitions per year. Figure 3 shows the occurrence of these terms over time. In a second step, the authors analysed the development of the selected definitions
over time and investigated whether the dimensions of the framework were mentioned
in each definition. The following examples show key terms related to each dimension. • Technical dimension: • Technical dimension: – Web 2.0 technologies as a single technology; – Networks and infrastructure as a collaboration technology. • Task dimension: • Task dimension: • Human dimension: • Human dimension: – Researcher as human; – Virtual organisations like social networks. – Virtual organisations like social networks. The next step was to analyse the relations between the three dimensions, human, task
and technology. • Task dimension: – Publishing, analysing or teaching as single tasks; – Collaborative projects which may have an interdisciplinary focus. Table 1 Number of definitions per year
1998–2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
5
5
5
16
17
15
14
12
10
17
11
11
10 Table 1 Number of definitions per year
1998–2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
5
5
5
16
17
15
14
12
10
17
11
11
10 6
C. Koschtial
Fig. 3 Relative frequency of terms related to time 6
C. Koschtial
Fig. 3 Relative frequency of terms related to time C. Koschtial 6 6 Fig. 3 Relative frequency of terms related to time Fig. 3 Relative frequency of terms related to time 5
Discussion of Initial Results Figure 3 shows that terms like cyberscience or cyberinfrastructure disappeared over
time. The presence of the term e-science is relatively stable over the time, which can
be seen as acceptance and establishment of this term. The frequency of the term grid
is decreasing, which may hint that the technological side of the concept is already
mature, established and needs no further development but that claim needs to be
checked for the next years. Additionally, the funding period of the UK e-Science
Core Programme stopped in 2006, resulting in a reduction of interest in the topic or
at least resulting in a reduced amount of publications. Figure4showsthecontentanalysisofthedefinitions.Thehumandimensionhasan
approximately stable occurrence over time. But technology is less often mentioned
throughout the analysed period. Regarding technology, the number of definitions
describing collaborative technology as a constitutive characteristic decreases over
time. The term grid is also used less and less over time. Technology seems to be no
longer a challenge, but an enabler. The single resource referring to web 2.0 tech-
nologies is stable over time. In the task dimension, collaborative/interdisciplinary
research projects do not play a significant role. The intention of financial supporting
institutions to encourage collaborative research may play an increasing role—but
such a trend is not visible, yet. Research as task is an increasing part of the defini-
tions, which might be a further hint that the technology itself is mature and the usage
is becoming more important. This allows the concept to be used in more different
fields. Understanding e-Science—What Is It About? 7 7 7 Understanding e-Science—What Is It About? Understanding e-Science—What Is It About? Understanding e-Science—What Is It About? 7
Fig. 4 Results of the analysis of the human, task and technology dimensions of e-science Fig. 4 Results of the analysis of the human, task and technology dimensions of e-science Regarding the relations between the dimensions, an important link is emerging
between task and technology. This may be understood as an indicator for increasing
automation. Furthermore, the relation between human and task is the relation that is
increasing most sharply. The use of the selected terms varied by geographical location and in relation to
public funding programmes in the respective area. The term e-science itself has been
used by the UK e-science Core Programme from 1999 until 2006. Cyberinfrastruc-
ture comes from the USA, and e-infrastructure emerged in Europe. 5
Discussion of Initial Results A further term
appeared in 2005 on an initiative of the Australian Research Councils, which was
entitled e-research. The focus here however is not on geographical differences and
funding; this issue requires further investigation. 6
Conclusion The aim of this paper was to show how the use of the term e-science is changing
through a literature analysis. The initial results show that the concept of e-science
changes over time. One aspect of the concept is technology, referring to infrastructure
and single resources: • Grid computing is “an important new field, distinguished from conventional
distributed computing by its focus on large-scale resource sharing, innovative
applications, and, in some cases, high-performance orientation” (Foster et al. 2001, p. 200). 8 C. Koschtial C. Koschtial • Web 2.0 technologies are an evolutionary stage in Internet use. Examples are
virtual communities, blogs or wikis (Nentwich 2009). • Web 2.0 technologies are an evolutionary stage in Internet use. Examples are
virtual communities, blogs or wikis (Nentwich 2009). Furthermore, e-science is oriented to tasks: processing vast amounts of data,
searching for information or publishing content. The task of establishing collab-
orative projects is weakly represented in the analysed literature. • Open access refers to “The first is a change in the publishing model to one more
suited to the age of the Web; the second, a change in how scientists connect with
society – their major funders through taxation” (e-science talk 2012). • Open access refers to “The first is a change in the publishing model to one more
suited to the age of the Web; the second, a change in how scientists connect with
society – their major funders through taxation” (e-science talk 2012). Additionally, the scientist plays an important role in the concept of e-science in two
ways: Additionally, the scientist plays an important role in the concept of e-science in two
ways: • as a single researcher; • as virtual communities, which exist only in the Internet. They form for a limited
period in time as interdisciplinary groups of regional segregated elements (Mosch
2005). The key characteristic of such units is collaboration. • as virtual communities, which exist only in the Internet. They form for a limited
period in time as interdisciplinary groups of regional segregated elements (Mosch
2005). The key characteristic of such units is collaboration. The changes related to e-science are apparent in all three of Heinrich’s dimensions. Important concepts like open access or the grid have been attributed to the different
dimensions. 6
Conclusion Therefore, the potential of e-science is not reduced to electronification,
but expanded to include redesign of tasks, the emergence of virtual organisations
and the rapidly increasing importance of collaboration. Right now, the technology
dimension still dominates the concept, but it is maturing and this will form the basis
for further changes. It seems necessary to do further research to analyse related technologies and tasks
behind the concept of e-science in more detail in order to provide a sufficient base
for scientists to be able to learn about the potentials of e-science and to convert those
potentials into realised benefits. Atkins, D.E.: Cyberinfrastructure and the next wave of collaboration. http://hydra-cog.fsl.noaa.gov/
site_media/docs/atkins_2005_wave.pdf (2005). Accessed 24 Feb 2013
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the copyright holder. 1
Introduction The central aim of this article is to identify forms of organisational governance
(social, output, or behavioural control) that are suitable for effective e-collaboration
in scientific communities. Are “e-learning” and “e-science” fundamentally different
things? Specifically, does e-learning concern teaching, and e-science, research? This
is factually correct, but from an organisation theory perspective, not a sufficient
criterion for differentiation. Above all, the clientele at issue here is the same: the
teaching and research staff of universities. In addition, both activities are carried out
within the same institution. In this respect, comparison is not only possible, it is
mandatory. Our evaluation is based on both a review of the relevant literature and empirical
studies, some of which were conducted by the authors. Following the classification
of virtual organisations, the main characteristics of organising academic activities
are presented and validated through suitable institutional examples. Thomas Köhler, Christoph Lattemann, and Jörg Neumann Thomas Köhler, Christoph Lattemann, and Jörg Neumann Abstract Research on organisational arrangements of scholarly networks in both
e-learning and e-research is located at the intersection of different theoretical justifi-
cations and developmental contexts such as organisational theory, computer science,
education science and media informatics. However, there is still a lack of research on
the organisational context of e-learning arrangements and its impact on collaboration
inacademiccommunities.E-learningresearchshowsthattheintegrationofelectronic
media in scientific communities negatively impacts their effectiveness and causes
conflicts within communities. Research networks however are far less investigated
as there is not direct didactic focus on how to collaborate. Recent theories on organi-
sational design, virtual organisations and governance provide concepts for organising
e-collaboration more effectively. Managerial instruments such as direct control of
results and behaviours need to be supplemented or even replaced by concepts of
social control; typically trust and confidence become the central mechanisms for
the new forms of inter- and intra-organisational coordination. This paper starts with
concepts. Then, to exemplify the organisational coordination mechanisms in schol-
arly e-communities, the authors critically discuss and reflect on these organisational
arrangements and managerial concepts for two higher education portals and one
research network in Germany. The conclusion is that, just as previous research has
confirmed for educational networks, governance within academic networks relies
heavily on the functionality of social and communicative forms of control. Keywords Research network · Education portal · Virtual organisation ·
Governance · Social control · Science collaboration · Scholarly collaboration ·
Online community T. Köhler (B)
Department of Education, Technische Universität Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de
C. Lattemann
Department of Business and Economics, Jacobs University, Bremen, Germany
e-mail: c.lattemann@jacobs-university.de
J. Neumann
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: joerg.neumann@tu-dresden.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_2 T. Köhler (B)
Department of Education, Technische Universität Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de C. Lattemann
Department of Business and Economics, Jacobs University, Bremen, Germany
e-mail: c.lattemann@jacobs-university.de J. Neumann
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: joerg.neumann@tu-dresden.de J. Neumann
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: joerg.neumann@tu-dresden.de 11 11 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_2 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_2 T. Köhler et al. T. Köhler et al. 12 2.1
Online Technologies in Higher Education The integration of new media in educational settings has been intensively discussed
in academic research and education for about 15 years. Various forms of online,
distance, and blended learning have been implemented and tested. After a series
of tentative, rather experimental tests to integrate new Internet technologies and
electronic media in teaching processes, the management of students and eventu-
ally the teaching itself, we now see the results in the forms of web-based tutorials
(WBT), virtual learning environments (VLE) and more recently in massive open
online courses (MOOC). With respect to developments in the online learning arena, in 1999 the German
expert group on Higher Education Development by New Media predicted the higher
education landscape would be as follows (cf. Köhler et al. 2010): 1. Global education providers and platforms offer worldwide accessible online
courses. 1. Global education providers and platforms offer worldwide accessible online
courses. 2. Traditional universities are in competition with private online providers, in partic-
ular with corporate universities, and students use the opportunities of the global
education market. 3. In order to survive in this competitive situation, many colleges have joined
together in networks and offer common learning opportunities, while univer-
sities are jointly offering their academic programs together under the umbrella
of a virtual university. Organising Academia Online 13 4. Student services are provided by facilitators and tutors, and less by classical
university teachers, because more than 50% of students study online. 4. Student services are provided by facilitators and tutors, and less by classical
university teachers, because more than 50% of students study online. As of today, these predictions can only partly be confirmed. However, besides
the established Open Universities like the British Open University or the German
Fernuniversität Hagen, new global education providers such as the edX, Coursera
or Udacity are emerging and become more relevant with the increasing need for
lifelong learning and with growing numbers of students seeking for flexible online
learning. Nevertheless, they still only play a niche role in higher education so far. But
it is no surprise that the Centre for Higher Education Development (Hener and Buch
2006) concluded more than a decade ago that “[i]n academic education […] uses of
digital media in teaching and learning and integration of information technology-
based administrative services have become widely established. Key questions of the
future are seen especially in the interlinking of different services” (p. 2). 2.2
Virtualisation in Higher Education Academic research has dealt with the use of Internet-based technology in teaching
for many years (see, e.g., Lievrouw et al. 2000; Issing and Klimsa 2003, 2010). While
initial claims were rather didactic (“classroom technology”), virtualised educational
scenarios (VLEs, MOOCs, etc.) are of increasing interest nowadays. The concept of
virtualisation is being used more and more often to describe the essential features and
expectations of information and communication technologies (ICT) and multimedia,
and to document the change. What exactly is behind it? Features of virtualisation
described by Köhler et al. (2010) include the facts that students no longer meet their
seminar leaders personally and that neither they nor the lecturers need to borrow
books from the library. Researchers submit their conference abstracts, and expert
opinions on other posts, via an Internet portal, while heads of research projects
identify potential research partners in a database—without having ever met in person
before. All in all, universities and virtual academies cooperate by uploading teaching
content to a joint learning management system to be used by students from other
institutions. In sum, such a far-reaching change in the educational landscape has
established itself in less than 15 years and is on the verge of becoming the standard. However, acceptance by the teaching staff, especially at universities, is rather low;
for example, professors in Toronto went on strike in 1997 and have managed to keep
their teaching offline until today. Similarly, a study published by the Centro Nacional
de Estadística, Geografía e Informática Mexico in 2004 (INEGI 2004) explained that
70% of professors in Mexico protested against the use of ICT in education. Their
main reason was and perhaps still is the form of presentation of course content
when using ICT in formats like PowerPoint and LaTeX. The distinctly reluctant
behaviour of university staff is illustrated, for example, by the words of a professor
from education sciences “you have to operate well didactically […] and a part of
this is the whole computer nonsense” (Misoch and Köhler 2005, p. 1). In the same T. Köhler et al. 14 T. Köhler et al. 2.2
Virtualisation in Higher Education way, the dean of the engineering department at a leading German university stated
in 2015 that “the nightmare is graduates who no longer draw without a computer, no
more writing”.1 The prevailing opinion is that this leads to a very impersonal design
of seminar rooms and lecture halls, whereby students may lose their communication
and personal contact with each other. Respondents continue to believe ICT should
only be used in education to communicate data and not to communicate between
people, nor do they see it as a new academic format or alternative for formation,
though it may be used in addition to a classroom setting. Hence, pivotal questions remain unanswered. What will the campus of 2025 look
like? Which organisational models of e-learning and e-science collaboration will
prevail? Despite the aforementioned reluctance in academia, other developments are
observable. For example, online learning is proliferating in media-related disciplines;
topics such as artificial intelligence, telemedicine and distance learning, MOOCs and
open science are frequently and extensively discussed as powerful new opportunities
for improving academic activity in general (Pscheida et al. 2014; Lattemann and
Khaddage 2013). Our first conclusion is that ICT has changed (academic) education. As the above
examples illustrate, this change is not limited to education, academic teaching and
learning. This raises the question of what exactly the virtualisation of education
means. As early as 1999, Landfried, then President of the German Rectors’ Confer-
ence, described unlimited access to stocks of knowledge independent of time and
space; yet this knowledge is disconnected (separated) from physical institutions and,
in particular, individuals (Landfried 2009). What is meant by this double separation? To answer this, it is important to analyse what is virtualised, which is more than the
learning objects or knowledge content. In fact, relations (micro- and macro-social,
but also those between learners and learning object) can be virtualised as well as
knowledge, sometimes both at the same time. 1This quotation was taken from an anonymised interview by the author. 3
Change of Organisational Theories and Paradigms What has been known from both management and operational practice for a long
time (cf. Frindte et al. 2000) now also appears to apply to education: ICT is becoming
more important in managing organisational processes, and these infrastructures are
becoming permanent. But these processes vary significantly, raising the question of
the ideal configuration of technology and organisation. The first research to address
this issue introduced new ICT to control operational processes in knowledge coopera-
tion.Munkvold(2003)setupsuchaheuristicthatcanbetransferredtotheeducational
context almost directly. He divided the “implementation of collaboration technolo-
gies” into four sub-areas, the (1) organisational context, (2) implementation project, 15 Organising Academia Online (3) technological context and (4) implementation phase. Similarly, with explicit refer-
ence to the introduction of online learning in higher education when used as dimen-
sions of change, Euler et al. (2004) proposed the following five dimensions: (1)
economic dimension, (2) pedagogical-didactic (educational) dimension, (3) organ-
isational/administrative dimension, (4) technical dimension and (5) sociocultural
dimension. Are these theories based on economics or technology? Neither. Organisation and
organisational culture are central to change. With this assessment, the authors align
with a strand in the German educational research tradition (Neumann and Schütte
2008) that is gaining ground but still rather new. This broadens the academic perspec-
tive on the use of media, which was previously dominated primarily by cognitive
(psychology), teaching (pedagogy), education-oriented (educational science) or even
technological (computer science, etc.) approaches. An organisational perspective
adds a social and management science-based momentum, and macro-social perspec-
tives. After 2005 more research programmes in Germany sought to meet the need
for such an approach, including New Media in Education II or the later Digitisation
Initiative (2014). In education and media studies, where approaches based on organ-
isation studies, education science, or media economics are preferred, researchers are
frequently challenged to take these approaches. Just after 2010, based on the concept of openness—used when coining the terms
of OER and MOOC—many became convinced that the technology used for univer-
sity operations would be revolutionised. Within the next decade, it is expected that
students will no longer attend lectures or work in a lab, but will join professors’
research activities online, whenever and wherever they want. Academic knowledge
will be tailored, or transferred from mass production to mass customisation. So what
is the core of the “digitisation of teaching” or the “advent of information and commu-
nication technologies in the university”? 3
Change of Organisational Theories and Paradigms Germany’s former Minister of Science,
Bulmahn (2004, p. 5), argued that “the new media in the combination of computer
andInternet[willpenetrate]allsocialandeconomicsectors[andwillrelease]afunda-
mental structural change” combined with unprecedented speed of market globalisa-
tion. Ortner and Nickolmann (1999) stressed that the success of open universities will
force conventional universities to adopt innovations in teaching organisation, such
as distance learning, on-campus students as independent learners, modular course
structures and the enrolment of mature part-time students. This goes along with
changing forms of social micro-study, from online learning communities (Kahnwald
and Köhler 2005) to more complex flexible online knowledge organisations (Köhler
et al. 2003). To speed up the new media restructuring of higher education, the Federal Ministry
of Education and Research (BMBF) has targeted the existing New Media in Educa-
tion Programme and the 2004 re-bid. The first phase of the programme from 2000
to 2004 aimed to develop high-quality e-learning content and concepts for mobile
learning, and to put them into regular practice, particularly in undergraduate studies. These developments were intended to be available from 2005 and to be sustained
and broadened by two conveyor lines. Conveyor line (A) was for projects in an inter-
disciplinary and university-specific context, called “e-learning integration”. This is T. Köhler et al. T. Köhler et al. 16 about developing organisational infrastructure and about changing management to
develop utilisation of the opportunities provided by ICT innovation potential in the
field of teaching, learning, and exams to universities systematically and sustain-
ably. Conveyor line (B), for projects in a university-wide and primarily subject-
specific context, referred to as “e-learning transfer”, was to lead to new organisa-
tional concepts and business models for services, related to the production and use
of online learning primarily supporting professional and technical areas (cf. BMBF,
2004, all translations from German by the authors). By 2010, most of these projects
were completed. What impact did the targeted re-organisation of online learning in
German universities have? 3.1
The Research Framework: Virtual (Educational)
Organisations In view of the different organisational theories applicable to online teaching and
learning in a university context, including its structural and procedural commonali-
ties, the following issues should be noted. At the institutional level, online learning
is integrated into the organisational structure of the university. This requires suffi-
cient integration of external service providers. Figure 1 presents the value chain of
e-learning from a university perspective, including the internal and external partners
at the Technische Universität Dresden in 2008. The e-learning value chain shows that teaching and learning in an electronically
mediated environment is multifaceted and involves various stakeholders. Because
of the various partners involved, the organisational concept shows many charac-
teristics of a virtual organisation with loosely coupled partners (external content
providers, platform providers, external and internal instructors and students, etc.). Hence, universities which provide online learning arrangements must also follow, or
at least adopt, mechanisms of virtual organisations. They must change their struc-
tures from their traditional departmental separation towards more process-oriented,
open and collaborative organisational settings. These kinds of new virtual organisations are primarily shaped by their virtual char-
acter and are limited by their lack of “real” organisational boundaries. This applies
to all organisational aspects: the location, bonds and stability of the organisation. Such a virtual organisation is “multisite, multi-organisational and dynamic” (Snow
et al. 1999). As shown by Köhler and Schilde (2003), virtual organisations can differ greatly in
terms of size, durability or stability. Furthermore, various forms of virtual organisa-
tion and cooperation are described in theory and can be observed in practice, under an
equally large number of names (network, cluster, virtual team, virtual organisation,
etc.). In order to make these phenomena comparable and assign experimental find-
ings, a further differentiation of the term is required. Okkonen (2002) proposed one 17 Organising Academia Online Fig. 1 Organisational framework of online learning using the example of the Technische Universität
Dresden (own figure after Neumann and Schütte 2008) Fig. 1 Organisational framework of online learning using the example of the Technische Universitä
Dresden (own figure after Neumann and Schütte 2008) way of doing this, presented by Köhler et al. (2003) as an advanced systematisation
of virtualised organisational forms (see the following Table 1). In the following, two case studies on online learning and one case study on
online research are presented and critically discussed from the perspective of virtual
organisations. able1 Differentiatedcharacteristicsofvirtualisedorganisationalforms(ownfigureafterOkkonen
002; Köhler et al. 2003) Table1 Differentiatedcharacteristicsofvirtualisedorganisationalforms(ownfigureafterOkkonen
2002; Köhler et al. 2003) We have chosen two case studies because the authors of this paper are involved
in the projects and they have deep insights. A triangulation approach was utilised
as this is “the most desired pattern for dealing with case study data” (Yin 2011). Seminal articles on the case study topics were selected for analysis (Yin 2013). For this particular example, differing sources have been consolidated to present
a comprehensive case study summary, including scientific publications, research
reports,andpublicdescriptionsonthewebsitesofthechoseninstitutions.Allmaterial
was either available publicly or from internal sources. Figures used come from self-
descriptions of those projects—the layout was not changed, but translated. 3.2
Research Methods This paper follows an inductive research approach in order to identify relevant organ-
isational mechanisms in an e-learning institution, based on three case studies. The
case study method is selected as it is a common and comprehensive investigative
tool for exploring individual, group, organisational or social phenomena (Yin 2013;
Bryman and Bell 2011). In this instance, the weaknesses in corporate data security are
investigated, in order to reveal potential causes, as discussed in the analysis section. 18 T. Köhler et al. Case I: Online learning in academic education through the education portal
of Saxony (since 2001) Since 2001, a university network has been supporting online teaching at public
universities in the German federal state of Saxony. After an initial phase with the
direct participation of the four universities which comprised this group since 2004,
a system corporation, BPS Education Sachsen GmbH, was founded in 2006. In
an evaluation of the state of development of online learning at Saxon universities
for the Saxon Minister of Science and Art, the German National Centre for Higher
Education Development (CHE), stated in 2006 that despite many years of funding by
means of the country and the special commitment of many scientists concluded that
online media is still used on a relatively small scale. Overall, however, acceptance
is increasing among both university staff and students. But Hener and Buch (2006)
noted a lack of liability for student usage, sustainability in higher education, and
overall management of e-learning in higher education. This has been confirmed by
further analyses (Köhler and Ihbe 2006) calling for a more systematic integration of
online learning at Germany’s largest technical university, the Technische Universität
Dresden. In 2007, control of the project passed to the newly established e-learning Organising Academia Online
19
Fig. 2 Model of the education portal of Saxony (cf. https://bildungsportal.sachsen.de/) Organising Academia Online 19 Fig. 2 Model of the education portal of Saxony (cf. https://bildungsportal.sachsen.de/) working group of the Rector’s Conference Saxony. Since then, all public universities
in Saxony and two private universities have joined the network. The following Fig. 2
shows the distribution of the educational portal in Saxony as of 2008: T. Köhler et al. T. Köhler et al. Fig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) ig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) Fig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) Case II: Online-supported continuous learning in the education portal of
Thuringian universities (2000–2013) Based on analysis of the need for media-based academic training and organisa-
tional structures at and between the universities of Thuringia, and to support more
sustainable development of such online training, the (online) education portal for
Thuringia was constructed in 2001 (www.bildungsportal-thueringen.de). As a conse-
quence of the above tests, this portal aimed to serve institutional training seekers
or their staff, that is, employees who want to selectively add to their skills profile
according to their academic or equivalent qualifications or needs. There was already
significant potential demand for this when the portal opened. An expert (Stifter-
verband 2001) estimated that 20,000 of almost 60,000 students of the Distance
University of Hagen alone are undergoing a hidden continuing professional devel-
opment (CPD). The education portal of Thuringia competed with several private
CPD providers. This fact should be mentioned because the expectations and attri-
butions of training seekers were influenced by their experiences with these market
leaders. Nevertheless, the participating universities have reconfigured themselves on
the virtual organisation model, consisting of a core information broker and a network
of partners meeting training needs, as in Fig 3. The education portal of the Thuringian universities remained at the project stage
until 2013 and was then closed by the responsible Ministry of Science. 20 Case III: The e-Science Saxony Research Network as a virtual science
organisation (since 2011) The e-Science Research Network project is a Saxony-wide comprehensive
research network of all state universities created to explore approaches and methods
in e-science (electronic science). The term e-science describes the different fields
of scientific research and development related to the use of computer technologies. While this term is mainly used in Germany and the UK, comparable concepts include
“cyber-infrastructure” in the United States or “e-research” in Australia. Currently,
the slogan “Science 2.0” frames the discussion, in particular concerning cooperative
digital scientific work (Weichselgartner 2010). The thematic range of infrastructures,
application architectures, grid and cloud technologies extends to the educational
technology known as e-learning. In addition, e-science systems support cooperative
research between universities and with the private sector (cf. Ziegler and Diehl 2009). Research in e-science can be subdivided into disciplines such as e-humanities, e-
medicine or e-engineering. In any case, it extends the scholarly process by integrating
e-technologies and methods based thereon. The methodology was found to screen
collaborative research activity, but knowledge organisation changed also dramati-
cally and has been systematically underdeveloped by these e-disciplines. Even when
research contexts are established or reused, it creates new paradigms, such as the
concept of a “living lab”. This is user-centred research and open innovation practice,
based on research work in multidisciplinary teams. One of the essential activities
of these teams is co-creation, bringing together technological innovations and their
applications through procedures such as crowdsourcing and crowdcasting. In these
driven-by-research community practices, a variety of opinions, needs and knowledge
exchanges can be used to brainstorm new scenarios, solutions and applications; yet
these may be one-sided (Fig. 4). Overall, starting with a steady drop in the “half-life of knowledge”, the changing
demands of industry and the economy, and social changes in the knowledge society,
the network partners have developed a new type of research and the accompanying
scientific activities. New information and communication technologies can be used
in this context, especially to provide, disseminate and use research information,
such as laboratory data from simulations using complex aggregate social science
information. Thus, media-based networking researchers are characterised by a high
degree of flexibility and variability; usage may translate into new contexts through
the restructuring of data and their usage. Through the coordinated action of the Saxon 21 21 Organising Academia Online Organising Academia Online Fig. 2http://www.hochschulforumdigitalisierung.de/, retrieved on 15 July 2015. Case III: The e-Science Saxony Research Network as a virtual science
organisation (since 2011) 4 Clusters and
organisational structure in
the e-science Saxony
research network
eScience
Network
Saxony
Cluster I
eLearning
Cluster III
eSystems
Cluster II
eResearchy
State Ministry for Science and Art and the Federal Republic of Germany, the Saxon
universities have achieved an excellent level of “computational science”, especially
in introducing e-learning support systems (Hener and Buch 2006). Summarised as e-
sciences, the current project focusses on e-business, e-learning and e-systems, which
are interwoven holistically at universities in the context of teaching and research. Fig. 4 Clusters and
organisational structure in
the e-science Saxony
research network State Ministry for Science and Art and the Federal Republic of Germany, the Saxon
universities have achieved an excellent level of “computational science”, especially
in introducing e-learning support systems (Hener and Buch 2006). Summarised as e-
sciences, the current project focusses on e-business, e-learning and e-systems, which
are interwoven holistically at universities in the context of teaching and research. 4.1
Theoretical Considerations About the Functioning
of Virtual Organisations in the Academic Sector 4.1
Theoretical Considerations About the Functioning
of Virtual Organisations in the Academic Sector Recent digitisation initiatives in academia demonstrate the pressing need of a serious
discourse about its fundamental principles and practical meaning for the whole sector. In Germany since its launch in 2014, the Higher Education Forum on Digitisation has
created an independent national platform to discuss the multiple facets of digitisation
in higher education by consulting in six thematic groups on issues surrounding the
digitisation of university teaching.2 Two decades ago, Malone and Davidow (1992) triggered the discussion about
new organisation and management concepts in the economic sciences with their path-
setting contribution “Virtual Corporation”. Until that moment, organisational change
was marked by various headings such as “Computational Organisation”, “Learning T. Köhler et al. 22 T. Köhler et al. Organisation”, “Organisational Communication”, “Society and Internet Develop-
ment”, “Trust Leadership and Decision Making” or “Augmented Reality” (cf. Köhler
and Schilde 2003). All approaches share a similar basis: organisational units are
reduced to their core competencies and have to cooperate in network-like struc-
tures. Complex tasks are realised by a number of independent organisational units
or enterprises with complementary skills. This calls into question traditional organi-
sational concepts, as published in governance research. Direct output and behaviour
control, which are feasible in traditionally structured enterprises with divisional and
functional organisation patterns, are supplemented or even replaced by concepts of
social control. In the 1980s, psychological studies of cooperation and communi-
cation in virtual communities depicted computer-mediated communication as typi-
cally rather anomic in nature (Sproull and Kiesler 1986), less tolerant (Funkhouser
and Shaw 1990) and lacking transferable behaviour (Köhler 2003). Postmes (1997)
see this analysis as based on the less medium-socialised population of the “early
years”. Therefore, these findings would be difficult to replicate. However, the cases
presented here show that today’s changed environment creates completely new ways
of medium-socialised collaboration. Once again, the majority are beginners in a
new (mediated) organisational culture. Consequently, Lattemann and Köhler (2005)
assumed that trust and security of contract would become key factors of cooperation
in virtual organisations. This implies that social control becomes a strategic factor in
competition among virtual organisations (Barney and Hansen 1994; Krysteck 1997)
laying the foundation for new forms of cooperation. 4.1
Theoretical Considerations About the Functioning
of Virtual Organisations in the Academic Sector Their analysis based on liter-
ature review, and our own empirical studies, lead us to observe that the less output
and behaviour can be assigned directly to specific individuals, the more important
social control of the community becomes. Our three case studies demonstrate that organisational development towards a
networking, virtualised organisational structure can be found in both the academic
education and research domains. For both domains, it is obvious that this develop-
ment is going beyond existing organisational patterns; however, it is not necessarily
sustainable, as the closure of the education portal of Thuringian universities after only
ten years shows. Is this development merely the interface of a larger organisational
change, or the beginning of a new era? Networking organisations need to move beyond the purely project stage. In all
cases, besides new organisational forms we found both close linkage to existing
units, including several management instances like steering committees, information
offices, and supervisory boards. Neither a classical hierarchy nor a clear linkage to
all partners were found in these cases. Structures and opportunities for influencing
the processes seem rather soft and depend on functioning communication. In sum, virtual networks with flexibly aligned partners, who deliver different
services and competencies, heavily rely on the coordination of and motivation for
social control and trust. Appropriate instruments need to be strengthened. Long-
established norms cannot be adopted because these are either insufficiently developed
or simply not applicable—which led to the central question studied by the authors
previously: Which governance concept is most efficient in the diverse forms of a
virtualorganisation?Intheirstudy,LattemannandKöhler(2005)examinedtheextent Organising Academia Online 23 to which new governance concepts (i.e. social control) may be applied to forms of
e-learning (i.e. virtual collaboration) and could propose a classification system for
virtual organisations. Already before and after Köhler et al. (2003, 2010) studied the
organisation of online learning. In a next step, the focus was directed on research
networks as an organizational artefact, their functionality and technology. What can
be concluded on how to steer the development and how to govern that functioning
of those structures effectively? 4.2
Forms, Instruments and Mechanisms of Control
in Virtual Organisations Organisational theory examines traditional forms of governance (behavioural and
output control) in detail, mostly uniformly. However, with the establishment of
network-like organisational structures, the concept of social control has only recently
been subjected to rigorous debate. Only the following forms of governance are
considered here: 1. direct governance—inspection of behaviour (behavioural control), such as on the
basis of standards won from experiences (Magretta 1998); 2. indirect governance—determination of output based on given goals (output
control) (Thomson 1967; Magretta 1998); 3. social governance (social control)—comparison of conformity to certain moral
and cultural rules (Ouchi 1979). 3. social governance (social control)—comparison of conformity to certain moral
and cultural rules (Ouchi 1979). As Lattemann and Koehler (2005) argue, instruments of social control can be
identified in relation to the level of objective and personnel management (Thomson
1967). Therefore, trust is not related to behavioural and output control mechanisms,
as some authors postulate (see, e.g., Manchen and Grote 2000; Bradach and Eccles
1989), but rather supplementary to these (Das and Teng 1998; Ebner et al. 2003). In
that sense, traditional control mechanisms and social control describe are different. How can flexible and light organisational structures be designed and imple-
mented? Based on the above discussion of the literature and cases, trust can be
promoted by appropriate social standards and basic institutional conditions. A
number of governance instruments can be applied to exercise social control, such
as promoting common cultures among networking partners with homogeneous
value creation processes, or reviewing and creating similar moral concepts through
rituals or ceremonies. The observed networks apply different means, ranging from
a project plan to an inter-institutional agreement. This method is particularly suit-
able for networking partners of a similar size, origin and organisational form (Ouchi
1979), that is, with almost no heterogeneity. Other effective means of social control
include operational guidelines (Heck 1999), intensive use of modern and uniform
ICT (Köhler 2003; Albers et al. 2002), promoters for public relations and conflict
management (Hausschild 1997), job rotation or jointly offered training courses. In
the three networks observed here, we found both inter-institutional agreements (such T. Köhler et al. T. Köhler et al. 24 as the integrated provision of academic master’s programmes) and other measures
(such as joint training) for using the platform. Can the social control model (cf. Fig. 4.2
Forms, Instruments and Mechanisms of Control
in Virtual Organisations 5) developed by Lattemann and Köhler
(2005) for learning networks be transferred to research organisations with presum-
ably less standardised activity? The efficiency of the three governance forms discussed and the possible fields of
their application depend upon the nature of the organisational arrangement. The more
governance mechanisms are used; the more competencies are required in the process
of cooperation. In contrast to traditional enterprises (Type 1 in Fig. 1), where mostly
traditional forms of control (behaviour and output control) based on structural gover-
nance tools are used to promote coordination (information and communication) and
motivation, virtual organisations may adopt concepts of social control with different
degrees of intensity. Virtual teams, virtual projects, temporary virtual organisations and meta-networks
are characterised as maximally closed networks with unilateral dependency on the Virtual Teams
or Projects, Tem-
porary Virtual
Org., Meta Net-
works
closed/ fixed
open
Traditional
Enterprises
Virtut al Teams
or Projo ects, Tem-
porary Virtut al
Org., Meta Net-
works
closed/ f
open
Traditional
Enterp
r rises
Importance of social control
high
Border of Virtual
Organizations
Connection between
Virtual Organizations
Degree of Virtualization
low
low
high
Permanent
Virtual Org.,
Cluster
Spherical
Network
(Miles &
Snow 86)
Borders of Virtual Elements
ixed
Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler
2005) Border of Virtual
Organizations Connection between
Virtual Organizations Virtual Teams
or Projects, Tem-
porary Virtual
Org., Meta Net-
works
closed/ fixed
open
Traditional
Enterprises
Virtut al Teams
or Projo ects, Tem-
porary Virtut al
Org., Meta Net-
works
closed/ f
open
Traditional
Enterp
r rises
Importance of social control
high
Organizations
Connection between
Virtual Organizations
Degree of Virtualization
low
low
high
Permanent
Virtual Org.,
Cluster
Spherical
Network
(Miles &
Snow 86)
ixed
Fig 5 Social control and organisational virtualisation (figure by authors cf Lattemann and Köhler Spherical
Network
(Miles &
Snow 86) Permanent
Virtual Org.,
Cluster Degree of Virtualization low low Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler
2005) Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler
2005) Organising Academia Online 25 value creation process. The partners provide a wide spectrum of services and prod-
ucts. Such networks do not require a high degree of competency for cooperation. This
reflects the fact that social governance tools were not applied intensively in these
forms of virtual organisations. 4.2
Forms, Instruments and Mechanisms of Control
in Virtual Organisations Business relations of this type are shaped by market-
oriented or structural management instruments, such as a centralised coordinating
body based on contractual arrangements (e.g. services or employment contracts). Virtual organisations like this frequently use ICT to collaborate and communicate. This is because both employees of the enterprise and long-term partners are often
closely associated. Thus, ICT structures are implemented and do not need to be built
up. Also—which is perhaps far more important—these structures do not need to be
mediated between the partners, as they are obligatory in most temporary projects. Moreover, members of permanent virtual organisations and clusters need strong
collaborative competencies due to their extremely intertwined mutual relations. A maximum of informal relations is presupposed in spherical networks (Miles
and Snow 1986). The roles of individual participants are distributed in a spherical
network;resourcesand/orparticipantsareboundlesslyexchangeable.Suchstructures
can be assumed in social networks; however, this article refers to profit-making, not
non-profit, environments, so spherical networks are not the focus here. Even its
proponents state that this structure cannot be observed in reality (Miles and Snow
1986). In practice, the extent to which ICT is used to support coordination processes
in virtual organisations varies greatly. However, in all virtual organisations, ICT
plays a pivotal role; without it, virtual organisation is impossible. Research which
was based on a set of unsystematic findings from case studies (Manchen and Grote
2000; Köhler and Schilde 2003; Köhler et al. 2003), recommended that the minimum
required ICT support be identified first. The arrangement of information and commu-
nication processes determines the complexity of the ICT infrastructure (e.g. enter-
prise resource planning or e-mail). In less complex virtual organisations (e.g. virtual
teams or projects), less sophisticated ICT solutions have been used in academic
practice for approximately 20 years. However, in these research organisations, ICT-
based groupware solutions were still rather exceptional (Köhler and Röther 2002;
Köhler and Schilde 2003). More recently, it has been found out that only a small
number of scientists are adopting social media technologies like Mahara, Mendeley
or ResearchGate. For example, a Germany-wide survey conducted by Pscheida et al. (2015) found that social media applications such as social networks, microblogs and
social bookmarking tools are used by a maximum of 8% of scientists in a research
context. 4.3
Limitations Given the recent nature of this study, both the available literature and empirical
access to the sectoral development were limited. Firstly, the empirical cases represent
developments in German academia only. In the next stage, research must include
data from other countries, to develop a more general understanding of organisational
dynamics in the academic sector and avoid a national-only explanation. Some sources, including website communications, were publicly available docu-
ments written by legal professionals or corporate representatives. Therefore, the case
study may contain less reliable data than that supplied from exclusively academic
sources. Although the authors attempted to adopt a wide range of literature from several
sub-disciplines in business, media and education studies, it is difficult to identify
whether other researchers intentionally focussed on organisational development or
whether this was a by-product of other considerations. Thus, the case made here is
largely based on the previous work of the authors. 4.2
Forms, Instruments and Mechanisms of Control
in Virtual Organisations Only in 2020 the influence of the Corona pandemic will perhaps lead to
a more massive adoption of such collaboration techniques, but not necessarily in a
conscious use. All in all, organisational models for academic institutions dealing with both educa-
tion and research need to adapt to organisational models of virtual organisations. Universities and other research institutions have to change in both structure and
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S. (eds.) The Routledge Companion to Creativity. Routledge, New York, NY (2009) S. (eds.) The Routledge Companion to Creativity. Routledge, New York, NY (2009) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
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Commons license, unless indicated otherwise in a credit line to the material. If material is not
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statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. B. Mohamed (B)
British Lincoln College, Riyadh, Saudi Arabia
e-mail: bahaa@bzoor.com
T. Köhler
Institute for Vocational Education, TU Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_3 Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly
communication · Doctoral training 1
Introduction Research collaboration is the foundation of research students’ efforts in academia. Independently of disciplinary background, research is based on the social patterns of
competition for the best explanation and joint evaluation of the quality of research. Therefore, research collaboration is a form of positive interaction between knowl-
edge producers that have taken on management roles by using certain resources
and tools to establish and pursue a scientific goal (Ynalvez et al. 2011). We define
research collaboration as the current and future regulations, processes, and concepts
which support interaction and cooperation between our doctoral candidates. Here,
it is important to note that collaboration is not simply students and professors co-
authoring a piece of research; instead, it requires establishing connections that might
extend to communication which, over time, develops into sustainable collaboration
among different researchers with similar interests. Accordingly, we may need to
better understand the nature of scientific tasks and the time frame in which they
should be completed, as well as how individual beliefs of using ICT and web 2.0 in
a research context can help to define how online activities should be organised. In
addition, the use of technology can be interpreted in relation to cultural contexts and
disciplines. Finally, incentives act as the engine that encourages students to under-
take collaborative research, and, in academia, this engine is covered and protected
by research ethics. In this paper, we focus on collaboration of all PhD students in
their first, second, or third year. This may take into consideration the form of any
formal or informal social action and scientific activities that could increase the output
and production of scholarly research, improve communication through the text, and
encourage resource sharing and collaborative writing. PhD students face new challenges in the age of digital research. In particular,
this paper focuses on challenges such as dealing with digital material and resources,
learning management systems, personal learning environments, social networks, and
collaboration in research networks. Current PhD students, who are largely from the
Generation Y demographic group (born between 1982 and 2000), are familiar with
technology and are likely to encounter one or more web 2.0 technologies in their
everyday life (Zaman 2010). In the academic context, web 2.0 technology shapes
how PhD students learn, self-regulate, and communicate. The Fish Model: When Do Researchers
Collaborate Online? Bahaaeldin Mohamed and Thomas Köhler Abstract The questions of whether and how doctoral students are motivated
for enhanced research collaboration deserve thorough consideration. Even though
collaboration in general and its mediated forms, such as computer-supported coop-
erative work and collaborative learning (CSCW and CSCL), are prominent research
topics, only a little is known about the methods necessary to design various activities
to support research collaboration. With the upcoming generation of tools such as
Mendeley, Conference Chair, ResearchGate, or Communote, scholars suspect that
web 2.0 services play a decisive role in enabling and enhancing research collabora-
tion. However, there is almost no data available on the extent to which researchers
adopt these technologies, and how they do so. Therefore, the authors first present an
overview of the current usage of web 2.0 among doctoral researchers in their daily
academic routines, based on a survey (n = 140) conducted in the German Federal
State of Saxony. It confirms a wide and often specified usage of web 2.0 services
for research collaboration. For theoretical analysis, the authors propose a concep-
tual framework that reflects the requirements of scientific participation and scholarly
collaboration within an average international doctoral programme adopting current
digitaltechnologies.Theaimofthisframeworkistounderstand,support,andenhance
research collaboration among doctoral researchers. Our fish model highlights the
mutual relationship between the following dichotomous factors: (a) tasks/time
factors; (b) beliefs/activities; (c) support/context; and (d) incentives/ethical issues. Our results indicate a significant relationship in terms of research collaboration. This relationship has particularly been identified between two dichotomous factors:
beliefs/activities and incentives/ethics. Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly
communication · Doctoral training Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly
communication · Doctoral training 29 29 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_3 B. Mohamed and T. Köhler 30 1
Introduction Accordingly, universities
have begun to use and provide these facilities of infrastructure to attract and connect
students and develop—step by step—a better practice for research collaboration. However, as Zaman (2010) reports, current doctoral programmes struggle to follow
up and meet these demands and requirements. Concerning social and scientific inter-
action and collaboration among our doctoral students, Mohamed et al. (2013) investi-
gated PhD students’ attitudes towards doctoral colloquium, online learning material The Fish Model: When Do Researchers … 31 via Edu-tech,1 and learning management systems via OPAL.2 These scientific activ-
ities were used simply to provide an informative website for learning material and
scientific events; PhD candidates usually found that the community of practice and
the feeling of belonging were lacking. We expect the digital form of research so-called e-research collaboration to
comprise the attempt to enhance and develop not only scientific activities such as
co-authorship or finding peers and peer reviewers, but what we refer to as “open-
kitchen research”. This term refers to sharing research activities not only as a finished
product, but also as processes. In fact, during the doctoral candidate education, they
attempt to communicate and collaborate only in the context of theoretical curriculum. Theselearningformalcoursesaretraditionallydesignedtoprovidestudentswithonly
structured theoretical knowledge but no real practices. In most cases, we observed
that part-time PhD students working in third-party projects at our laboratory give
priority than ever before to the projects they are working in where there is more
community support than working individually with their own dissertation. The relevance of this study can be confirmed by the fact that doctoral educa-
tion in Germany is rapidly growing in all academic disciplines, to a recent total
number of 200,400 doctoral candidates being supervised at German universities (in
the winter semester 2010/2011), while only half of this group (n = 104,000) was
officially registered (Forschung & Lehre 2012; Wolters and Schmiedel 2010). How
do those registered scholars participate in research activities? Do they follow their
academic activities at the same pattern and do they regularly use the same research
online tools? We can just guess that the new openness of social media and web 2.0
communication helps to provide similar conditions and borderless collaboration for
all scholars depending on their access to the Internet. 1This study focused on the European doctoral network “Education & Technology” (cp. http://edu-
tech.eu).
2OPAL, an open-source Learning Management System, used by all universities of the Federal
German State of Saxony (cp. https://bildungsportal.sachsen.de/). 1This study focused on the European doctoral network “Education & Technology” (cp. http://edu
tech.eu).
2 2OPAL, an open-source Learning Management System, used by all universities of the Federa
German State of Saxony (cp. https://bildungsportal.sachsen.de/). 2
The Fish Model: A Conceptual Framework
for E-Research Collaboration The authors conceptualised e-research collaboration as follows. Based on a meta-
analysis, approximately 200 papers focussing on different aspects and approaches
in e-science and e-humanities were recruited, organised, and analysed, in order to
formulate a proposed conceptual framework, the fish model, previously published
in Mohamed et al. (2013). The framework may be used to deepen our under-
standing of the daily scientific tasks, activities, technologies, and incentives that
shape everyday academic practices for doctoral scholars, regardless of their disci-
plinary heritage. Databases consulted include Science Direct, Pro-quest, EBSCO,
Scirus, and Mendeley. Inclusion criteria were limited to full-text papers concerning
the use of web 2.0 in research communication and collaboration. Keywords used
for collecting scientific articles directly from the mentioned databases included
the following: researchers’ digital habits, use of web 2.0 in research, e-research,
social media in research, research collaboration, and scholarly communication. The
following selection criteria were used for papers: (1) written in English, (2) situated
only on the PhD and researcher levels, (3) either empirical or review articles only. In
addition, a conceptual definition of collaboration factors from Patel et al. (2011) and
the Folk Model of Intentionality (DeAndrea 2012) were used as guides to identify
the fish model (Ringle et al. 2005). The first step in analysing the selected papers was
to interpret online research behaviours and the academic activities associated with
using web 2.0 technologies, in order to predict the future of research collaboration,
using the Fish Model (Mohamed et al. 2013). As the model clarifies the factors and
concepts behind the best practices associated with research collaboration using web
2.0 technologies, it was proposed to develop an understanding of daily scientific
research tasks and activities. As the authors suggested earlier, online research behaviour is controlled by some
key factors and indicators, which was first framed in the Model of Collaborative
e-Research (Reebs 2011). This model can be used to describe the factors that
support online collaboration in e-science. The fish model (Mohamed et al. 2013),
however, extends this research by giving evidence that individual factors (beliefs,
self-regulation, etc.), in addition to group interaction organised by the institution, and
time management, obviously influence the active production of research, communi-
cation among researchers, and subsequent collaboration. Using the fish model, the
core factors in online research behaviours and the academic activities associated with
using web 2.0 technologies all were investigated. 1
Introduction In the German Federal State of
Saxony, where the data of this study was collected, the number of PhD degrees has
increased more than tenfold, from n = 111 in 1993 to n = 1,206 in 2009 (Saxony
State, Statistical Branch 2009). In order to provide an adequate statement about how our novice researchers collab-
orate via using web 2.0 services, we explore which factors might shape this collab-
oration, particularly the collaborative opportunities offered by web 2.0, we begin by
developing a theoretical framework for our investigation, and apply it to the current
situation of PhD students in Germany. 32 B. Mohamed and T. Köhler 2
The Fish Model: A Conceptual Framework
for E-Research Collaboration It is argued that a doctoral scholar would behave “like a fish living in a specific
environment, taking part in a particular community, showing different individual
behaviours to respond to an action, led by their own beliefs and framed by a certain
culture” (Mohamed et al. 2013, p. 3275). Typical behaviours and activities are
managed by incentives related to the qualification addressed and controlled by the
scholar’s role in the research ecology. The fish metaphor emerged when framing
a body of collaboration patterns for the authors’ previous study (Frewox 2010). 33 The Fish Model: When Do Researchers … “Collaboration in research is managed by a dorsal fin to stabilise research against
rolling and protect scientific environment from isolation and weakness. Inhalation
through the mouth passes over the gills in fish to obtain fresh oxygen, communi-
cation is the oxygen of research project which is necessary for bringing activities
and ideas to the project and achieve the tasks related. The backbone of our fish is
web 2.0 technologies which connect and facilitate all functions of the whole body,
these functions are divided concerning a dichotomous aspect (fish spine) – as we
will describe it complementarily in the frame of this paper – in a task/time, activi-
ties/beliefs, support/context, and ethics/incentives division” (Tannen 2006, p. 3267
ff.). Research collaboration is usually considered as a planned activity where knowl-
edge can be produced and transferred. The authors predicted previously (Mohamed
et al. 2013) that collaborative e-research (using web 2.0 technology to improve best
research practices) will take place alongside dichotomies. Tannen (Wang 2010), in his
book, The Argument Culture (1998), proposes the concept of perceived dichotomies,
that is, binarisms between two connected concepts, while not distinguishing between
them through the use of vocabulary such as “good” and “bad”. Building on Tannen’s
work, the fish model proposes the integration of both factors. Research collaboration
in this study can be interpreted as a relationship between eight concepts formed in
pars making up the total of four groups: (a) between scientific tasks or candidates’
needs and time available for implementing them; (b) between planned activities and
individual research beliefs in dealing with these activities; (c) support from tech-
nology and understanding the uses of this technology within a certain context and
culture of an institution; and (d) intentions/motivations for collaboration, which are
directed by research ethics, as illustrated in Fig. 1. 2
The Fish Model: A Conceptual Framework
for E-Research Collaboration CommunicaƟon
Ethics
IncenƟves
Time
AcƟviƟes
Context
web 2.0
Tasks
Beliefs
Support
CollaboraƟon
Fig. 1 Fish model: conceptual framework for developing e-research collaboration for PhD students
and novice researchers (Mohamed et al. 2013) CollaboraƟon Fig. 1 Fish model: conceptual framework for developing e-research collaboration for PhD students
and novice researchers (Mohamed et al. 2013) 34 B. Mohamed and T. Köhler B. Mohamed and T. Köhler H1: p
H1-0: An academic task to be done via web 2.0 is driven by a timeframe (when the
task should be done/how much time is needed to do it). H1-0: An academic task to be done via web 2.0 is driven by a timeframe (when the
task should be done/how much time is needed to do it). H1-1: An appropriate timeframe for a task to be carried out via web 2.0 can lead to
academic collaboration H1-1: An appropriate timeframe for a task to be carried out via web 2.0 can lead to
academic collaboration 2.1
The Reality of Managing Scientific Tasks in Terms
of the Available Time It can be expected that novice researchers are likely to collaborate and work with
each other because they are more likely than experienced researchers to break their
work down into various tasks, activities, and actions. Such individual behaviour is
controlled by time management as short-/long-term academic tasks, primarily related
to different actions such as information search, data analysis, reading, or possibly
writing (Illeris 2004). Overall, the doctoral education system differs significantly
from programmes at masters and bachelor level, as doctoral programmes prepare
candidates for high-level careers in industry or provide long practical experience
(Zaman 2010). In their previous studies (Mohamed et al. 2013; Mohamed et al. 2013),
the authors identified two key tasks that doctoral students undertake in order to carry
out their research. The first is marketing, that is, building a scientific competence
profile in order to develop a scientific reputation. The second is doing research, that is
activities in daily research practice, including mainly reading, writing, investigating,
searching, and reviewing. H1:
Novice researchers are more likely to collaborate and work with each other
when the work task (types, stages, and technologies) and timeframe are
specified. 2.2
Online Research Activities Led by Work-Based Beliefs PhD students’ daily research activities include specific online activities, as identified
previously (Mohamed et al. 2013): accessing resources, information, and research
funds; engagement in scientific discussions and being an active member in one
or more academic communities of practice; communication in reviewing, sharing,
and exchanging ideas; awareness of recently published scientific papers and events;
presenting oneself online in social media and social networking in order to build up
a profile and identification (Mohamed 2011; Lahenius 2010; Peggy and Borkowski
2007). Typically, it is expected that PhD research work is completed through three main
development phases (Terrell et al. 2009; Zaman 2010; Mohamed et al. 2013): (a)
becoming a researcher by training, and reading activities for first-year PhD students;
(b) becoming an expert in any required methods and the pressure to start publishing
for second-year PhD students; and (c) becoming an author which includes partici-
patinginpeer reviewing, co-authoring, andwritingpublications. Eachof thosephases
requires a number of planned online activities. Additionally, gradual engagement The Fish Model: When Do Researchers … 35 with the literature of one’s own scientific discipline should be considered, because it
leads to particular work beliefs. Three main explanations for scholars’ success were
identified (Patel et al. 2011): social culture, the culture of disciplines, and the indi-
vidual beliefs (values, motivation, learning style, self-regulation, cognitive compe-
tence, confidence, and trust). Usually, beliefs are addressed by psycho-educational
research, whereas the role of trust (versus control) as a governance concept has been
addressed in earlier research on virtual organisations (Lattemann and Köhler 2005). Only the combination of these accepted beliefs defines a researcher’s individual
approach to scientific activities. H2:
Novice researchers are more likely to collaborate and work with each other
when they believe in the work and participate in academic and research
activities (online). H2:
Novice researchers are more likely to collaborate and work with each other
when they believe in the work and participate in academic and research
activities (online). H2-0: Academic activities (online) affect a researcher’s belief in using web 2.0
toward collaboration. H2-0: Academic activities (online) affect a researcher’s belief in using web 2.0
toward collaboration. H2-1: Researchers’ belief in using web 2.0 for research may increase their chances
of collaboration 2.4
Incentives Protected by Research Ethics PhD candidates need incentives to be strongly engaged in online collaboration (Pidd
2011); these incentives are intrinsic motivation, satisfaction, and reputation. Purely
financial motivation is less important, but the motivation should be protected and
controlled by research ethics related to the digital environment (Mutula 2010). The
issue of trust should be considered by faculty involved in digital research processes
(Jirotka et al. 2006), as it has a special role in steering online networks (Lattemann and
Köhler 2005). Young researchers need to develop e-strategies to use research portals
to ensure and facilitate authentic human sources for knowledge transfer. While the
majority of them have adopted web 2.0 tools already, their willingness to shift from
offline to online digital research practices is crucial (Pscheida et al. 2013; 2014) to
build trust and protect scientific work in a virtual environment (Lam 2011). H4:
Novice researchers are more likely to collaborate and work with each other
when they receive incentives (as external motivation) that are protected and
combined with their trust and the value of their work (as internal motivation). H4-0: Incentives as an external motivation can influence ethics as an internal
motivation for enhancing research collaboration. H4-1: Research ethics as an internal motivation is closely related to research
collaboration H4-1: Research ethics as an internal motivation is closely related to research
collaboration 2.3
Support for Technology Use in Context Even though web 2.0 is a rather young technology, multiple studies have investigated
its benefits for learning, especially in the production and communication of scientific
research, or e-science (Pscheida et al. 2013; Kahnwald et al. 2015). A core aspect of
ICT infrastructure (web 2.0) is its strong linkage to the sociocultural context and the
disciplinary culture. While academic work triggers social interactions among PhD
scholars, the cultural context drives and assists their use of web 2.0 technologies
in order to interact. ICT and web 2.0 services in learning and research comprise
all methods, techniques, online behaviours of scientists, tools used by researchers,
knowledge sharing and transfer, acceptance/adoption, and building social networks
via e-research identified by literature reviews (Meyer and McNeal 2011). A doctoral
candidate’s use of web 2.0 technologies is both supported by and understood through
institutional context and discipline culture (Pscheida et al. 2013). Those have a partic-
ular need for being involved in one or more academic communities on a national or
international level in order to share and develop practice successfully, usually realised
through web 2.0 services (Veletsianos and Kimmons 2012; Eyman et al. 2009; Illeris
2004; Gillet et al. 2009; Lam 2011). H3:
Researchers are more likely to collaborate when they have received technical
support in their academic context. H3-0: web 2.0 technology may enhance research communication, leading to future
collaboration. H3-1: Research context has a direct influence on collaboration B. Mohamed and T. Köhler B. Mohamed and T. Köhler 36 3
Method For this paper, data was collected and analysed through the combination of two main
methods: (a) description of a quantitative online survey conducted in the German
Federal State of Saxony from 22 July 2012 until 22 October 2012, at the Technische
Universität Dresden and (b) forming and testing the structured model. The main aim
was to investigate novice researchers’ intentionality to collaborate with each other
through the use of web 2.0 and digital online technologies in academia. Our survey
included two main parts: the first part reveals demographic data and the second part
includes a 5-interval Likert scale with points ranging from 1 (strongly disagree) to
7 (strongly agree). The survey addressed doctoral students as novice researchers
who are using web 2.0 technology to communicate and collaborate in research daily
life. This 45-item measure was created for this study to assess participants’ percep-
tions, profiling the nine main factors that shape the final structure of the fish model:
task, time, activity, belief, support, context, incentive, ethics, and collaboration. The
instrument was then tested by three independent experts in research collaboration
before being given to respondents from the target audience. The authors received a
total return of n = 140 doctoral students who completed the survey. The data was
examined using factor analysis and our fish model was tested with the Partial Least
Squares (PLS) technique. SmartPLS, Version 2.0 M3 software was used to test the
model (Ringle et al. 2005, p. 1). The Fish Model: When Do Researchers … The Fish Model: When Do Researchers … 37 4
Results The majority of respondents (57.71%) were male, 66.74% were not married and
had no children, and 30.45% of respondents were from the School of Science, which
includes the 13.41% which were PhD students from the Faculty of Mechanical Engi-
neering. This can be considered typical for Saxony’s higher education landscape, as
it has a special focus on technical subjects. 4.1
The Measurement Model PLS is “the second-generation structural equation modelling technique that assesses
both the measurement and structural model in a single run” and was chosen for two
reasons: it works well for smaller sample sizes and eliminates restrictions on data
distribution such as normality (Serenko 2008, p. 465). Before analysing this model,
its reliability was measured. Cronbach’s alpha exceeded the required threshold of
0.7 for all items, implying high internal consistency of the scales (Serenko 2008). In order to submit an accepted level of eligibility for the questionnaire, half of the
items (24 of 45 items) were removed which do not have sufficient weight vis-à-vis
their main factor (Table 5, see Appendix). Once these items were removed, the model
was re-estimated. Reliability results are given in Table 1. The data shows that the
measures are robust in terms of their internal composite reliability. The composite
reliability of the different items ranges from 0.8 to 1.0, above the recommended
starting value of 0.70 (Serenko 2008). In addition, consistent with the guidelines of
Fornell and Larcker (Birnholtz 2005), the average variance extracted (AVE) for every
component is above 0.50. Table 2 presents the results of measuring the discriminant
validity for variable constructs. The matrix diagonal reports that the square roots of Table 1 Assessment of the measurement model
Variable constructs
Composite reliability (internal
consistency reliability)
Average variance
extracted/explained (AVE)
Time
0.80
0.57
Task
0.80
0.57
Support/tech
0.88
0.66
Incentives
0.83
0.62
Ethics
1.00
1.00
Context
0.82
0.69
Collaboration
0.84
0.58
Beliefs
0.83
0.62
Activities
0.85
0.59 Table 1 Assessment of the measurement model B. Mohamed and T. Köhler 38 Table 2 Discriminant validity (inter-correlations) of variable constructs
Latent variables
1
2
3
4
5
6
7
8
9
1. Time
1.00
2. Task
0.67
1.00
3.Support/Tech
−0.43
−0.39
1.00
4. Incentives
−0.23
−0.20
0.59
1.00
5. Ethics
−0.32
−0.30
0.37
0.33
1.00
6. Context
−0.027
−0.10
0.30
0.23
0.00
1.00
7. Collaboration
−0.31
−0.30
0.50
0.50
0.46
0.06
1.00
8. Beliefs
−0.44
−0.36
0.66
0.53
0.49
0.11
0.65
1.00
9. Activities
−0.28
−0.22
0.35
0.37
0.34
0.25
0.41
0.54
1.00 the AVEs are greater in all cases than the off-diagonal element in their corresponding
row and column, which supports the discriminant validity of the instrument. The instrument was tested additionally through PLS-Graph and for convergent
validity. Table 4 (see Appendix) shows the factor loading of all items to their respec-
tive latent constructs. 4.1
The Measurement Model All items loaded on their respective construct from a lower
pound of 0.70 to the upper pound of 0.85. In addition, the T-test of outer model
loading in the PLS-Graph output was highly significant (p < 0.001) for each factor’s
loading on its respective construct. The results confirm the convergent validity as
demonstrating a distinct latent construct. 4.2
The Structured Model Figure 2 presents the results of the structured model with interaction effect. In order to
assess the structured model, a bootstrapping technique was applied. The examination
of t-values was based on a 1-tail test with statistically significant levels of p < 0.05
(*), p < 0.01 (**), and p < 0.001 (***). Dotted lines highlight the insignificant paths. Structured components were formulated by multiplying the corresponding indicators
of the predictor and moderator construct. For clarity purposes, the outcomes of the structural model in terms of direct
effects, bootstrapping, and t-statistics confirmed the majority of the hypotheses, at
varioussignificancelevels.However,theresultsshowthatonlytwofactorsinresearch
collaboration are associated significantly (Fig. 2). Specifically, “Academic activities”
is very significantly associated with “Researchers’ beliefs” (H2-0 at β = −0.67, p <
0.001 level). In this first path, “Researchers’ beliefs” has a significant relation with
“Collaboration” (H2-1 at β = 0.41, p < 0.001 level). In the second path, “Incen-
tives” and “Ethics” contribute significantly to “Collaboration”. Accordingly, (H4-0)
confirms a significant relation between “Incentives” and “Ethics” (H4-0 at β = 0.71, 39 39 The Fish Model: When Do Researchers … Fig. 2 Structure model (PLS bootstrapping “path coefficient”). *significant at 0.05 level (1.96);
**significant at .01 level (2.58); ***significant at 0.001 level (3.29) ig. 2 Structure model (PLS bootstrapping “path coefficient”). *significant at 0.05 level (1.96);
*significant at .01 level (2.58); ***significant at 0.001 level (3.29) p < 0.001 level) along with the relationship (H4-1) between “Ethics” and shaping
“Collaboration” (β = 0.06, p < 0.05). The other two paths of predicting research collaboration are not significant. First,
“Technology and support” has a significant relationship with “Context” (H3-0 at β
= 0.64, p < 0.05), but, as a second path, the “Context” cannot predict research “Col-
laboration” (H3-1 at β = 0.00 not significant). Second, academic “Task” connected
strongly with the factor “Time” (H1-0 β = −0.70, p < 0.001). On the other hand, the
relationship between “Time” and shaping academic “Collaboration” (H1-1 β = −
0.00, not significant) was unrelated in the context of shaping academic collaboration
(Table 3). 5.1
Conclusions Theresultsofthisstudydemonstratethefactorsthatmightinfluenceresearchcollabo-
ration among novice researchers in Germany. The study conceptualised and validated
thefishmodelforunderstandingresearchcollaborationinthedigitalage,highlighting
where the model can be extended. A brief review of the findings raises the question
of what drives researchers’ propensity to collaborate using web 2.0 services. B. Mohamed and T. Köhler B. Mohamed and T. Köhler 40 Table 3 Research hypotheses and conclusions
Hypothesis
β (path-coefficient)
t-value
p-value
Validation
H1-0: An academic task to be done via web
2.0 is driven by a timeframe (when the task
should be done/how much time is needed
to do it)
0.70
12.61
< 0.001
Supported
H1-1: An appropriate time frame for a task
to be carried out via web 2.0 can lead to
academic collaboration
−0.00
0.03
n.s. Rejected
H1: Novice researchers are more likely to
collaborate and work with each other when
the work task (types, stages, and
technologies) and time frame are specified
Rejected
H2-0: Academic and research activities
(online) affect a researcher’s belief in using
web 2.0 for collaboration
0.67
9.71
< 0.001
Supported
H2-1: Researchers’ belief in using web 2.0
to support research may increase their
chances of collaboration
0.41
5.77
< 0.001
Supported
H2: Novice researchers are more likely to
collaborate and work with each other when
they believe in the work and participate in
academic and research activities (online)
Supported
H3-0: web 2.0 technology may enhance
research communication, leading to
collaboration
0.64
3.74
< 0.05
Supported
H3-1: Research context has a direct
influence on collaboration. 0.00
0.00
n.s. Rejected
H3: Researchers are more likely to
collaborate when they have received
technical support in their academic context
Rejected
H4-0: Incentives as an external motivation
can influence ethics as an internal
motivation for enhancing research
collaboration
00.71
3.79
< 0.001
Supported
H4-1: Research ethics as an internal
motivation is closely related to research
collaboration
0.06
1.74
< 0.05
Supported
H4: Novice researchers are more likely to
collaborate and work with each other when
they receive incentives (as external
motivation) that are protected and
combined with their trust and the value of
their work (as internal motivation)
Supported The Fish Model: When Do Researchers … 41 The first collaboration path showed that doing online doctoral research activities
might shape beliefs in using web 2.0 technologies for academic purposes and, thus,
enhance collaboration. An example is that using social media to connect with like-
minded people eventually shapes one’s belief about the importance of web 2.0. 5.1
Conclusions Researchers who believe in using such media are more likely to collaborate and
more open to empathy. Overall this study illustrates how the fish model can be applied to an online
setting in order to understand how the interaction between academic activities and
researchers’ beliefs can influence research collaboration. The results are consistent
with the previous mentioned literature as it was discussed by Terrell et al. (2009),
being successful can shape a person’s individual beliefs. Engaging in online research
activities in order to communicate and collaborate reflects individual beliefs that
controltheactionsthatcanenhancefurthercollaborationoffline,ashasbeenobserved
in a professional context (Köhler 1997). Researchers’ activities may reveal some
of the individual beliefs that back and catalyse collaboration. When researchers
engaged in online research activities, their belief in the use of web 2.0 in research
increased. Use of web 2.0 services such as social media can also predict productive
and conductive research collaboration (Pscheida et al. 2013). The second collaboration path shows that in keeping a balance between internal
“ethics” and external “incentives”, motivation can confirm collaboration. An example
is that researchers’ trust in sharing their ideas via web 2.0 services only grows when
they benefit from using such technology and, accordingly, it may lead to collabo-
ration. These findings have important implications for the fish model. Internal and
external motivations support future research collaboration. We argue that external
and internal motivations are closely related; consequently, in academia both types
of motivation help researchers become engaged in collaboration. Higher incentives
predict higher levels of trust; researchers are more likely to collaborate when they
trust the technologies they use. What motivates researchers to enhance collabora-
tion into the web 2.0 sphere depends on the technologies they can trust and use
to extend their professional networks. For collaboration among researchers, trust is
synonymous with benefit, which is the catalyst for collaboration. 5.2
Limitations In this study, research collaboration was defined as the use of web 2.0 technologies
for communication and daily research routines (reading, searching, writing, etc.). The authors addressed a subset of the concept labelled e-science or science 2.0. They
empirically observed doctoral scholars. These PhD students came mainly from the
Faculty of Mathematics and School of Science at the Technische Universität Dresden
in Germany. These aspects may limit the range and meaning of the findings presented. 42 B. Mohamed and T. Köhler Another limiting aspect is that the fish model reported only two significant paths
that may predict research collaboration. It would, however, be more informative if
measures of the other paths of the fish model (that appeared as non-significant in
our study) were measured once again in a different research context with another
sample. Appendix See Tables 4, 5, and 6. See Tables 4, 5, and 6. See Tables 4, 5, and 6. The Fish Model: When Do Researchers … 43 Table 4 Factor loadings (bolded) and cross loadings
Factor
Time
Task
Support/Tech
Incentives
Ethics
Context
Collaboration
Beliefs
Activities
TIM1
0.70
0.46
−0.29
−0.14
−0.19
0.05
−0.08
−0.20
−0.17
TIM2
0.81
0.52
−0.49
−0.25
−0.32
−0.07
−0.33
−0.50
−0.33
TSK1
0.57
0.81
−0.26
−0.20
−0.27
−0.03
−0.29
−0.30
−0.15
TSK2
0.47
0.70
−0.24
−0.11
−0.27
−0.09
−0.17
−0.21
−0.31
SUP1
−0.42
−0.44
0.83
0.44
0.30
0.23
0.44
0.60
0.29
SUP2
−0.35
−0.28
0.82
0.45
0.35
0.27
0.39
0.49
0.29
SUP3
−0.31
−0.24
0.86
0.57
0.29
0.29
0.40
0.58
0.29
INC1
−0.21
−0.11
0.40
0.85
0.32
0.07
0.38
0.45
0.34
INC2
−0.22
−0.26
0.67
0.75
0.21
0.35
0.42
0.50
0.32
INC3
−0.10
−0.14
0.37
0.74
0.23
0.18
0.40
0.31
0.20
ETK
−0.32
−0.30
0.37
0.33
1.00
0.00
0.46
0.49
0.34
CON1
0.02
−0.05
0.25
0.24
0.05
0.84
0.08
0.09
0.21
CON2
−0.064
−0.129
0.26
0.14
−0.04
0.83
0.02
0.09
0.21
CLB1
−0.25
−0.29
0.40
0.48
0.25
0.18
0.70
0.50
0.22
CLB2
−0.25
−0.24
0.31
0.32
0.39
0.01
0.76
0.49
0.42
CLB3
−0.19
−0.17
0.38
0.37
0.32
0.05
0.77
0.45
0.30
CLB4
−0.24
−0.22
0.43
0.36
0.41
−0.03
0.81
0.53
0.25
BEL1
−0.22
−0.25
0.48
0.32
0.35
0.04
0.41
0.78
0.50
BEL2
−0.39
−0.29
0.54
0.53
0.50
0.09
0.63
0.84
0.39
ACT1
−0.14
−0.11
0.16
0.26
0.18
0.20
0.22
0.27
0.72
ACT2
−0.34
−0.30
0.39
0.35
0.33
0.15
0.42
0.56
0.84
ACT3
−0.26
−0.16
0.25
0.21
0.28
0.13
0.30
0.44
0.75
(continued) B. Mohamed and T. Appendix Köhler 44 Table 4 (continued) 45 The Fish Model: When Do Researchers … The Fish Model: When Do Researchers … 45 Table 5 Items removed
Factor
Item
TSK3
It is more effective to ask colleagues for a declaration about unclear work tasks by
E-Mail or Skype than face-to-face
TSK4
The task of reading an online paper is more effective than a printed one
TSK5
Task of searching/sorting for literature review by using web 2.0 services more difficult
than my traditional way
TSK5
When I need to effectively discuss something related to my research with colleagues,
web 2.0 services are not the right solution
TIM3
It is necessary to invest a lot of time for communicating, researching, and working via
web 2.0 services
TIM4
Web 2.0 services save time for organising and managing our teamwork and working in
a scientific community
TIM5
Usage of synchronous web 2.0 services (in real time interaction) such as chat or video
conferences is more useful for managing online discussions than asynchronous tools
(e.g. Appendix online forum)
SUP4
The usage of web 2.0 services in a scientific research is difficult and I can’t understand
it
SUP5
I use web 2.0 services when others recommend something really interesting for me
SUP6
Peers and colleagues warn me to use web 2.0 services in research
CON3
My institute/faculty does not formally support using web 2.0 services among doctoral
students
CON4
The best way to contact my supervisor is through e-mail
CON5
Collaboratively reading, writing, and reviewing a paper via web 2.0 services in our
project/research group is not familiar yet
INC4
Receiving daily information about a recent paper, event, or colleagues’ activity, is a big
motivation for me to use web 2.0 services
INC5
Editing, commenting, reading, and reviewing dissertation tasks by using desktop word
processing software are more familiar to me than using web 2.0 services
ETK2
Taking on more responsibility in scientific editing, reviewing, commenting via web 2.0
services among researchers is ambiguous and uncertain
ETK3
Web 2.0 services signify for me a place where there is a lower level of data security
ETK4
Data security for me is an important issue for participating in any scientific editing,
reviewing, commenting, and reading via web 2.0 services
ETK5
My data can be stolen easily via web 2.0 services
ACT5
Giving online lectures is one of my usual online activities
BLF3
I believe that putting my data through cloud services is safe and enhances mobility
BLF4
Web 2.0 services may slow down my work load and research progress
BLF5
Managing time, procedures, reading, writing, reviewing, and daily events are
effectively done without using web 2.0 services
CLB5
I intend to communicate only through e-mail in scientific research, due to the fact that
research is an individual contribution Table 5 Items removed
Factor
Item
TSK3
It is more effective to ask colleagues for a declaration about unclear work tasks by
E-Mail or Skype than face-to-face
TSK4
The task of reading an online paper is more effective than a printed one
TSK5
Task of searching/sorting for literature review by using web 2.0 services more difficult
than my traditional way
TSK5
When I need to effectively discuss something related to my research with colleagues,
web 2.0 services are not the right solution
TIM3
It is necessary to invest a lot of time for communicating, researching, and working via
web 2.0 services
TIM4
Web 2.0 services save time for organising and managing our teamwork and working in
a scientific community
TIM5
Usage of synchronous web 2.0 services (in real time interaction) such as chat or video
conferences is more useful for managing online discussions than asynchronous tools
(e.g. Appendix online forum)
SUP4
The usage of web 2.0 services in a scientific research is difficult and I can’t understand
it
SUP5
I use web 2.0 services when others recommend something really interesting for me
SUP6
Peers and colleagues warn me to use web 2.0 services in research
CON3
My institute/faculty does not formally support using web 2.0 services among doctoral
students
CON4
The best way to contact my supervisor is through e-mail
CON5
Collaboratively reading, writing, and reviewing a paper via web 2.0 services in our
project/research group is not familiar yet
INC4
Receiving daily information about a recent paper, event, or colleagues’ activity, is a big
motivation for me to use web 2.0 services
INC5
Editing, commenting, reading, and reviewing dissertation tasks by using desktop word
processing software are more familiar to me than using web 2.0 services
ETK2
Taking on more responsibility in scientific editing, reviewing, commenting via web 2.0
services among researchers is ambiguous and uncertain
ETK3
Web 2.0 services signify for me a place where there is a lower level of data security
ETK4
Data security for me is an important issue for participating in any scientific editing,
reviewing, commenting, and reading via web 2.0 services
ETK5
My data can be stolen easily via web 2.0 services
ACT5
Giving online lectures is one of my usual online activities
BLF3
I believe that putting my data through cloud services is safe and enhances mobility
BLF4
Web 2.0 services may slow down my work load and research progress
BLF5
Managing time, procedures, reading, writing, reviewing, and daily events are
effectively done without using web 2.0 services
CLB5
I intend to communicate only through e-mail in scientific research, due to the fact that
research is an individual contribution B. Mohamed and T. Appendix Köhler 46 Table 6 Final measured items (items used)
Factor
Item
TSK1
Web 2.0 services may hinder my tasks in everyday research activities
TSK2
When I need to effectively discuss something related to my research with colleagues,
web 2.0 services are not the right solution
TIM1
Web 2.0 services are not helpful services in situations when information is needed on
the same day
TIM2
It is a waste of time to use web 2.0 services to establish communication or
collaboration with other colleagues in the context of doing research
SUP1
The uses of web 2.0 services are useful for my research
SUP2
I enjoy using web 2.0 services in editing, commenting on, and reading a piece of
research
S3
Using web 2.0 services may help a lot to inform me about important scientific events
CON1
My institute provides a proper knowledge management system/web 2.0 services (e.g. Appendix website) for improving communication and collaboration among doctoral students
CON2
Officially, Wiki is used as a platform for group activities and collaborative work
reports in my research group
INC1
Creating a personal profile in web 2.0 services would enhance my reputation
INC2
Using web 2.0 services in research helps me to satisfy my interests in my scientific area
INC3
Web 2.0 services facilitate the presentation of myself and marketing my research
ETK1
I trust sharing my data through web 2.0 services
ACT1
I usually engage in one or more online scientific discussions
ACT2
Sharing files, links, videos, or photos with colleagues is one of my daily uses of web
2.0 services
ACT3
Peer review of scientific work via web 2.0 services is one of my usual online activities
ACT4
Commenting and writing in one or more scientific online forums, weblogs, or wikis is
also one of my daily/weekly activities
BLF1
I believe that using web 2.0 services has become one of my everyday research routines
BLF2
I would say, to enhance academic collaboration, you should use web 2.0 services
CL1
I intend to engage and involve myself in a community of practice by using web 2.0
services
CLB2
I intend to share my reading, writing, review, and resources with other colleagues
when it is mediated by web 2.0 services
CLB3
I intend to coordinate and work together more when this coordination is facilitated by
web 2.0 services
CLB4
Willingness to communicate and collaborate in research with other disciplines could
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(2010) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
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adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license and
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statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. The Use of Digital Tools in Scholarly
Activities. Empirical Findings
on the State of Digitization of Science
in Germany, Focusing on Saxony Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida,
and Thomas Köhler Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida,
and Thomas Köhler Abstract Scholars are only beginning to understand what digitization means for
their work, that is, the conduct of science. Taking a broad perspective on e-science,
this paper provides empirical insights about two important aspects of the digitization
of science, namely the use of digital tools in scholarly activities and scholars’ percep-
tions of the change such use entails. The results of a German-wide survey of scholars
and supplementary qualitative interviews in the years 2012 and 2013 show that the
majority of scholars have adopted digital tools and that scholarly practice is affected
profoundly by the use of such tools. This does not apply to web 2.0 tools, which
remain a niche medium for some scholars. Small but significant differences exist
between disciplines, and decisions about individual tool use are utilitarian. Further
research is needed to assess the changes from a longitudinal perspective. Keywords E-science · Digitization · Scholarly practice · Survey results 1
E-Science, Cyberscience, Science 2.0: The Digitization
of Science Is on the Move EversinceGalileo’ssuccessfuluseofthetelescope,scientistshavereliedonnewtools
in their scholarly practice (Hankins and Silverman 1995). The advent of computer C. Minet
Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany
e-mail: Minet@hs-mittweida.de
S. Herbst · D. Pscheida · T. Köhler
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: Sabrina.herbst@mailbox.tu-dresden.de
T. Köhler
e-mail: Thomas.koehler@tu-dresden.de
S. Albrecht (B)
Berlin, Germany
e-mail: Steffen.albrecht@berlin.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_4
49 C. Minet
Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany
e-mail: Minet@hs-mittweida.de
S. Herbst · D. Pscheida · T. Köhler
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: Sabrina.herbst@mailbox.tu-dresden.de
T. Köhler
e-mail: Thomas.koehler@tu-dresden.de
S. Albrecht (B)
Berlin, Germany
e-mail: Steffen.albrecht@berlin.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_4
49 C. Minet
Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany
e-mail: Minet@hs-mittweida.de
S. Herbst · D. Pscheida · T. Köhler
Media Center, Technische Universität Dresden, Dresden, Germany
e-mail: Sabrina.herbst@mailbox.tu-dresden.de
T. Köhler
e-mail: Thomas.koehler@tu-dresden.de
S. Albrecht (B)
Berlin, Germany
e-mail: Steffen.albrecht@berlin.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_4
49 C. Minet
Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany
e-mail: Minet@hs-mittweida.de 49 49 50 S. Albrecht et al. S. Albrecht et al. technology and digital networks was no exception, impacting not only the commu-
nication of research, but also the production of new knowledge. The World Wide
Web with its network of hypertexts and its gradual change to web 2.0 with the addi-
tional manifestation of online social networks reinforce this impact and generate
more potential. Although this cooperative process is not new (Bijker and Law 1992;
Mayntz 1993), we are still only beginning to understand the changes that digitiza-
tion entails for science. This paper furthers our understanding by providing empirical
insights from an online survey of German scholars related to two specific aspects
of the digitization of science, namely the use of digital tools in research, teaching
and other scholarly activities, and scholars’ perceptions of the change that such use
brings. g
Several terms have been proposed to apprehend how science is influenced by
networked computer technologies. In 1999, the term e-science was introduced by
John Taylor, General Director of the Research Council at the Office of Science and
Technology of the UK. Taylor realized that new technological infrastructures were
needed to foster global cooperation and data-intensive research in science. 1Other notions of the digitization of science, include “digital scholarship” (Weller 2011) and “digital
science” (European Commission 2013). 1
E-Science, Cyberscience, Science 2.0: The Digitization
of Science Is on the Move In other
words, “e-science is not a new scientific discipline; rather, the e-science infrastructure
developed […] should allow scientists to do faster, better or different research” (Hey
and Trefethen 2005: 818). Jim Gray specified what such “different research” could
look like. He identified a “fourth paradigm” of scientific inquiry, “data-intensive
science” that is characterized by the use of massive amounts of data to generate new
theoretical models (Gray 2009: xix). Michael Nentwich (2003) took a more holistic view of “cyberscience,” including
how academic work is organized, how it functions, and what its products are. While
emphasizing its novelty compared to “traditional science,” he technically assesses the
digitization of science. In a recent update with René König, Nentwich used the term
“cyberscience 2.0” to acknowledge the emergence of web 2.0 and its relevance to
scholarly communication (Nentwich and König 2012). “science 2.0” is another term
that emphasizes the importance of web 2.0 in facilitating openness and collaboration,
focusing on online communication tools such as weblogs or wikis that open up
science communication to external audiences (Waldrop 2008).1 Despite their nuances, all these terms are more similar than different. A broad
notion is best suited to address the diverse issues involved in the digitization of
science. Here and in the e-Science Research Network Saxony (www.escience-sachse
n.de), we use the term e-science to comprise science, social science, and humanities
disciplines, not only in research and collaboration, but also in teaching and science
communication. In terms of technology, e-science comprises digital tools used in
scholarly work that go beyond the individual computer and represent digital media
or online-based, networked software systems. Taking a broad perspective on digitization means normatively assessing this pro-
cess without bias. This involves considering not only the changes in technology,
but also changes induced by the social environment. Soon before e-science got onto The Use of Digital Tools in Scholarly Activities … 51 the agenda, several authors recognized fundamental changes in how science was
generally understood. “In response to the challenges of policy issues of risk and the
environment, a new type of science – ‘post normal’ – is emerging,” wrote Silvio
Funtowicz and Jerome Ravetz (1993: 739). In a similar vein, Michael Gibbons and
colleagues (1994) observed the emergence of what they called “mode 2” science,
which was transdisciplinary and involved stakeholders from outside the scientific
community. 1
E-Science, Cyberscience, Science 2.0: The Digitization
of Science Is on the Move Both diagnoses overlap in noting an increasing external influence on
science from politics, the economy, and civil society. The interrelations between
technological and social change are not the main focus here, but developments within
science such as the role of web 2.0 in opening up the research process might be part
of a broader social change, in which technology plays only a moderating role. The aim of this paper is to provide empirical observations of changes in scientific
practice in relation to technological change, focusing on media use in science. Our
approach is based on two fundamental assumptions. First, we find that considerable
attention is devoted to the potential and affordances of digital technologies, but much
less notice is taken of what scholars actually do with these technologies in their day-
to-day practices, including potential non-adoption and refusal to use them (cf. Barassi
and Trer 2012: 1282). Second, while there are a number of empirical case studies of
scholars’ use of technology in specific fields, we think a broad view on all aspects
of scholarly practice is necessary to identify the changes, before the nature of such
change in specific areas can be analyzed. 2
The Empirical Question: Is Digitization Really
on the Move? The empirical perspective of this paper goes beyond the rhetoric and euphoric expec-
tations of some e-science discourse. We ask three questions. To what extent do
scholars use digital media and online tools in their day-to-day academic activities? What kind of new practices emerge from such use? How do such changes in the
conduct of science contribute to the bigger structural changes? Technological innovation always takes place in form of co-evolution of engi-
neering and social domains (Köhler 1998). Adoption theorists have pointed out that
the adoption process is not just a matter of time, but also of individual differences,
system characteristics, social influence, and facilitating conditions (Venkatesh and
Bala 2008). Against this background, we can assume that the adoption of digital tools
is not as straightforward a process as is depicted by some of the theoretical accounts
discussed above: it is ongoing and has to be observed empirically to determine its
state and direction. Our paper adds to the small, but growing empirical literature
about the impact of using digital tools in science. Previous research has shown that investigating scholars’ use of digital tools poses
methodological problems. There are a number of different approaches, all with
specific merits and pitfalls. We can broadly distinguish a qualitative orientation with 52 S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. a focus on in-depth analysis of a limited number of cases, often based on stakeholder
interviews or case studies (see, e.g., Currier 2011; RIN/NESTA 2010; Bullinger
et al. 2010), and a quantitative orientation with a focus on assessing the whole field,
often based on standardized surveys. As our aim is to provide a holistic and realistic
assessment of the state of adoption, we mainly review previous quantitative research. Lattemann et al. (2010), ZBW (2011), Donk (2012), and Pscheida and Köhler
(2013) all address a limited target group (principal investigators in funded research
projects, economics researchers and students, researchers at one specific university,
and scholars at universities in Saxony, respectively). Thus, none of this research is
particularlyhelpfulintermsofeithermethodologyorresults.Inanearlystudyof1477
UK re-searchers, Procter et al. (2010) found that 60% used a web 2.0 tool (blogging,
commenting, sharing resources, or contributing to wikis) in their scholarly activities,
but only 13% did so frequently. The authors consider this figure “rather low” and
observe that frequent users are most likely to be computer scientists or mathemati-
cians, engineers, or scholars in the arts and humanities. 2
The Empirical Question: Is Digitization Really
on the Move? Ponte and Simon (2011)
also focus on web 2.0 use, but based on a self-selected sample of 345 persons from
across Europe. They report the use of wikis and blogs by about 40% of respondents,
academic social networking sites by 35%, and microblogging by 18% of researchers. Results for specific groups are not presented. Bader et al. (2012) analyzed 1053 responses to an online survey of scholars at
German universities. They found that communication tools such as e-mail (94%),
mailing lists (24%), and Skype (21%) were widely adopted, web 2.0 tools like blogs
or research portals were much less used (6% use wikis, 5% use research portals
or social networking sites, 4% use academic blogs, and 2% use Twitter). The tools
used varied greatly by discipline: wikis were mostly used in science and engineering,
whereas mailing lists and blogs were more popular in humanities and social sciences,
especially in law, and research portals were favored by social scientists. In general,
the authors consider German researchers to be at an “early stage” of adopting digital
communication tools. Despitethesmallnumberofstudiesofsufficientscopeandmethodologicalquality,
these results raise doubts about the predicted impacts of digital tools on science. In
the best case, adoption is too early to have had a significant impact. In the worst
case, apart from some small groups, scholars are not tempted to actually use digital
tools in their work. The existing research shows that digital tool adoption in scholarly
activities is low (apart from very popular tools such as search engines), that web 2.0
tools are much less likely to be used than more conventional ones, and that disciplines
seem to play a role in the choice of tool. 3
Hypotheses, Data, and Methods To remedy the obvious lack of comprehensive, quantitative research, our paper seeks
to empirically assess the state of adoption of digital tools by scholars and their impacts
on the basis of new data from the Science 2.0 Survey 2013 (Pscheida et al. 2014). The Use of Digital Tools in Scholarly Activities … 53 Based on our above analysis of previous research, we assume that to have an impact
on scientific activity, digital tools have to be used for scholarly purposes in the first
place. This leads us to the following hypotheses and research questions. Based on our above analysis of previous research, we assume that to have an impact
on scientific activity, digital tools have to be used for scholarly purposes in the first
place. This leads us to the following hypotheses and research questions. Hypotheses. Our first two hypotheses concern the extent to which scholars use
digital tools in their activities. H1: The adoption of digital tools in scholarly activities is still in an early phase,
with diffusion levels (Rogers 1995) below 50% of the population (“early majority”). H2: Web 2.0 tools like weblogs, wikis or microblogging are used by a minority
of scholars for professional activities, with diffusion levels below 16% (“early
adoption”). p
Our third hypothesis concerns the differences between disciplines and is formu-
lated as research question, since previous research is inconclusive. RQ1: Do scholars in different disciplines use digital tools differently? RQ1: Do scholars in different disciplines use digital tools differently? Finally, we are interested in how digital tool use impacts on the conduct of science
leading to another research question. Finally, we are interested in how digital tool use impacts on the conduct of science,
leading to another research question. Finally, we are interested in how digital tool use impacts on the conduct of science,
leading to another research question. RQ2: What changes in the conduct of science as a result of digital tool use do
scholars perceive? RQ2: What changes in the conduct of science as a result of digital tool use do
scholars perceive? Data. We collected data in two related steps. First, an online survey of 778
scholars at German universities was conducted in autumn 2013, addressing ques-
tions such as scholars’ use of 17 different tools and services, their academic and
sociodemographic background, their motives for and attitudes to using digital tools
(see Pscheida et al. 2The data set of the Science 2.0 Survey 2013 is open access: see www.escience-sachsen.de. 3
Hypotheses, Data, and Methods 2014).2 Although quota sampling of universities was applied
in the recruitment procedure, the sample shows some deviations from the popula-
tion with regard to gender (women are slightly overrepresented), professional status
(professors are overrepresented, research assistants or “WHK” underrepresented),
discipline (with medicine strongly underrepresented, humanities, mathematics, and
natural sciences slightly overrepresented), location, and type of university. While
the latter two could be adjusted by weighting, the other deviations should be kept in
mind in interpreting the results. In addition, all scholars at universities in the German
federal state of Saxony were invited to participate in the same survey, with 442 ques-
tionnaires being submitted. The Saxony sample shows similar patterns of deviations
from the population, except that with regard to disciplines, engineers and mathemati-
cians/natural scientists are strongly overrepresented, whereas medicine and the fine
arts are underrepresented. The quantitative survey was supplemented in the first half of 2013 by 19 interviews
with scholars in Saxony, chosen to map the various disciplines and status groups. The semi-structured interviews focused on the scholars’ perception of the use of
digital tools and of the changes this entails. Due to the variety of scholarly practices
and lack of knowledge about the precise impact of digital tools on them, qualitative
interviews were chosen to address our second research question. Methods. The hypotheses and research questions were statistically analyzed,
comparing the Saxony and German-wide samples. Adoption was measured by asking
scholars “to what extent do you use the following?” followed by a list of 17 different S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. 54 online tools. Answers were categorized by frequency of use. In the analysis, only
uses for scholarly work (research, teaching, research administration, and science
communication) were taken into account. Based on Schmidt’s (2007) definition,
social networking sites, wikis, video/photo community portals, weblogs, microblogs,
and social bookmarking services are regarded as “social software” or “web 2.0 tools,”
astheyconstitutesocialorhypertextualrelationshipsof(atleastpartially)publicchar-
acter (Schmidt 2007: 32). The disciplines were categorized based on the definition
of the German Federal Bureau of Statistics (2012) into arts and humanities; (natural)
sciences (including mathematics); engineering and social sciences (including law and
economics). Finally, the qualitative interviews were transcribed and anonymized, and
qualitative content analysis methods were applied to the responses. 4
Results 4.1
General Level of Adoption of Digital Tools in Scholarly
Activities 4.1
General Level of Adoption of Digital Tools in Scholarly
Activities Scholarly activity at German universities in 2013 was affected considerably by the
use of digital tools. Of all 17 tools the survey asked about, ten were used by more
than 50% of all respondents in a professional context (with two others by 49%, see
Fig. 1). Only general-purpose social networking sites, online editors like Etherpads 0
10
20
30
40
50
60
70
80
90
100
Wikipedia
Online Archives
Mailing Lists
Content Sharing
Videoconferencing/VoIP
Online Forums
Other Wikis
Video-/Photo CommuniƟes
Reference Management
Learning Management Systems
Academic Social Networks
Chat/IM
Social Networks
Online Editors
Weblogs
Microblogs
Social Bookmarking
Germany
Saxony
Fig. 1 Level of adoption (in %) of digital tools in scholarly use in Germany and Saxony Fig. 1 Level of adoption (in %) of digital tools in scholarly use in Germany and Saxony The Use of Digital Tools in Scholarly Activities … 55 or Google Docs, weblogs, microblogs like Twitter, and social bookmarking services
are used by less than about half of all respondents. Wikipedia is the tool with the
broadest diffusion in academia, with 95% of respondents reporting to have used
Wikipedia in their scholarly work. Comparably extensive more than three quarters
of the respondents use online archives like Arxiv.org and mailing lists. The pattern for scholars in Saxony is quite similar to the national one. Wikipedia,
online archives, and mailing lists are the tools with the highest level of adoption
in the context of scholarly work. Social networking sites, online editors, weblogs,
microblogs, and social bookmarking services are used by less than half of the respon-
dents, including professional social networking sites like Xing or Academia.edu. The
general level of adoption of digital tools in Saxony is a bit lower than in Germany
as a whole. The reverse is true for online forums (64% in Saxony, 56% in Germany)
and wikis other than Wikipedia (62% in Saxony, 55% in Germany). Of course, such
seems still to be a contradictory observation as many scientists recommend their
students not to use digital tools like Wikipedia due to the “non-scientific” nature. So
is especially valuable exploring in more detail practices of adoption among scientists. In some cases, digital tools may be used more for general than work-related
purposes (see Table 1). 4.1
General Level of Adoption of Digital Tools in Scholarly
Activities Content sharing and cloud services, video conferencing
and VoIP (“online telephone”) services, online forums, video/photo communities, Table 1 General and work-related use (in %) of digital tools in Germany and Saxony. Note the
high level of general use
Digital tool
Germany
Saxony
General
Work
General
Work
Social networking sites
57.9
32.9
51.1
21.0
Academic networking sites
52.7
48.8
41.0
37.6
VoIP
71.7
58.0
64.3
46.2
Microblogs
15.1
10.5
5.9
1.6
Weblogs
29.2
22.2
28.3
22.6
Wikipedia
98.9
95.2
100
96.2
Other wikis
56.5
55.1
63.6
61.5
Content sharing/cloud server
73.5
67.7
64.3
54.5
Online editors
26.7
24.9
24.4
21.0
Online forums
65.3
56.0
74.0
64.0
Mailing lists
77.4
76.2
74.0
71.5
Chat/IM
69.1
48.7
69.2
44.3
Online archives
79.8
79.3
76.7
76.2
Reference management
52.2
52.2
49.1
48.4
Social bookmarking services
5.9
5.2
4.3
3.8
Video/photo communities
80.4
54.8
78.3
45.7
Learning management systems
52.3
52.2
56.1
55.7 able 1 General and work-related use (in %) of digital tools in Germany and Saxony. Note the
igh level of general use S. Albrecht et al. 56 S. Albrecht et al. chat/instant messaging (IM), social networking sites, and microblogs all show a
significantly higher level of personal than professional use. Where data for compar-
ison exists, the use of digital tools is more widespread among scholars than in the
German population in general (cf. data from the ARD/ZDF Online Study 2013, van
Eimeren and Frees 2013). With regard to our first hypothesis, we can thus infer that the adoption of digital
tools in scholarly activities has left the phase of early adoption and has reached a more
mature state with more widespread use. Although a considerable number of scholars
do not use certain digital tools, and some tools have not reached broad adoption, the
majority of tools our survey asked about are used by more than 50% of respondents. 4.2
Use of Web 2.0 Tools Among Scholars The situation is different for web 2.0 tools such as wikis, blogs, social networking
sites, social bookmarking services, and video/photo communities. While about half
of respondents use wikis, video/photo communities and academic social networking
sites in work-related contexts, only between 5 and 32% of scholars use general-
purpose social networking sites, weblogs, and microblogs as well as social book-
marking services for work. Considering the broad adoption of digital tools in general
and the length of time that web 2.0 tools have been in use, the latter have to be
considered a niche product with regard to scholarly use. The figures for Saxony are
comparable, but generally lower than for the national level (except for wikis, see
above). However, with regard to our second hypothesis, web 2.0 tools have a higher
adoption level than the 16% “early adoption” rate, at both the national and the Saxony
level, with the exception of microblogs and social bookmarking services. At the
same time, only a minority of scholars use web 2.0 tools that have not been designed
specifically for academics. Given that these tools have been in use for a long time
and are well known among scholars (except for social bookmarking services, which
about 50% of respondents said they didn’t know about), we have to conclude that
web 2.0 tools have only reached specific groups of scholars (cf. Pscheida et al. 2014:
18). It seems to be difficult for most scholars to find useful applications for these
tools. From the results of the survey, we can more generally infer that tools are adopted
when a specific use is found for them. Most of the tools with high levels of adoption
are specialized for one or more areas of scholarly work. Most respondents said that
the digital tools they use are practical or make their work easier and faster (Pscheida
et al. 2014: 24f.), indicating the prevalence of utilitarian motivation. This was not
equally the case for all tools. General-purpose social networking sites and microblogs
show a different pattern of use: both tools are used twice as often in a personal than a
professional capacity, that is, utilitarian motivation was less important. 4.2
Use of Web 2.0 Tools Among Scholars The two main
reasons for not using general-purpose social networking sites in a scholarly context
are disagreement with the terms of use (indicated by 24% of those researchers who The Use of Digital Tools in Scholarly Activities … 57 do not use them for work) and personal use (indicated by 18%). For microblogs,
the most salient obstacle is the lack of additional benefit (indicated by 56% of those
researchers who don’t use microblogs for work). Besides the prevalence of pragmatic reasons, researchers who use web 2.0 tools
(like academic network sites, weblogs, or microblogs) also mentioned an interest
in new technologies or that these tools help to boost their reputation. This shows
awareness of the social and hedonistic (as one could say) affordances of web 2.0
tools. 4.3
Disciplinary Differences Our third hypothesis was about the differences between disciplines in scholars’ adop-
tion of digital tools. The results of the survey indicate a more nuanced picture than
previous studies have drawn. Cross-tabulation and computation of Cramer’s V (a
bivariate measure of association) for the German study show small but significant
differences in professional use of Wikipedia, wikis, online editors, mailing lists,
online archives, reference management systems, social bookmarking services, and
video/photo communities (see Table 2). In all other cases, no difference between
disciplines in the use of digital tools for scholarly purposes is found. Digital tools are most highly adopted in the (natural) sciences and in arts and
humanities, whereas engineering and social sciences show lesser degrees of adop-
tion. However, engineering scientists use wikis and video/photo communities quite
heavily, and social scientists use mailing lists and online archives to a similar degree
as the (natural) scientists. For Saxony, significant differences between the disciplines are more frequent
and related to other tools than in the German-wide study. Social networking sites,
academic networking sites, VoIP, microblogs, weblogs, content sharing services,
chat/instant messaging services, reference management systems, and learning
management systems all show small but significant differences between disciplines
(see Table 3). Social scientists use tools most across all categories, followed by
scholars in arts and humanities. The only tools which are used more extensively by
natural scientists and engineers are Wikipedia and other wikis, but these findings are
not statistically significant. The differences between the Saxony and German-wide results are striking. They
might be explained by the special disciplinary structure of universities in Saxony,
which have a strong emphasis on natural sciences and engineering. For Germany as
a whole, such differences might exist, but are leveled off due to the mix of academic
cultures and institutional structures across the various federal states. However, the
differences are generally small, with low values of Cramer’s V, so we can conclude
with regard to our first research question that there are only small differences between
the disciplines, highly dependent on the disciplinary context in which each tool is
used. 58 S. Albrecht et al. S. Albrecht et al. 4.3
Disciplinary Differences Table 2 Professional use (in %) of online tools by scholars at German universities in 2013 across the
most relevant disciplines: arts and humanities; (natural) sciences; engineering and social sciences
Digital tool
General
n=778
Humanities
n=225
Natural
sciences
n=243
Engineering
n=116
Social
sciences
n=133a
Cramer’s
Vb
Social
networking
sites
32.9
37.6
32.2
24.1
35.1
−
Academic
networking
sites
48.8
48.7
53.5
44.0
53.8
−
VoIP
58.0
57.8
60.7
57.8
56.4
−
Microblogs
10.5
12.0
10.7
8.6
11.9
−
Weblogs
22.2
25.8
23.0
16.2
23.3
−
Wikipedia
95.1
93.8
98.8
94.9
90.2
.112
Other wikis
55.1
52.2
68.7
56.0
44.4
.114
Content
sharing/cloud
server
67.7
69.9
70.8
59.5
69.9
−
Online editors
24.8
28.0
26.7
22.2
21.2
.092
Online forums
56.0
58.0
59.3
65.5
45.1
−
Mailing lists
76.2
81.0
76.9
63.8
75.2
.093
Chat/IM
48.7
51.8
54.5
40.5
49.6
−
Online archives 79.3
86.3
78.2
67.5
78.9
.110
Reference
management
52.2
53.3
63.6
33.3
43.6
.158
Social
bookmarking
services
5.3
4.4
9.1
2.6
3.8
.100
Video/photo
communities
54.8
64.2
48.6
57.8
43.3
.116
Learning
management
systems
52.2
56.9
44.7
51.3
59.0
−
aincluding law and economics
bsignificance α<.05
−indicates that no significant correlation is observed aincluding law and economics g
bsignificance α<.05 g
bsignificance α<.05 −indicates that no significant correlation is observed If discipline does not explain differences in the use of digital tools, how else
might we explain them? Some indications can be found in the 19 semi-structured
interviews that were conducted to supplement the quantitative investigation. Content
analysis methods according to Mayring (2000) were used to analyze these. In a
first step, categories of analysis were generated based on the interview guideline. 4.3
Disciplinary Differences These categories were then tested against the empirical material, and continuously The Use of Digital Tools in Scholarly Activities … 59 Table 3 Professional use (in %) of online tools by scholars at universities in Saxony in 2013
across the most relevant disciplines: arts and humanities; (natural) sciences; engineering and social
i Table 3 Professional use (in %) of online tools by scholars at universities in Saxony in 2013
across the most relevant disciplines: arts and humanities; (natural) sciences; engineering and social
sciences
Digital tool
General
n=442
Humanities
n=49
Natural
sciences
n=124
Engineering
n=191
Social
sciences
n=47a
Cramer’s
Vb
Social
networking
sites
21.3
28.6
21.8
13.6
34.0
.165
Academic
networking
sites
37.6
32.7
37.9
31.9
66.0
.165
VoIP
46.8
42.9
53.2
39.3
63.8
.145
Microblogs
5.9
6.1
4.8
1.6
21.3
.197
Weblogs
24.0
30.6
25.0
16.2
38.3
.133
Wikipedia
96.2
91.8
98.4
96.3
93.6
−
Other wikis
61.5
59.2
64.5
61.8
61.7
−
Content
sharing/cloud
server
55.0
71.4
50.8
47.1
72.3
.146
Online editors
27.8
20.4
25.8
15.7
31.9
−
Online forums
64.0
49.0
67.7
64.9
68.1
−
Mailing lists
71.5
77.6
75.8
64.4
85.1
−
Chat/IM
45.0
42.9
54.8
36.1
55.3
.140
Online archives 76.2
71.4
77.4
74.9
85.1
−
Reference
management
48.4
51.0
51.6
40.8
66.0
.138
Social
bookmarking
services
3.8
4.1
5.6
3.7
2.1
−
Video/photo
communities
46.4
53.1
45.2
41.9
59.6
−
Learning
management
systems
55.7
77.6
53.2
49.2
80.9
.175
aincluding law and economics
b i
ifi
05 g
−indicates that no significant correlation is observed revised and amended with sub-categories during analysis. In a third step, relations
and causalities between categories and sub-categories of analysis were carved out. revised and amended with sub-categories during analysis. In a third step, relations
and causalities between categories and sub-categories of analysis were carved out. 60 S. Albrecht et al. S. Albrecht et al. The results do not point to disciplinary differences, but instead to the influence of
the tangible working practices in which scholars are involved. These can be collabo-
rations, such as in projects with many partners (interview 8), working groups (inter-
views 1, 7) or institutions (interview 7), but also institutional contexts, such as when
“interdepartmental” wikis are created (interview 8) or the institutional website is
used for information sharing, because “those who are concerned and who will look
at the information [are] mainly limited to the institute” (interview 19). 4.3
Disciplinary Differences y
Another important determinant for the use of a digital tool is its quality and
suitability for specific working contexts. Digital tools are expected to make working
processes more efficient: “the biggest obstacle and a huge inefficiency is how we
communicate data. We copy, we process data again and again” (interview 3). Wikis,
for example, are used to facilitate collaborative work: “to manage data, I do not have
to send e-mails around where nobody knows what the current state is” (interview 8). Similar motivations underlie the use of cloud services like Dropbox (interview 5) or
instant messaging clients and VoIP services such as Skype and ICQ (interview 8). The use of e-mail for collaborative work is considered rather inefficient (interviews
3, 5, 8). Wikis can be used as “encyclopedias,” to provide information in a structured and
clearly arranged way, “where you can collect things that you maybe will have to look
up in future” (interview 19). Wikis are repositories “where all kinds of information
are collected” (interview 19); “just to preserve collected knowledge that you can
look up again” (interview 7); “where knowledge for all is provided” (interview 1);
“to upload files in the current state, where it can then be downloaded” (interview 8). This also refers to the exchange of administrative information, such as in managing
technical infrastructure (interview 9) or as an organizational manual (interviews 9,
15). However, once data protection becomes an issue, web-based tools and services
are not used despite their efficiency savings: “I would have proposed Dropbox, but
because of data protection requirements we cannot use it” (interview 11). Instead,
local network servers are used to exchange data, especially in cases where the cooper-
ation is limited to partners in the same institution: “to some extent we have this in our
working group internally, using the university file system. There we have our account
and there is our stuff, i.e. the programs, and everybody in our working groups who
wants can use it” (interview 1). Yet, web-based applications are important “espe-
cially if you collaborate with external partners” (interview 8). From a qualitative
perspective, too, the conclusion is that the requirements of collaborative work and
the affordances of the technology have a stronger influence on scholars’ choice of
digital tools than professional affiliations. 4.4
Changing Scholarly Practices The above analysis sheds some light on an important prerequisite for any changes
in the conduct of science induced by digitization, namely the actual use of digital The Use of Digital Tools in Scholarly Activities … 61 tools in scholarly activity. But this is just a necessary, not a sufficient, condition for
change. The semi-structured interviews indicate what kind of changes scholars in
Saxony perceive. Of course, such perceptions might not give an accurate account of
the situation, but until better data is available (e.g., from long-term observations of
scholarly practices), qualitative interpretation of perceptions from actors within the
field with a variety of perspectives gives a good approximation. Our interview partners indicated a number of changes in their work practices
which they did not see as related to technology use, but rather to a changing social
environment in science. The importance of collaborative work is seen as growing. Short-term research projects can require the use of certain digital tools (interview
8) or new competencies, such as writing research proposals (interview 7). Work
biographies are seen as becoming more flexible. Temporary retirement affects the
way of working and the adoption of new technologies: “so I did not slowly get used to
[web-based tools], I knew work without them and when I was re-entering, I had to use
and become acquainted with the different tools” (interview 1). This flexibility also
includes geographical mobility and increasing independence from local contexts: the
use of Skype “has actually naturalized through stays abroad, only to stay in touch”
(interview 14). Interviewees mentioned several changes in their personal way of working that they
related to technological conditions. The entire process of scientific enquiry, including
literature research, has tremendously accelerated: “you simply find something imme-
diately rather than writing letters to ask: ‘what did you do there actually?’” (interview
19). Before using digital archives, “we had to […] ask for interlibrary loan literature
and had to wait” (interview 16). Technology is explicitly mentioned as an attractive
agent of change: “so I still remember card indexes in libraries and of course when
the online catalog was there, then you liked to use it” (interview 14). This also relates
to the management of literature: “I think the trigger was that the university offered
Refworks and that we got an account for the group” (interview 1). 4.4
Changing Scholarly Practices Communication processes seem to be particularly affected: “if I have a meeting
withsomeonetoday, I just searchfor her or himontheInternet beforeandlookupwho
it is. If I’m lucky, I have a small CV or at least I see what she or he does” (interview
13). Communication is increasingly shifting into virtual spaces (interview 17): “in
times of my diploma one rather met personally, […] so if calling on the telephone did
not work, then one rather met personally somehow” (interview 7). What is more, the
way information is stored and made available has changed: “I have scarcely printed or
written documents, […] all of my documents are digitized. Either as a PDF or HTML
page or in another format, like video or other scripts or programs” (interview 2). This
in turn influences the access to information: “in the past, I can still remember that I
used a usual lexicon from the bookshelf, which I not so long ago just sold because
I have not been using it anymore and it stood around useless” (interview 9). Again,
the affordances of new technologies are described as attractive: “I notice that I still
prefer printed paper, but this changes step by step and in ever more cases, I do not
print the reports I read, but rather read them on the screen somewhere and if I have
the opportunity also highlight sections as it is possible with various apps on the iPad, 62 S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. then for me this actually replaces printed and nicely annotated reports because I thus
have the same opportunities to work” (interview 18). Advancements in data infrastructure, including the availability of faster and more
efficient Internet connections or better computing capacities, primarily affect infor-
mation sharing and data analysis, “just because it was somehow difficult to load ten
megabytes from the Internet with the first emerging DSL connections” (interview
15), and “if one then changed from modem to ISDN and DSL, then you increasingly
used it, it went faster” (interview 14). The ubiquity of computing and network power
eases the work process “because you don’t have to rack your brain, should I resize
photos in the dataset or not, instead you just send it” (interview 12). 5
Summary and Discussion Our study empirically observes the digitization of science and its effects on schol-
arly practices. Starting from the individual use of digital tools by scholars as the
most important element in the digitization process, we have measured the adoption
of digital tools in scholarly work in Germany, focusing on Saxony. By critically
extending previous work, our results show that the majority of scholars adopted such
tools and that scholarly practice is affected profoundly by their use. We have also
shown that this does not apply to all kinds of tools. Web 2.0 and its affordances for
scholars might stimulate much debate, but a minority of scholars only uses tools such
as weblogs and social networking sites. Presumably, a neglect of epistemological and
technological sociological analyses of scientists’ activities can be identified, which
has to be overcome. This goes hand in hand with the need for a review with regard to
digital science technologies, which has so far been reflected neither in the curricula
for training nor in the self-image of the scientists. Our survey indicates that there are small but significant differences in disciplinary
adoption of digital tools. The arts and humanities show higher levels of adoption than
engineering and the social sciences. However, the degree of use greatly depends on
the tool in question. Similarly, the change which the tools induce varies greatly by
scholarly activity. Our analysis of the qualitative interviews has confirmed that tools
are chosen based on utilitarian motives, and given rise to new hypothesis about the
interrelation between individual, technological, and systemic factors of change in
the digitization of science. In comparison with the discourse on e-science, cyberscience, and science 2.0,
but also to the results of previous empirical studies, our results show that the digi-
tization of science is indeed on the move in Germany. The level of adoption is
higher than in previous studies, with many digital tools reaching broad professional
diffusion. The full potential of e-science has yet to be exploited. Our interviews indi-
cate that institutional cultures and the affordances of the technologies do not fit well
enough to let these online applications evolve into widely used professional scholarly
tools. Still there is need for further consideration, including individual competency
development. Our results certainly do not provide definite answers to the questions raised at the
beginning of this paper. 4.4
Changing Scholarly Practices Parts of data
analysis are replaced by automated processes: “30 years ago or maybe more, you
went with stacks of punch cards to the computing center and tried to compute a t-test
or something similar, and now you just have to push the button” (interview 5, cf. interview 19). The availability of portable devices, “that we have just passed on to
equip all staff with laptops, [i.e.] no location-bounded work on the computer we sit
in front of anymore” (interview 15), supports highly flexible working practices. Finally, the attitude of researchers toward new technologies, their openness and
curiosity to try something new also affect their working practices: “then I had a
telephone bill of about 80 marks which was very high for a student, just because
I intensively explored the Internet” (interview 16). Or, as another interviewee said:
“whenever a new technology emerges, I deal with it and watch to see if it makes
sense to use it” (interview 3). Last but not least, cost-benefit considerations also play
an important role: “If I have the feeling that there is something that helps me on […]
then I try it” (interview 19, cf. interview 16). Coming back to our second research question about perceived changes in the
conduct of science, the qualitative interviews confirm the result from the survey that
in science, digital tools are widely adopted. Scholars are not only using digital tools
for work, but also perceive their work as being changed by these tools, partly even
dramatically. The change is described as making research more efficient and faster,
and this acceleration also affects communication and collaboration. Theprecisenatureofthischangerequiresmorethoroughanalysis.Fromtheresults
presented here, it is clear that technology is just one of the driving forces underlying
the change, and that the increasing collaboration and mobility of scholars is another
important factor interacting with the use of technology. With regard to the motivations
for decisions about technology use, both the qualitative and the quantitative analysis
underscore the importance of a pragmatic, utilitarian orientation. The affordances of
digital technologies and the institutional contexts appear less perceptible, but also
relevant factors in determining which technologies are used and to what extent they
affect scholarly work. Based on our study, more detailed research into the interplay
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ital-scholar-how-technology-is-transforming-scholarly-practice. Digital Research Infrastructure Maik Stührenberg, Oliver Schonefeld, and Andreas Witt Abstract Digital research infrastructures can be divided into four categories: large
equipment, IT infrastructure, social infrastructure, and information infrastructure. Modern research institutions often employ both IT infrastructure and information
infrastructure, such as databases or large-scale research data. In addition, information
infrastructure depends to some extent on IT infrastructure. In this paper, we discuss
the IT, information, and legal infrastructure issues that research institutions face. Keywords Digital research infrastructure · IT infrastructure · Information
infrastructure References Accessed 11 Mar 2020 ital-scholar-how-technology-is-transforming-scholarly-practice. Accessed 11 Mar 2020 ZBW: World Wide Wissenschaft – Wie professionell Forschende im Internet arbeiten. Kiel: ZBW
Leibniz-Informationszentrum Wirtschaft (2011) ZBW: World Wide Wissenschaft – Wie professionell Forschende im Internet arbeiten. Kiel: ZBW
Leibniz-Informationszentrum Wirtschaft (2011) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license and
indicate if changes were made. g
The images or other third party material in this chapter are included in the chapter’s Creative
Commons license, unless indicated otherwise in a credit line to the material. If material is not
included in the chapter’s Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. 1Combinations of more than one category are possible as well. M. Stührenberg (B)
Universität Bielefeld, Bielefeld, Germany
e-mail: maik.stuehrenberg@uni-bielefeld.de 1
Introduction This paper was originally submitted late 2014 and the final publication was delayed
until 2019. The authors are well aware that the view and state of the art for digital
research infrastructures have evolved in the last 5 years. A research infrastructure can be defined as a public or private institution that has
been established mainly for research, teaching, and the support of young researchers. Research infrastructures can be divided into four main categories (Wissenschaftsrat
2011b, 17f.)1: – large equipment, including research platforms such as scientific research vessels,
planes, or satellites; – large equipment, including research platforms such as scientific research vessels,
planes, or satellites; 1Combinations of more than one category are possible as well. M. Stührenberg (B)
Universität Bielefeld, Bielefeld, Germany
e-mail: maik.stuehrenberg@uni-bielefeld.de
O. Schonefeld · A. Witt
Institut Für Deutsche Sprache, Mannheim, Germany
e-mail: schonefeld@ids-mannheim.de
A. Witt
e-mail: witt@ids-mannheim.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_5 M. Stührenberg (B)
Universität Bielefeld, Bielefeld, Germany
e-mail: maik.stuehrenberg@uni-bielefeld.de
O. Schonefeld · A. Witt
Institut Für Deutsche Sprache, Mannheim, Germany
e-mail: schonefeld@ids-mannheim.de
A. Witt
e-mail: witt@ids-mannheim.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_5 M. Stührenberg (B) O. Schonefeld · A. Witt
Institut Für Deutsche Sprache, Mannheim, Germany
e-mail: schonefeld@ids-mannheim de A. Witt
e-mail: witt@ids-mannheim.de 67 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_5 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_5 67 M. Stührenberg et al. 68 – IT infrastructure, such as computer hardware and software; – social infrastructure, that is, research institutions that offer scholars a place to
exchange ideas and collaborate (Wissenschaftsrat 2011a, 20f.), for example, the
Leibniz Center in Dagstuhl Castle, Germany; – information infrastructure, that is, research institutions that collect and curate
primary data and make them accessible to a larger group of scholars. – information infrastructure, that is, research institutions that collect and curate
primary data and make them accessible to a larger group of scholars. While large technical equipment is only seldom used in digital humanities disci-
plines, and social infrastructure is beyond the scope of this paper, combinations of
IT infrastructure and information infrastructure are quite common. Therefore, the
purpose of this paper is to give insight into various aspects of modern research
infrastructures with an emphasis on both the latter categories. 1
Introduction In addition, we have
conducted a qualitative analysis by interviewing twelve German research institutions
(Fiedler et al. 2012). The institutions were interviewed and asked to participate in
a survey. The 74 survey questions were structured into different topic areas, such
as organizational aspects, data management, hardware and software, environmental
aspects, and legal issues. We will reflect on some of these topics in the respective
sections of this article. 2
IT Infrastructure Digital humanities research institutions working with huge amounts of data (e.g.,
language corpora) have special needs regarding IT infrastructure, such as a growing
demand for storage space, computing capacity (for querying and analyzing linked
data), and durability (including distributed access over large-scale networks such as
the Internet for a huge number of potential users). This results in significant amounts
of money spent on hardware and software. In addition, operating costs (divided
into maintenance and personnel costs) have to be taken into account, including IT
staff, hardware maintenance, software updates, and licensing. Especially energy costs
should not be underestimated, as the price of electricity is increasing over time. A green-IT strategy can help an institution to reduce some of these costs. A key
way of doing this is buying new equipment and replacing old (less energy-efficient)
hardware. However, green IT consists of more aspects, such as efficient cooling
(like separation of warm and cold aisles in the data center or using free cooling
techniques), institutional policies (e.g., obliging employees to turn their computers
off before leaving the workplace), or using supplies made of recycled material (like
recycled paper). Implementing a green-IT strategy is generally a project of its own
for a research institution and is currently a low priority for the institutions that we
analyzed. Therefore,oneoftheissuesmodern-dayresearchinstitutionshavetodealwithisto
optimize these costs, usually by undertaking the following steps. Firstly, a transparent
accounting system, including every single asset for salaries, maintenance costs, and
so forth, has to be established, allowing for a more accurate estimation of current Digital Research Infrastructure 69 and future demands for IT infrastructure. Replacing proprietary software with open-
source software may only slightly decrease licensing costs, but may be cheaper in
the long run since the latter can be adopted to the institution’s needs and usually
has better support of open formats (see Sect. 3.2). However, two points have to be
considered regarding this assumption: 1. Additional costs for user training may be necessary if the open-source application
differs from the formerly used product; 1. Additional costs for user training may be necessary if the open-source application
differs from the formerly used product; 2. In-house IT expertise is necessary to adapt open-source software, which may
result in even higher personnel costs. 2. In-house IT expertise is necessary to adapt open-source software, which may
result in even higher personnel costs. 2See http://www.clarin.eu for further details.
3See http://www.eprints.org/ for further details.
4See https://www.escidoc.org/ for further details. 3
Information Infrastructure Research data, especially primary data (e.g., recordings, measurements, and curated
corpora), are among the most valuable assets for a research institution. Research
institutions that can be categorized as information infrastructures (such as libraries,
archives, collections, and smaller non-academic research institutions) that collect
and curate primary data, scientific and non-scientific knowledge, and databases,
and provide access to researchers [34], who may use this data for research projects
on their own. To ensure access to the information infrastructure, various technical
aspects have to be taken into account. 2
IT Infrastructure For these reasons, it is advisable, especially for smaller research institutions, to
collaborate in the field of IT infrastructure to reduce costs. Examples of such coop-
eration include a shared Internet connection, server housing, or archival storage. A majority of the interviewed research institutions already collaborate with other
external facilities to lower IT costs and to distribute archival and backup storage Since research institutions are nowadays connected to the Internet, storage of and
access to the information infrastructure involves special security requirements. Two
main issues have to be considered: 1. preventing unauthorized access to systems, processes, or data (including infor-
mation infrastructure); 1. preventing unauthorized access to systems, processes, or data (including infor-
mation infrastructure); 2. ensuring that hardware and software continue to function. Although there is no such thing as a completely secure network, the first step to
prevent unauthorized access is a complete risk analysis for the relevant computer
systems, including estimating possible losses and limitations on daily work (e.g.,
due to vandalism or sabotage). The outcome of this analysis should be a prioritized
list of data and systems to be protected. The concrete security measures (the security policy) are defined by the IT security
officer and the data protection officer and are mandatory for the whole staff of the
research institution (ISO/IEC 27002:2013 2013; BSI 2014). Important points for a
security policy are: – prioritization of data according to their value for the research institution; – identification of possible risks (including computer viruses and network infras-
tructure attacks); – backup strategy; – data encryption. While a backup strategy for research data is considered crucial (nine out of twelve
interviewees have a central backup strategy and the remaining institution plans to
implement one), only a third of the institutions surveyed have a central in-house IT
security policy. M. Stührenberg et al. 70 5Note that we are talking about the binary .doc, not the XML-based .docx format used by Office
2004 onwards and that is standardized as ISO/IEC 29500-1:2011 (2011). However, even the latter
format uses a number of features that cannot easily be interpreted by application programs without
further knowledge. 3.1
Repositories and Publication Server Repositories have already been used in large-scale collaborative projects, often inter-
national ones, such as CLARIN.2 The CLARIN centers provide repositories storing
academic research data (such as curated corpora) accessible via the Internet. Retrieval
of a desired information item is highly dependent on metadata. Following on from
existing metadata standards such as Dublin Core (ISO 15836:2009 2009; DCMI
2012), IMDI (ISLE Metadata Initiative 2003; Broeder and Wittenburg 2006; ISLE
Metadata Initiative 2009), or OLAC (Simons et al. 2008; Bird and Simons 2009),
the Component Metadata Structure (CMDI) (Broeder et al. 2011, 2012; Trippel et al. 2012) has been created to facilitate documenting research information and querying
it over the distributed repositories. In our survey, five out of the twelve interviewed
institutes already run a repository on their own, while four are in the process of
building one. Another aspect of information infrastructure is the archiving and accessibility of
publications. Establishing and maintaining an in-house publication server can be a
way for a research institution to retain both copyright (see Sect. 4.1) and access
control over information that has been produced by its academic staff. Open-source
implementations, such as ePrints3 or eSciDoc,4 often combine the functionalities of
publication servers and primary data repositories. For all these tasks, staff working on
IT and information infrastructure need to collaborate closely. In particular, research
institutions having their own libraries can benefit from the expertise of IT and
information departments regarding archives, metadata, and retrieval. Seven of the
interviewees already run a publication server. 71 Digital Research Infrastructure Digital Research Infrastructure 3.2
Data Formats Although the creation of research data is often quite expensive, a large portion of this
information gets lost shortly after the end of the project in which it was gathered. Apart from the hardware failures or insufficient metadata discussed above, another
possible reason can be a proprietary storage format, for which the corresponding
application is not available any more. Data formats usually exist for two reasons: (1) as serialization of a specification,
or (2) as the import and export format of an application. A format as such may
be open or proprietary, which may be important for processing and archiving the
information encoded in it. An example of a proprietary de facto standard format is
the ubiquitous.doc format, produced by Microsoft Word.5 Since it is a binary format,
it is not possible to extract information with arbitrary text editors; instead, one has
to use specific programs, and applications other than MS Word may not be able to
successfully render the document as it was intended by the author. For research data which are curated by an information infrastructure, open text-
based formats should be preferred. Formats based on the open meta language XML
(Bray et al. 2008) are quite common in academic research and can be defined by
document grammar formalisms such as XML DTD (part of the aforementioned
specification), XML Schema (Gao et al. 2012; Peterson et al. 2012), or RELAX NG
(ISO/IEC 19757-2:2008 2008), allowing for on-the-fly validation during the creation
of instances. Examples of open XML-based annotation formats in the digital humani-
tiesaretheTEIGuidelines(BurnardandBauman2014)orDocBook(Walsh2010)for
technical documentation. Information encoded in those formats is not only readable
with common text editors, but separates content from formatting, since the rendering
is usually controlled by separate XSLT (Kay 2007, 2014) or CSS (Bos et al. 2011)
stylesheets. This not only prevents vendor lock-in, but significantly eases the process
of archiving. The attitude to open standards and open-source software compared
with proprietary in-house development is mixed; however, there is a tendency to use
standardized APIs and formats, or at least consider open-source applications. Seven
surveyed institutes keep data in proprietary formats, while four aim to use standard
formats and one is still determining its strategy. Often, institutes lack the human
resources to convert data into standard formats. 6See http://creativecommons.org for further details.
7See http://opensource.org/licenses/bsd-license.php for further details.
8See http://www.gnu.org/licenses/#GPL for further details.
9Especially NC may have undesired side effects, see Klimpel (2012) for a discussion.
10The categories have recently been extended by Kupietz and Lüngen (2014).
11See Görl et al. (2011) for a discussion about the impacts of information infrastructure in
universities of North Rhine-Westphalia. 4
Legal Issues Research institutions are confronted with a number of legal issues, the most important
of which are: (1) copyright and (2) personal data protection and privacy. M. Stührenberg et al. 72 4.1
Copyright Issues Research data is often based on material contributed by third parties. The primary
data of text corpora, for example, often originate from newspaper articles or similar
non-academic sources. German copyright law protects literary, artistic, and scientific
works (including software) that are the author’s own intellectual creation. Copyright-
protected works may only be modified (and, arguably, annotated) with the authoriza-
tion of the copyright holder. Copyright expires 70 years after the death of the original
author. In Germany (unlike in most other jurisdictions), copyright cannot be trans-
ferred and is reserved by the author until his death (and 70 years after it), but it can
be licensed. In practice, authors often license their rights out to publishers. Although the German copyright law (UhrG) does not contain the American
concept of “fair use”, there are copyright limitations (§§ 44a–63a UrhG) that apply
to certain specific uses of copyright-protected works (e.g., citations, personal use,
scientific use) (Mönch 2006). However, in order to be covered by a copyright limita-
tion of § 52a UrhG, scientific use has to be restricted to “small groups of researchers”
(Hoeren 2014, 157). This is especially important if a research institution wants to
publishannotatedcorpora-inthatcase,theprimarydatahastobelicensedbeforehand. Research data to which a research institution holds the copyright (e.g., primary
data produced in-house) should be made available to others under a liberal license,
e.g., an open-access license such as Creative Commons.6 Creative Commons (CC) is
a free license (similar to the software license, BSD,7 or the General Public License,
GNU8) that was originally developed for creative work and that consists of several
building blocks, such as Attribution (BY: minimal requirement), NoDerivatives
(ND), NonCommercial (NC),9 and ShareAlike (SA). The current version (4.0) also
addresses specific database rights that exist in EU Member States. Apart from human-readable CC license deeds, laundry symbols (similar to those
established in the CLARIN research group (Oksanen et al. 2010) for its own specific
licenses) provide a quick overview of the license requirements.10 For a detailed
discussion about legal implications of institutional repositories see Bargheer et al. (2006). Regarding publications, a research institution’s staff may agree to publish their
works on the institution’s publication server under an open-access license (Degkwitz
2007). 12See the text of the declaration at http://openaccess.mpg.de/3515/Berliner_Erklaerung.
13See Stempfhuber (2009, 119) and http://opcit.eprints.org/oacitation-biblio.html for a number of
studies about open-access impact factors. 4.1
Copyright Issues Open-access publications have steadily gained ground in countries such as
the US, Denmark, or Japan, while there is still an ongoing discussion about them
in Germany, especially in the digital humanities disciplines11—although the Berlin 73 Digital Research Infrastructure Declaration on Open Access to Knowledge in the Sciences and Humanities12 has
boosted their reputation. While open-access journals are still sometimes seen as less
reputable than traditional journals (although both publication types monitor quality
throughpeerreview),theyoftenhavehighercitationnumbers.13 Researchinstitutions
can play an active role in the process of building the reputation of open access by
publishing in this format. It is therefore pleasant to see that an open-access strategy
is already present in five of the institutions interviewed, while three of them plan on
implementing one. Declaration on Open Access to Knowledge in the Sciences and Humanities12 has
boosted their reputation. While open-access journals are still sometimes seen as less
reputable than traditional journals (although both publication types monitor quality
throughpeerreview),theyoftenhavehighercitationnumbers.13 Researchinstitutions
can play an active role in the process of building the reputation of open access by
publishing in this format. It is therefore pleasant to see that an open-access strategy
is already present in five of the institutions interviewed, while three of them plan on
implementing one. 4.2
Personal Data Protection Personal data protection issues may arise when living persons are involved in the
process of creating research data, such as voice or video recordings. Publication
of personal data is only allowed if the persons recorded have given their (written)
consent. For every collection of personal data, a register of processing operations
has to be created (according to §4 g, §§18 and 4e of the German data protection law,
BDSG. The type of personal information, how it is processed, and the data protection
measures, are recorded in this register. Despite the variety of legal issues that may arise for research institutions, most of
the interviewees rely either on their own (general) legal department or on cooperation
with external law firms. Licensed (IT law) attorneys are seldom employed. However,
since German research institutions are required to employ a data protection officer
if they deal with personal data, they already have at least some existing in-house
expertise. This expert should be involved in any data collection activities as soon as
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www.wissenschaftsrat.de/download/archiv/10466-11.pdf (2011b) 76 M. Stührenberg et al. Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license and
indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative
Commons license, unless indicated otherwise in a credit line to the material. If material is not
included in the chapter’s Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. MOVING: A User-Centric Platform
for Online Literacy Training
and Learning MOVING: A User-Centric Platform
for Online Literacy Training
and Learning Keywords MOVING platform · MOVING web application · Recommender
system · Adaptive training support Keywords MOVING platform · MOVING web application · Recommender
system · Adaptive training support MOVING: A User-Centric Platform
for Online Literacy Training
and Learning Aitor Apaolaza, Tobias Backes, Sabine Barthold, Irina Bienia, Till Blume,
Chrysa Collyda, Angela Fessl, Sebastian Gottfried, Paul Grunewald,
Franziska Günther, Thomas Köhler, Robert Lorenz, Matthias Heinz,
Sabrina Herbst, Vasileios Mezaris, Chifumi Nishioka,
Alexandros Pournaras, Vedran Sabol, Ahmed Saleh, Ansgar Scherp,
Ilija Simic, Andrzej M.J. Skulimowski, Iacopo Vagliano, Markel Vigo,
Michael Wiese, and Tanja Zdolšek Draksler Abstract In this paper, we present an overview of the MOVING platform, a user-
driven approach that enables young researchers, decision makers, and public admin-
istrators to use machine learning and data mining tools to search, organize, and
manage large-scale information sources on the web such as scientific publications,
videos of research talks, and social media. In order to provide a concise overview
of the platform, we focus on its front end, which is the MOVING web application. A. Apaolaza · M. Vigo
University of Manchester, Manchester, UK
e-mail: aitor.apaolaza@manchester.ac.uk
M. Vigo
e-mail: markel.vigo@manchester.ac.uk
T. Backes
GESIS, Cologne, Germany
e-mail: tobias.backes@gesis.org
S. Barthold · P. Grunewald · F. Günther · T. Köhler (B) · R. Lorenz · M. Heinz · S. Herbst
Media Centre, TU Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de
S. Barthold
e-mail: sabine.barthold@tu-dresden.de
P. Grunewald
e-mail: paul.grunewald@tu-dresden.de
F. Günther
e-mail: franziska.guenther1@tu-dresden.de
R. Lorenz
e-mail: robert.lorenz@tu-dresden.de
M. Heinz
e-mail: matthias.heinz@tu-dresden.de
S. Herbst
e-mail: sabrina.herbst@tu-dresden.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_6 A. Apaolaza · M. Vigo
University of Manchester, Manchester, UK
e-mail: aitor.apaolaza@manchester.ac.uk
M. Vigo
e-mail: markel.vigo@manchester.ac.uk
T. Backes
GESIS, Cologne, Germany
e-mail: tobias.backes@gesis.org
S. Barthold · P. Grunewald · F. Günther · T. Köhler (B) · R. Lorenz · M. Heinz · S. Herbst
Media Centre, TU Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de
S. Barthold
e-mail: sabine.barthold@tu-dresden.de
P. Grunewald
e-mail: paul.grunewald@tu-dresden.de
F. Günther
e-mail: franziska.guenther1@tu-dresden.de
R. Lorenz
e-mail: robert.lorenz@tu-dresden.de
M. Heinz
e-mail: matthias.heinz@tu-dresden.de
S. Herbst
e-mail: sabrina.herbst@tu-dresden.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_6 A. Apaolaza · M. Vigo
University of Manchester, Manchester, UK
e-mail: aitor.apaolaza@manchester.ac.uk A. Apaolaza · M. Vigo
University of Manchester, Manchester, UK
e-mail: aitor.apaolaza@manchester.ac.uk M. Vigo
e-mail: markel.vigo@manchester.ac.uk T. Backes
GESIS, Cologne, Germany
e-mail: tobias.backes@gesis.org 77 78 A. Apaolaza et al. A. Apaolaza et al. By presenting the main components of the web application, we illustrate what func-
tionalities and capabilities the platform offer its end-users, rather than delving into
the data analysis and machine learning technologies that make these functionalities
possible. 1
Introduction Scholarsandprofessionalsinvarioussectorsoftheeconomy,includingpublicadmin-
istrators, corporate compliance officers, and auditors, deal with an ever-increasing
flow of information (new scientific publications, business documents and multimedia
files, laws, etc.). They need sophisticated tools to evaluate all this information fast
and accurately and to visualize the analysis results. Specifically this means that, on
the one hand, they need tools that enable state-of-the-art search and semantic analysis
of large digital contents, by providing: (i) access to an extensive source inventory, (ii) MOVING: A User-Centric Platform for Online Literacy Training and Learning 79 advanced search and visualization methods, and (iii) functionalities for generating
new knowledge from these digital assets. On the other hand, these tools need to be
reasonably easy for their users to understand and support them through: (i) a detailed
and scientifically proven help system (tutorials, guidance), individually configurable
training programmes (learning modules, videos), and a lively community of people
that have similar interests or problems to be solved. To face these challenges, the inter-
disciplinary trans-European project called MOVING (“TraininG towards a society
of data-saVvy inforMation prOfessionals to enable open leadership INnovation”)
(Vagliano et al. 2018) has built an innovative training platform that enables users
from various societal sectors to fundamentally improve their information literacy
by training in how to choose, use, and evaluate data mining methods in their daily
research and business tasks, and to become data-savvy information professionals. 2
Digitized Science Initiatives by the European Union (which has long been pursuing a digital agenda)
to support research in the field of digitized science illustrate the need to investigate
related change processes (European Commission 2016). Obviously, empirical and
theoretical justification is needed to develop the practice of science. The innova-
tive approach dealt with here was developed in the MOVING project, which offers
an innovative training platform to support scientists and other users from all areas
of society to fundamentally improve their information literacy in research-oriented C. Nishioka
University of Kyoto, Kyoto, Japan
e-mail: nishioka.chifumi.2c@kyoto-u.ac.jp A. Saleh
ZBW, Kiel, Germany
e-mail: a.saleh@zbw.eu A. Scherp
Ulm University, Ulm, Germany
e-mail: ansgar.scherp@uni-ulm.de 80 A. Apaolaza et al. A. Apaolaza et al. contexts.1 The project is about training users to select, apply, and evaluate technolo-
gies and data mining methods, so that the relevant research staff can develop into
‘data-savvy’ information professionals in their daily research routines (Scherp et al. 2016; Köhler et al. 2016a, b). In terms of content, the research methodological changes in scientific action
cannot easily be explained as domain-specific activities. This requires analyses of
both current technological developments and the changes in how scientists use these
technologies (or methods). The eScience Saxony research network provides state-
ments on both perspectives (see, e.g., [Pscheida et al. 2013, 2014]). The network has
observed the following: – there is great potential for the use of new digital tools in research; – preferred topics for development are scientist collaboration and the visualization
of (often large or new) databases; – transitions between the subject areas of research and teaching can also be observed
in technology development; – almost all scientists do most of their work using computer-based technologies and
have access to appropriate infrastructures; – scientists sometimes find it difficult to adopt new media technologies in research
and teaching (e.g. social media), although there are also subject-specific differ-
ences; – there is still uncertainty regarding the requirements, possibilities, and assumed
risks of open-access publishing; – research methodology has not been fully systematically discussed and is often
inadequately implemented; – there are no clear standards for high-quality research technology and no recog-
nizable institutionalization to support open-access trends in science, so these still
need to be worked out together; – digital change in science is comparatively rapid from an individual (scientist)
perspective, the outcome is not known, especially regarding location-determining
infrastructures. 1Platform.moving-project.eu, last accessed 7 May 2020. 2
Digitized Science Indeed the listing matches to a larger proportion with the demands of these cases
addressedbytheMOVINGproject.NeverthelessMOVINGdidsetfocusontwomore
main characteristics. First there was a serious interest to address research activity not
only in academia but as well in public administration and industry. Second, when
developing the approach the project consortium decided to include as well a direct
focus on the related skill development, i.e. include a serious effort on innovation in
the educational dimension (the Online Literacy Training and Learning) that needs to
go along with any new technology in every sector. Indeed the listing matches to a larger proportion with the demands of these cases
addressedbytheMOVINGproject.NeverthelessMOVINGdidsetfocusontwomore
main characteristics. First there was a serious interest to address research activity not
only in academia but as well in public administration and industry. Second, when
developing the approach the project consortium decided to include as well a direct
focus on the related skill development, i.e. include a serious effort on innovation in
the educational dimension (the Online Literacy Training and Learning) that needs to
go along with any new technology in every sector. MOVING: A User-Centric Platform for Online Literacy Training and Learning 81 3
Overview of the MOVING Platform An overview of the MOVING platform architecture is illustrated in Fig. 1, which
shows the most important components and their relationships. The main component Fig 1 MOVING platform architecture Fig. 1 MOVING platform architecture 82 A. Apaolaza et al. A. Apaolaza et al. A. Apaolaza et al. blocks are (i) data acquisition, (ii) data processing, (iii) back-end data storage, user
tracking, search and recommendation, and (iv) the MOVING web application that
includes the front-end search. In this section, we briefly describe the overall platform. The MOVING web application is the core of the platform and the interface to the
user. The main entry points to the web application are the community section, the
learning environment, and the search interface. The search interface offers different
visual representations of search results. These visualizations allow the user to explore
the search results in various ways. For this purpose, four visualizations have been
added to the MOVING platform, namely: (i) the Concept Graph, which displays the
search results as an interactive network, (ii) uRank, a dynamic document ranking
view, (iii) Top Properties, a bar chart visualization that aggregates the results based
on their properties, and (iv) a Tag Cloud, showing the most frequently occurring
keywords. Moreover, the Adaptive Training Support (ATS) widget supports users
learning how to search and provides material suited to their needs (Fessl et al. 2018)
and the Recommender System (RS) widget (bridging the front and back ends of
the platform) points users to potentially relevant documents by evaluating their last
search queries. Thanks to its responsive design, all the views adapt to different screen
sizes, automatically changing the layout according to the capabilities of the device. Private user data and public documents are stored in three separate databases:
The web application database holds the data for the communities, the learning envi-
ronment, and the ATS. The index holds the public documents and generated meta-
data information such as topics, authors, and extracted entities. The user-interaction
tracking captures user interactions with the web application and stores them securely
in a third database. User tracking provides additional data for both the ATS and the
RS, which form the basis for user support by these two widgets. The index used by the search interface is populated by various data acquisition
components (e.g. web crawlers and a Bibliographic Metadata Injection service), to
increase the amount of data accessible through the MOVING platform. 3
Overview of the MOVING Platform To date,
it hosts over 22 million documents and metadata records. These records include
books, scientific articles, laws and regulations, documents about funding opportuni-
ties, videos (e.g. of lectures and tutorials), and social media posts. Data processing
components have been incorporated into and applied to these records, to improve the
quality of data and make it easier to search. Additional features, the Data Integration
Service, Author Name Disambiguation, Deduplication, Named Entity Recognition
and Linking, and Video Analysis, all refine and enrich the documents stored in the
index. Author name disambiguation addresses the problem that many author names
belong to different real-world authors. To deal with this problem, a novel method
(Backes 2018a, b) has been developed which applies, for a given author name,
agglomerative clustering on features extracted from documents containing the
author mention in question, such as affiliation, co-authors, referenced authors, email
addresses,keywords,andpublicationyears.Thedisambiguationprocedurecalculates
the probability with which author mentions with the same name belong to the same
person. Name mentions having a high probability to belong to the same author are MOVING: A User-Centric Platform for Online Literacy Training and Learning 83 Fig. 2 MOVING search and results page Fig. 2 MOVING search and results page assigned a unique internal authorID. By this, authors with the same name are distin-
guished if they refer to different real-world persons. As a result, users who click on
the name of an author of a document in the result list of a search will only see docu-
ments from authors who have the same author ID as the selected author (instead of
showing all documents authored by any person with that name). A modified version
of this method has been applied for document deduplication. In the following, we present the front end of the MOVING platform in detail, in
order to provide a concise summary of what a user can do with it. For details on how
individual data processing, data acquisition, and other back-end components work,
the interested reader is referred to the relevant publications, such as (Nishioka and
Scherp 2016; Galanopoulos and Mezaris 2019; Tzelepis et al. 2018), as well as the
documentation available on the MOVING project web site.2 3www.elastic.co, last accessed 7 May 2020. 2www.moving-project.eu, last accessed 7 May 2020. 2www.moving-project.eu, last accessed 7 May 2020.
3www.elastic.co, last accessed 7 May 2020. 4.1
Search Search is a key functionality in the MOVING web application. At the back end, the
MOVING search engine is based on Elasticsearch,3 given appropriate parameters,
and fine-tuned to efficiently index dozens of millions of documents. At the front end,
the user sees a search page (Fig. 2), with various search options and filters on the left,
visualizations of the results in the centre of the window, and training functionalities 84 A. Apaolaza et al. Fig. 3 Search history view Fig. 3 Search history view Fig. 3 Search history view such as ATS on the right. The search history of the current user can also be viewed,
to support future searches. To enable platform users to view and replicate their previous searches, the search
history view is connected with WevQuery (Apaolaza and Vigo 2017). WevQuery
serves as an interface to the data generated by UCIVIT (Apaolaza et al. 2013),
the tracking tool of which logs user-interaction data. From WevQuery, we get the
information about the previous user searches, time when the user performed the
searchquery,andthenumberofdocumentsretrieved.Thisinformationisthenutilized
to build the search history view, an example of which is shown in Fig. 3. y
p
g
To present the results of a user query effectively, several visualizations have been
implemented. Four characteristic ones are: – Concept Graph. For the discovery and exploration of relationships between
documents and their properties. – uRank. A tool for the interest-driven exploration of search results. – Top Properties. A bar chart displaying aggregated information about the
properties of the retrieved documents. – Tag Cloud. A visualization for the analysis of keyword frequency in the retrieved
documents. Concept Graph: an interactive network visualization the Concept Graph (Fig. 4)
visualizes direct and indirect connections between retrieved search results. For
example, a single, disambiguated author of two different publications is visualized as
a node in the graph connecting the corresponding publications. Further extracted and
disambiguated entities are visualized in a way that users can grasp, quickly, such as
research networks. The initial graph visualization starts with a few collapsed nodes. These nodes can be expanded to visualize initially hidden nodes and to incrementally
add more information to the graph. Thus, users are not overwhelmed with too much
information when they start their search. These nodes can be expanded to visualize initially hidden nodes and to incrementally
add more information to the graph. 4.1
Search Thus, users are not overwhelmed with too much
information when they start their search. MOVING: A User-Centric Platform for Online Literacy Training and Learning 85 Fig. 4 Concept Graph with opened filter menu Fig. 4 Concept Graph with opened filter menu uRank: interest-based result set exploration. Based on the search query the top
100 retrieved results are displayed as a ranked list. The keywords extracted from the
results are presented in the Tag Cloud in the right sidebar of uRank (Fig. 5, point A). By selecting keywords of interest, the results in the list (Fig. 5, point C) are re-ranked
in such a way that the results containing the selected keyword move to the top. The
ranking view (Fig. 5, point D) provides visual feedback on the relevance of the result. It is possible to select multiple keywords and even fine-tune their importance by using
the slider under the selected words (Fig. 5, point B). Clicking on a result opens a
dialogue box, which presents additional information about the retrieved document. The user can export the current view of uRank, with the current search configuration,
by clicking on the export button, which initiates the download of a zip file containing
an image and a report text file. Top Properties: the Top Properties visualization uses 100 of the most relevant
results from the current search query. It shows a bar chart visualization presenting one
of the following properties of the available results: Authors, Keywords, Concepts,
Sources, and Year of Publication. The results are ordered according to the most
frequent values of the selected property, as can be seen in Fig. 6. When the publi-
cation year is selected, the sorting order changes so that the years are displayed in
chronological order to make it easier to identify year-on-year changes. Clicking on
one of the bars shows the results associated with this property in a small dialogue
box. The results in this dialogue are sorted in the order provided originally by the A. Apaolaza et al. 86 Fig. 5 uRank and its components—(A) tag cloud, (B) tag box, (C) result list, (D) ranking view Fig. 5 uRank and its components—(A) tag cloud, (B) tag box, (C) result list, (D) ranking view search engine. The Top Properties visualization also supports an export functionality,
which exports the current view of the visualization with its search configuration. Tag Cloud: the Tag Cloud visualization (Fig. 7) retrieves the 100 most rele-
vant results from the search query and displays them by showing the most frequent
keywordsthatoccurinthecorrespondingtitlesandabstracts.Thedisplayedkeywords
are initially sorted by their frequency and can be filtered by occurrence, year, or text. Clicking on one of the keywords shows the results associated with this property. The
results are sorted in the order provided originally by the search engine. Fig. 6 The Top Properties visualization with the dialogue box showing the result list for a bar of
interest Fig. 6 The Top Properties visualization with the dialogue box showing the result list for a bar of
interest MOVING: A User-Centric Platform for Online Literacy Training and Learning 87 Fig. 7 Tag Cloud visualization with a dialogue box showing the result list for a keyword 4.2
Recommender System The RS widget, depicted in Fig. 8, is part of the search page. It gives users addi-
tional suggestions for resources of which they may not be aware. The RS interacts
with the search engine, user-interaction tracking, and dashboard (WevQuery), hence
bridging the back and front ends of the MOVING platform. To build user profiles,
it obtains the search history from the user data previously logged through UCIVIT
and then retrieves the documents to suggest from the index, depending on the user’s
profile. The MOVING RS is based on HCF-IDF (Nishioka and Scherp 2016), a novel
semantic profiling approach that can exploit a thesaurus or ontology to provide better
recommendations. Further information on the MOVING RS is available elsewhere
(Vagliano and Nazir 2019). 88 A. Apaolaza et al. Fig. 8 The Recommender
System widget suggesting
three new items to the user: a
video, an article, and a web
page (Vagliano and Nazir
2019) Fig. 8 The Recommender
System widget suggesting
three new items to the user: a
video, an article, and a web
page (Vagliano and Nazir
2019) 4www.ckeditor.com, last accessed on 7 May 2020.
5www.twitter.com, last accessed on 7 May 2020.
6www.youtube.com, last accessed on 7 May 2020. 4.3
Communities Open collaboration and communication are the foundations of open innovation and
open science. MOVING communities offer users a powerful tool to organize group
collaboration and communities of practice on the MOVING platform (see Fig. 9). MOVING communities are part of the working environment of the platform and
offer a range of social technologies with knowledge and information management,
including wikis, forums, blog functions, and group news. MOVING communities are
based on the project management tools and technologies of the eScience platform
on which the MOVING platform is based. The existing eScience modules, which
enabled cooperation in closed teams of researchers, were adapted to the goals of
the MOVING platform to provide an open innovation environment and foster open
collaboration, communication, and knowledge exchange between its users. Registered users who want to create a new community are offered different
options. First, users can create public communities that are visible to everyone in the
MOVING platform and can be accessed and edited by anyone interested in the topic. Second, users who want to organize specific project teams or research groups can
create private communities that users have to join before they can access and edit
content. Private communities are not visible to other users but can be shared with
collaborators via email. MOVING: A User-Centric Platform for Online Literacy Training and Learning 89 Fig. 9 MOVING communities Fig. 9 MOVING communities The MOVING CK Editor4 enables the creation of formatted text and the integra-
tion of multimedia content in HTML pages that are created by users in the MOVING
communities. Videos, pictures, GIFs or documents, and social media content from
Twitter5 and YouTube6 can all be easily integrated. Features like the accordion and
the option to include expandable items make it easy to structure content in the page. It is a WYSIWYG editor (What You See Is What You Get) so even users that are not
familiar with HTML can use it easily to create and edit web-based content within
MOVING communities. The wiki module is useful for creating and collaboratively managing large
knowledge repositories with a community. The forum module provides space for 90
A. Apaolaza et al. Fig. 10 MOVING MOOC community 90
A. Apaolaza et al. Fig. 10 MOVING MOOC community 90 A. Apaolaza et al. Fig. 10 MOVING MOOC community open communication and information exchange—a precondition for open innova-
tion processes. 7moving.mz.tu-dresden.de/mooc, last accessed 7 May 2020. 8www.orcid.org, last accessed on 7 May 2020. 4.3
Communities The forum module contains a user rating functionality that allows
the community to publicly rate the content of individual forum entries. Users can
vote posts and replies up and down, based on the quality of the contribution. The
highest-rated input is highlighted to help users find the best response in a thread,
and the summarized score for all received votes is shown on each user profile. The
rankingfunctionalityhelpscommunitiesself-organizeandpeerassessuser-generated
content. Community administrators can also choose to assign badges to reward users
or motivate them to get actively engaged. Badges can be assigned automatically or
manually. The ease of user-generated content creation and integration combined with the
social features of MOVING communities open up a wide range of possible applica-
tions. Users can organize group work in small project teams, or create open commu-
nities around scientific or technical topics to discuss research or ask questions to an
expert community. MOVING communities can be organized as an open innovation
tool but also as a learning management system, as the following example shows. One practical application of MOVING communities is the four-week MOVING
MOOC (massive open online course) Science 2.0 and open research methods that
was organized on the MOVING platform (see Fig. 10).7 The MOOC is organized on
the platform as a private team community, so that participants have to register to gain 91 MOVING: A User-Centric Platform for Online Literacy Training and Learning 91 Fi
11 MOVING MOOC b d access to the learning materials and the forums. For each week of the MOOC, we
created a sub-community containing learning materials in different media formats as
well as weekly assignments. The forums were used to organize group communication
and allow users to share their assignment results. A wiki was created and contained
additional information about the course, learning goals, and technical details about
using the editor or the MOOC badges that users can earn on the course (Fig. 11). Badges are displayed on the user’s profile, My page, along with their personal and
contact details (profile picture, science field, skills, hometown, institution, email,
ORCID8). access to the learning materials and the forums. For each week of the MOOC, we
created a sub-community containing learning materials in different media formats as
well as weekly assignments. The forums were used to organize group communication
and allow users to share their assignment results. A wiki was created and contained
additional information about the course, learning goals, and technical details about
using the editor or the MOOC badges that users can earn on the course (Fig. 11). Badges are displayed on the user’s profile, My page, along with their personal and
contact details (profile picture, science field, skills, hometown, institution, email,
ORCID8). 92
A. Apaolaza et al
Fig. 12 MOVING learning environment 92 A. Apaolaza et al. 92
A. Apaolaza et al. Fig. 12 MOVING learning environment Fig. 12 MOVING learning environment 4.4
Learning Environment MOVING offers a unique combination of working and training features in one plat-
form. The heart of the training programme is the MOVING learning environment. Here, all the learning content is organized and directly accessible to the users. The
landing page (Fig. 12) gives an overview of the learning materials including the plat-
form demo videos and video tutorials, the Learning Tracks for Information Literacy
2.0, and the MOVING MOOC that was discussed in the previous subsection, Science
2.0 and open research methods. The platform demos are videos hosted on videolec-
tures.net and are embedded in the learning environment so that users can learn about
the different platform features and technologies developed within the MOVING
project. Users can improve their data and information literacy as well as digital
competences through Learning Tracks for Information Literacy 2.0 (Fig. 13). 4.5
Adaptive Training Support The ATS (Fessl et al. 2018) comprises two widgets for learning how to search and
curriculum reflection. The Learning-how-to-search (Fig. 14) widget visualizes information about the
use of features provided by the MOVING platform. The widget presents to users
how they used the features of the platform in a bar chart to motivate them to explore
new features and reflect about their usage behaviour. More information about the
widget and its evaluation can be found in (Fessl et al. 2019). The curriculum reflection widget (Fessl et al. 2019) consists of two parts: the
curriculum learning and reflection and the overall progress. The first part consists of
two main areas. The upper area either contains a learning prompt (suggesting that MOVING: A User-Centric Platform for Online Literacy Training and Learning MOVING: A User-Centric Platform for Online Literacy Training and Learning 93 Fig. 13 Start page of Learning Tracks for Information Literacy 2.0 Fig. 13 Start page of Learning Tracks for Information Literacy 2.0 the user learn more about the next topic in the current sub-module) and a button
which opens the respective learning unit in a new tab (Fig. 15 left), or it presents a
reflective question that motivates the user to think about the current topic of their
learning (Fig. 15 right). The user’s progress in the current sub-module is displayed
at the bottom of the widget. The overall progress part of the widget shows the user’s learning progress through
the curriculum using a sunburst visualization. Figure 16 shows that the curriculum
is divided into three modules. Each module is represented as a section in the inner
circle of the visualization and divided into three sub-modules in the outer circle. Every time a user completes a new learning unit, the percentage in the respective
section in the sunburst diagram is updated. Progress in each sub-module is encoded
by colour. If the user has not completed any learning units in a sub-module (0%), the
respective section will be red. Making progress in a sub-module will turn the section
yellow (50%) and completing it will turn the section green (100%). This is also explained by the legend below the visualization. Moreover, the
sections in the sunburst diagram are ordered to mirror the structure of the curriculum. Starting from the top, the sub-modules are completed clockwise, gradually turning
the visualization green. 94 A. Apaolaza et al. Fig. 14
Learning-how-to-search
widget: The tracked features
are separated into features of
the search input interface and
search result presentation
Fig. 15 Curriculum reflection widget: curriculum learning (left) and reflection (right) Fig. 14
Learning-how-to-search
widget: The tracked features
are separated into features of
the search input interface and
search result presentation Fig. 15 Curriculum reflection widget: curriculum learning (left) and reflection (right) Fig. 14
Learning-how-to-search
widget: The tracked features
are separated into features of
the search input interface and
search result presentation MOVING: A User-Centric Platform for Online Literacy Training and Learning The Know-Center is funded within
the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the
auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian
Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed
by the Austrian Research Promotion Agency FFG. p
g
ackes, T.: The impact of name-matching and blocking on author disambiguation. In: CIKM ’18:
The 27th ACM International Conference on Information and Knowledge Management Torino, Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant
agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been
supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within
the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the
auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian
Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed
by the Austrian Research Promotion Agency FFG. 5
Conclusion In this chapter, we presented the MOVING platform, focusing on the MOVING
web application with its search interface and novel results visualizations, commu-
nity features and learning environment, and components such Adaptive Training
Support. These functionalities help users to not only search within and visualize a
large multimedia collection using various advanced tools and functionalities, but also
to explore the platform more easily, e.g. by showing statistics about their platform
use or providing learning guidance. Productive use of the prototype platform in real
educational environments, such as the MOVING MOOC, showed how its integrated MOVING: A User-Centric Platform for Online Literacy Training and Learning Apaolaza, A., Harper, S., Jay, C.: Understanding users in the wild. In: Proceedings 10th International
Cross-Disciplinary Conference on Web Accessibility (W4A’13), Rio de Janeiro, Brazil (2013)
Apaolaza, A., Vigo, M.: WevQuery: testing hypotheses about web interaction patterns. In:
Proceedings ACM Human Computer Interaction 1(EICS), 4:1–4:17. (2017) ,
p
g
g
g
The 27th ACM International Conference on Information and Knowledge Management Torino, MOVING: A User-Centric Platform for Online Literacy Training and Learning 95 Fig. 16 Overall progress
widget: The first module was
completed and the second
module is in progress
training and working environment contributes to making information professionals
data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant
agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been
supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within
the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the
auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian
Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed
by the Austrian Research Promotion Agency FFG. Fig. 16 Overall progress
widget: The first module was
completed and the second
module is in progress training and working environment contributes to making information professionals
data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant
agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been
supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within
the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the
auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian training and working environment contributes to making information professionals
data-savvy and improving users’ information literacy skills. training and working environment contributes to making information professionals
data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant
agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been
supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within
the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the
auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian
Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed
by the Austrian Research Promotion Agency FFG. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant
agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been
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adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
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indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative
Commons license, unless indicated otherwise in a credit line to the material. References If material is not
included in the chapter’s Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. CLARIN-D: An IT-Based Research
Infrastructure for the Humanities
and Social Sciences Gerhard Heyer and Volker Böhlke Abstract The paper discusses the idea of bridging the gap between computer
sciences and the humanities by referring to an e-humanities infrastructure that
provides tools and services for well-defined and frequently encountered tasks. The
main goal of this infrastructure is to enable researchers in the humanities and social
sciences to better exploit their potential by reusing available digital resources, and
thus to increase the efficiency of e-humanities projects. CLARIN-D is an example of
such a research infrastructure. The paper provides a brief overview of the basic prin-
ciples and services of the CLARIN-D infrastructure, such as metadata harvesting,
federated content search, and chaining Web services. Keywords Digitalization · Humanities · CLARIN-D Keywords Digitalization · Humanities · CLARIN-D G. Heyer (B) · V. Böhlke
Leipzig University, Leipzig, Germany
e-mail: heyer@informatik.uni-leipzig.de
V. Böhlke
e-mail: boehlkev@informatik.uni-leipzig.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_7 1
Introduction To date, computer science and the humanities have taken different approaches to
working methodologies, rather than focusing on the potential synergies. However,
recent advances in digitizing historical texts, and the search and text-mining tech-
nologies for processing these data, indicate an area of overlap that bears great poten-
tial. For the humanities, the use of computer-based methods may lead to more effi-
cient research (where possible) and raise new questions that could not have been
dealt with otherwise. For computer science, turning to the humanities as an area of
application may pose new problems that require rethinking the approaches hitherto
favored by computer science. As a result, new solutions may develop that help to
advance computer science in other areas of media-oriented application. At present,
most of these solutions are restricted to individual projects and do not allow the
digital humanities community to benefit from other advances in computer science, V. Böhlke
e-mail: boehlkev@informatik.uni-leipzig.de 99 99 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_7 100 G. Heyer and V. Böhlke G. Heyer and V. Böhlke like service engineering. Hence, in this paper we attempt to spell out in detail the
idea of an infrastructure for e-humanities. Focusing on the notion of reusability of
data and algorithms such as morphological annotation and part-of-speech (POS)
tagging, we sketch how a loosely coupled infrastructure based on Web services and
a service-oriented architecture (SOA) can help the humanities to better exploit their
potential by reusing available digital resources, and thus increase the efficiency of
e-humanities projects. As an example, we present a rough overview of Common
Language Resources and Technology Infrastructure D (CLARIN-D), a Web-based
research infrastructure for the humanities and social sciences. 2
The Impact of Digitization in the Humanities—From
Digital Humanities to E-Humanities These methods impact in the following ways: • qualitative improvement of the digital sources (standardization of spelling and
spelling correction, unambiguous identification of authors and sources, marking
of quotes and references, temporal classification of texts, etc.); • qualitative improvement of the digital sources (standardization of spelling and
spelling correction, unambiguous identification of authors and sources, marking
of quotes and references, temporal classification of texts, etc.); • the quantity and structure of sources that can be processed (processing of very
large amounts of text, structuring by time, place, authors, contents and topics,
comments from colleagues and other editions, etc.); CLARIN-D: An IT-Based Research Infrastructure … 101 • the kind and quality of the analysis (broad data-driven studies, strict bottom-
up approach using text-mining tools, integration of community networking
approaches, etc.). • the kind and quality of the analysis (broad data-driven studies, strict bottom-
up approach using text-mining tools, integration of community networking
approaches, etc.). At present, most of these solutions are restricted to individual projects and do not
allow the scientific community in the e-humanities to benefit from advances in other
areas of computer science. We therefore wish to distinguish between two important
aspects of e-humanities: 1. creation, dissemination, and use of digital repositories; 2. computer-based analysis of digital repositories using advanced computationa
and algorithmic methods. While the first has originally been triggered by the humanities and is commonly
known as digital humanities, the second implies a dominance of computational
aspects and might thus be called computational humanities. A practical consequence of this distinction in organizational terms would be to
set up research groups in both scientific communities, computer science, and the
humanities. The degree of mutual understanding of research issues, technical feasi-
bility, and scientific relevance of research results will be much higher in the area
of overlap between computational and digital humanities than with any intersection
between computer science and the humanities. To empower the humanities to enter into a substantial and mutually beneficial
dialog with computer science, however, a research infrastructure is needed that
enables researchers in the e-humanities to reuse distributed digitized data and tools
for their analysis as much as possible. To use such computational methods, an indi-
vidual researcher can proceed by employing two strategies, depending on his or her
own degree of computer literacy. One strategy is the individual software approach. 2
The Impact of Digitization in the Humanities—From
Digital Humanities to E-Humanities To the extent that applications of computer science have always led to a replacement
of analog by digital media and processes, digital media and processing models are
having an increasing impact on traditional work flows based on analog media in
the humanities and social sciences. The interdisciplinary combination of methods
from computer science and traditional humanities with large amounts of digital data
and advanced tools for processing these is commonly known as e-humanities (cf. McCarty 2005). Although there is no standard definition of terms yet, e-humanities in
a broader sense are concerned with the intersection of computing and the humanities
in the eScience paradigm, and thus pertain to any digitized data that are subject to
investigation in the humanities and the social sciences, such as text, images, and
objects (e.g., in archeology). For the humanities, the use of computer-based methods may lead to more effi-
cient research (where possible) and raise new questions that could not have been dealt
with otherwise. For computer science, turning to the humanities as an area of appli-
cation may pose new problems that lead to rethinking approaches hitherto favored
by computer science. As a result, new solutions may develop that help to advance
computer science in other areas of media-oriented application. By focusing on text
as the main data type in the humanities, we can highlight the benefit that can be
gained from the combination of digital document collections and new analysis tools
from computer science, mainly derived from information retrieval and text mining. In this way, all kinds of sciences that work with historical or present-day texts and
documents are enabled to ask completely new questions and deal with text in a new
manner. 2
The Impact of Digitization in the Humanities—From
Digital Humanities to E-Humanities Given a selection of digital text data, the research question is transferred into a set of
issues and methods that can be dealt with by a number of individual programs. This
approach allows for highly dynamic and individual development of research issues. It requires, however, a high degree of software engineering know-how. The other
approach is to use standard software. For well-defined and frequently encountered
tasks, an e-humanities infrastructure will offer solutions that provide the users with
data and analysis tools that are well understood, have already delivered convincing
results, and can be learned without too much effort (cf. Boehlke et al. 2013). Both approaches are interdependent. Probably good solutions in one domain of
text-oriented humanities can be transferred to other domains by just using different
kinds of text. A good infrastructure must be capable of making such solutions
accessible as best practices. 102 G. Heyer and V. Böhlke 3
CLARIN-D—An Infrastructure for Text-Oriented
Humanities Research infrastructures are concerned with the systematic and structured acqui-
sition, generation, processing, administration, presentation, reuse, and publication
of content. Content services make available the resources and programs needed for
that. Public digital text and data resources are linked together and made accessible
by common standards. New software architectures integrate digital resources and
processing tools to develop new and better access to digital contents. CLARIN-D1
is part of CLARIN Europe, which recently2 became an independent legal entity
according to the ERIC3 statutes. CLARIN-D is primarily designed as a distributed,
center-based project (cf. Wittenburg et al. 2010). This means that centers are at the
heart of an infrastructure that aims at providing consistent data services. Different
types of resource centers form the backbone of the infrastructure, provide access to
data and metadata, and/or run infrastructure services. Access to data, metadata, and
infrastructure services is usually (but not solely) based on Web services and Web
applications. The protocols and formats of infrastructure services (like persistent
identifiers or metadata systems and standards that are of interest to the CLARIN
initiative on the European level) have been agreed upon in the preparatory phase of
the project. Additional infrastructure or discipline-specific services are built upon
those basic infrastructure services. The usage of general services like registering and
resolving persistent identifiers is not limited to CLARIN itself. Other infrastructure
initiatives can and do use such services. Important metadata on CLARIN centers—for example, technical access points,
standards and contact information—is stored in a centralized centers registry that acts
as a starting point for service users and enables the automation of various procedures,
such as monitoring and visualizing the state of all infrastructure services. 1http://de.clarin.eu.
2http://ec.europa.eu/research/index.cfm?pg=newsalert&lg=en&year=2012&na=na-290212-1.
3http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=eric.
4https://www.clarin.eu/content/component-metadata. 4
Metadata, Citation, and Search In CLARIN, metadata is usually represented in a component metadata infrastruc-
ture (CMDI).4 The underlying technology of CMDI is XML-Schema (components,
profiles), XML (instances), and REST (component registry). CMDI addresses the
problem of various specialized metadata standards used for specific purposes by
different research communities. Instead of introducing yet another standard, CMDI 103 CLARIN-D: An IT-Based Research Infrastructure … Fig. 1 Components, profiles, and component registry Fig. 1 Components, profiles, and component registry aims at describing and reusing, and (when used in combination with ISOcat5) inter-
preting and supporting the integration of existing metadata standards. CMDI compo-
nents act as basic building blocks that define groups of field definitions. These compo-
nents can be combined into profiles that define the syntax and semantics of a certain
class of resources and act as blueprints for metadata instances describing items of this
class. These components are managed in a component registry, which allows users to
archive and share existing components, thus enabling their reuse (see Fig. 1). Through
this approach, CMDI supports the free definition and usage of metadata standards
dedicated to specific use cases. As long as metadata is stored in XML, CMDI is able
to “embrace” other standards. By combining the data itself with semantic informa-
tion stored in the ISOcat data-category registry, CMDI forms a solid basis for using
sophisticated exploration and search algorithms. Metadata is the backbone of the infrastructure and publicly available in CLARIN
from the resource centers (cf. Boehlke et al. 2012) via the Open Archives Initiative
Protocol for Metadata Harvesting (OAI-PMH).6 The openness of metadata is impor-
tant to CLARIN since it guarantees high visibility of the provided resources in the
research community. OAI-PMH is a well-established standard and is supported by numerous repository
systems like DSpace7 and Fedora.8 The OAI-PMH protocol is based on REST and
XML and provides the ability to do two things. It offers full access to the metadata
provided by the resource centers and allows for selective harvesting of metadata (see
Fig. 2) for search portals like the Virtual Language Observatory (VLO). The VLO
enables users to perform a faceted search on the metadata that was harvested from the
repositories of all CLARIN centers. By using the information stored in the ISOcat
data-category registry (cf. Kemps-Snijders et al. 2008) and the CMDI profiles (see
Fig. 5http://www.isocat.org/.
6http://www.openarchives.org/pmh/.
7http://www.dspace.org/.
8http://fedora-commons.org/. 9https://www.clarin.eu/content/federated-content-search. 4
Metadata, Citation, and Search 3) associated to the CMDI metadata instances, the VLO map information is
stored in these instances onto a predefined set of facets (see Fig. 4). The VLO also
supports the extraction and usage of additional, CLARIN/CMDI-specific, metadata 104 G. Heyer and V. Böhlke 104
G. Heyer and V. Böhlke
Fig. 2 OAI-PMH harvesting
Fig. 3 Metadata records,
profiles, and ISOcat. Source
https://www.clarin.eu/sites/
default/files/styles/opensc
ience_3col/public/cmdi-ove
rview.png
such as ResourceProxy (e.g., link to download, dedicated search portal) and federated
content search (FCS) interfaces. CLARIN also provides support for content-based search. The CLARIN-D FCS9
is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL)
and allows users to perform a CLARIN-wide search over all repositories that offer a
FCS interface by using a simple Web application. This Web application and external
applications send a request to an aggregator service This service first queries a Fig. 2 OAI-PMH harvesting Fig. 3 Metadata records,
profiles, and ISOcat. Source
https://www.clarin.eu/sites/
default/files/styles/opensc
ience_3col/public/cmdi-ove
rview.png
such as ResourceProxy (e.g., link to download, dedicated search portal) and federated
content search (FCS) interfaces. CLARIN also provides support for content based search The CLARIN D FCS9 Fig. 3 Metadata records,
profiles, and ISOcat. Source
https://www.clarin.eu/sites/
default/files/styles/opensc
ience_3col/public/cmdi-ove
rview.png Fig. 3 Metadata records,
profiles, and ISOcat. Source
https://www.clarin.eu/sites/
default/files/styles/opensc
ience_3col/public/cmdi-ove
rview.png such as ResourceProxy (e.g., link to download, dedicated search portal) and federated
content search (FCS) interfaces. such as ResourceProxy (e.g., link to download, dedicated search portal) and federated
content search (FCS) interfaces. CLARIN also provides support for content-based search. The CLARIN-D FCS9
is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL)
and allows users to perform a CLARIN-wide search over all repositories that offer a
FCS interface by using a simple Web application. This Web application and external
applications send a request to an aggregator service. This service first queries a
repository registry and searches for compatible interfaces. The initial query is then CLARIN also provides support for content-based search. The CLARIN-D FCS9
is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL)
and allows users to perform a CLARIN-wide search over all repositories that offer a
FCS interface by using a simple Web application. This Web application and external
applications send a request to an aggregator service. This service first queries a
repository registry and searches for compatible interfaces. 11Stuttgart Tübingen Tagset. See http://www.sfb441.uni-tuebing-en.de/a5/codii/info-stts-en.xhtml 10An organization which maintains a format for digital text representation. See http://www.tei-c.
org/index.xml.
11Stuttgart Tübingen Tagset. See http://www.sfb441.uni-tuebing-en.de/a5/codii/info-stts-en.xhtml. 10An organization which maintains a format for digital text representation. See http://www.tei-c
org/index.xml.
11 4
Metadata, Citation, and Search The initial query is then CLARIN-D: An IT-Based Research Infrastructure … CLARIN-D: An IT-Based Research Infrastructure … 105 Fig. 4 VLO Fig. 4 VLO sent to all of these interfaces and the individual results are aggregated and sent back
to the user or application (see Figs. 5 and 6). Since CLARIN is designed as an open
infrastructure, third-party content providers may easily plug their own repository and
FCS interface into this process by registering it to the CLARIN repository registry. sent to all of these interfaces and the individual results are aggregated and sent back
to the user or application (see Figs. 5 and 6). Since CLARIN is designed as an open
infrastructure, third-party content providers may easily plug their own repository and
FCS interface into this process by registering it to the CLARIN repository registry. Web services in CLARIN are also described via CMDI (which may very well
contain a link to a WSDL file). If more specific metadata is provided (i.e., the infor-
mation enforced by a certain CMDI profile is given), these Web services can be used
in a workflow system called WebLicht (cf. Hinrichs et al. 2010). WebLicht allows
users to build and execute chains of Web services by analyzing the metadata available
for each service and ensuring that the format of the data is compatible; that is, that
the output of a predecessor service satisfies the specification of a successor service. Web services in CLARIN are also described via CMDI (which may very well
contain a link to a WSDL file). If more specific metadata is provided (i.e., the infor-
mation enforced by a certain CMDI profile is given), these Web services can be used
in a workflow system called WebLicht (cf. Hinrichs et al. 2010). WebLicht allows
users to build and execute chains of Web services by analyzing the metadata available
for each service and ensuring that the format of the data is compatible; that is, that
the output of a predecessor service satisfies the specification of a successor service. Fig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. png ig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. ng Fig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. png 106 G. Heyer and V. Böhlke Fig. 6 CLARIN-D FCS Web application
Table 1 Example input
specification for a POS tagger
Web service
Format
MyFormat
Input
text = UTF-8
language = German
tokens = present Fig. CLARIN-D: An IT-Based Research Infrastructure … 107 CLARIN-D: An IT-Based Research Infrastructure … Table 2 Example output
specification for a POS tagger
Web service
Format
MyFormat
Output
POS tags = STTS into tokens encoded in an imaginary format. It produces a document of the same
format by adding POS tags based on the STTS tagset. The chaining algorithm of WebLicht (cf. Boehlke 2010) is based on the idea
that NLP services usually consume a document of a well-defined standard and will
also return such a document. The successful invocation of a service for an input
document hence depends on which information is available in that document. A POS
tagger Web service may only work if sufficient information on sentence and token
boundaries is available, while a named entity recognizer (NER) requires appropriate
POS tags. Therefore, the standard used for the input document needs to allow for a
representation of this kind of information, and, of course, this information needs to
be present in the input document itself. This fact is also represented in the interface
definition. Thus, for service chaining to work, it must be ensured that this information
is available by using a type checker on each step of a chain. This check can be done when building the chain, since all the necessary informa-
tion is already available. Based on a formal Web service description according to the
proposed structure, a chaining algorithm, which is basically a type checker, can be
implemented. A service can be executed if the previous services in the chain meet
the following constraints: the format specified in the output is equal to the format specified in the input
specification of the service; every parameter-type/standard pair defined in the input specification needs to be
one of the pairs in the output specifications of services which have been executed
(or scheduled for execution previously in the chain, if we stay on build time). every parameter-type/standard pair defined in the input specification needs to be
one of the pairs in the output specifications of services which have been executed
(or scheduled for execution previously in the chain, if we stay on build time). These two constraints are of course a simplification. But in many simple cases, an
algorithm like this will be sufficient. A short and simplified example of the chaining
logic is given in Figs. 4
Metadata, Citation, and Search 6 CLARIN-D FCS Web application Table 1 Example input
specification for a POS tagger
Web service
Format
MyFormat
Input
text = UTF-8
language = German
tokens = present When thinking about interchanging neuro-linguistic programming (NLP) data like
text, there are several established standards defining how texts can be encoded and
how annotations like POS tags may be added. These standardization efforts are
supported by WebLicht, hence the following interface definition of a Web service
compatible with WebLicht: • the format used is TCF (or TEI10 P5, etc.); • the format used is TCF (or TEI10 P5, etc.); • the document contains German text and is annotated with POS tags; • the POS tags are encoded according to the STTS11 tagset. • the POS tags are encoded according to the STTS11 tagset. A complete interface definition of a WebLicht Web service consists of two iden-
tically structured specifications for input and output. Each of these specifications
defines the format of a document that is used to represent the data. Additionally,
a set of pairs of parameter types is mandatory to invoke the service for the input
specification, or is computed and added by the service for the output specification. Each of these parameter types is bound to a standard definition, which binds it to a
standardized encoding of the information. Tables 1 and 2 give example input and output specifications of a POS tagger Web
service. This service consumes documents that contain German text that was split CLARIN-D: An IT-Based Research Infrastructure … CLARIN-D: An IT-Based Research Infrastructure … 7 and 8, which show part of a chain consisting of Web services
A (a tokenizer) and B (a POS tagger). In Fig. 7, Service A can be executed since all
constraintsdefinedinitsinputspecificationaremet.Theformatoftheinputdocument
is compatible and its content fulfills the requirements because it contains German text
encoded in UTF-8. The tokenizer segments the text into sentences and tokens. After
its execution, this information is added to the resulting output document. Service B
is checked against this updated knowledge about the content of the output document
of Service A (see current metadata in Fig. 8). Service B is compatible since all of its
input requirements, format and parameters, are available in the output document of
Service A. 108 G. Heyer and V. Böhlke 108
G. Heyer and V. Böhlke
Fig. 7 Tokenizer service
specification
Fig. 8 POS tagger service
specification
5
Summary and Conclusion
Research infrastructures for the humanities can help to share digital resources and
content services. In particular, they can help researchers in the digital humanities
to save time and effort when developing software to deal with specific research
issues, while the development of such infrastructures and their key software compo-
nents is a software engineering task that increasingly poses interesting and chal-
lenging research problems for computer scientists. In this paper, we have presented Fig. 7 Tokenizer service
specification e Fig. 8 POS tagger service
specification Fig. 8 POS tagger service
specification 5
Summary and Conclusion Research infrastructures for the humanities can help to share digital resources and
content services. In particular, they can help researchers in the digital humanities
to save time and effort when developing software to deal with specific research
issues, while the development of such infrastructures and their key software compo-
nents is a software engineering task that increasingly poses interesting and chal-
lenging research problems for computer scientists. In this paper, we have presented
the European Strategy Forum on Research Infrastructures (ESFRI) project CLARIN
and some of its key elements as a research infrastructure for the humanities. In detail, CLARIN-D: An IT-Based Research Infrastructure … 109 we have presented component metadata infrastructure as a means for unifying meta-
data descriptions of linguistic resources in the humanities. Based on these metadata,
we have also shown how Web services can be built that share data and algorithms
in the research infrastructure. Both aspects are closely related: The content-driven
use of digitized data and software tools in a specific application scenario in the
humanities, and the software and service engineering issues relating to an efficient
research infrastructure in the humanities. These two aspects, content and service,
clearly need to complement each other in order to establish a culture of best practice
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(ELRA) (2010) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license and
indicate if changes were made. g
The images or other third party material in this chapter are included in the chapter’s Creative
Commons license, unless indicated otherwise in a credit line to the material. If material is not
included in the chapter’s Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. Toward Process Variability Management
in Online Examination Process
in German Universities: A State
of the Art Maryam Heidari and Oliver Arnold Abstract In contemporary organizations, multiple variants of the same business
process are often considerable. Such business process variability has caused consid-
erable challenges, both while modeling processes and in their execution. In order
to develop a new approach to managing process variants, or extend an existing one,
in this research, we review the state of the art in a particular area: online examina-
tion processes. We show to what extent variability should be considered in exam
processes, whether this is due to special legal restrictions and regulations, different
exam frameworks, or even different technical infrastructure. This could be the foun-
dation for developing an approach to managing process variability in the field of
e-assessment. Initial findings indicate that examination processes have many simi-
larities, but also considerable differentiation. Therefore, there an appropriate model
needs to be developed in order to manage variability in e-assessment and the devel-
oped approach must then be validated in identifying faculties. This paper constitutes
a first step in this direction. Keywords Process variability · Online examination · E-assessment process
model · Accreditation M. Heidari
TU Bergakademie Freiberg, Freiberg, Germany
e-mail: maryam.heidari@bwl.tu-freiberg.de M. Heidari
TU Bergakademie Freiberg, Freiberg, Germany
e-mail: maryam.heidari@bwl.tu-freiberg.de
O. Arnold (B)
Westsächsische Hochschule Zwickau, Zwickau, Germany
e-mail: oliver.arnold.1@fh-zwickau.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_8 1
Introduction In today’s dynamic world, there are often multiple variations of identical business
processes. Rosemann and colleagues noted, for instance, that SAP offers 27 different
industry solutions with corresponding business process reference models (Rose-
mann and van der Aalst 2007). These models usually include decisions in the work-
flow, which could be made before executing process instances. It is impossible for M. Heidari
TU Bergakademie Freiberg, Freiberg, Germany
e-mail: maryam.heidari@bwl.tu-freiberg.de O. Arnold (B)
Westsächsische Hochschule Zwickau, Zwickau, Germany
e-mail: oliver.arnold.1@fh-zwickau.de 111 111 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_8 112 M. Heidari and O. Arnold both variants of such decisions to coexist in a certain domain or process context. However, conventional modeling approaches do not offer the opportunity to differ-
entiate between such decisions and regular decisions during the runtime of a process
instance. An important element of controlling the variability in business process
models is to separate the usual runtime decisions from decisions at configuration
time, called variation points. The results of such steps are complex artifacts. The
number of artifacts makes the manageability of related workflows more complex. Basedonthereviewedliterature,organizationstakedifferentapproachestomanaging
process variability (Ayora Esteras 2012). The existing approaches have limitations
in terms of supporting an entire set of elements like control flow, rules, and legal
regulations during the construction and execution of business processes. For this paper, we chose an educational field as an example of process variability,
in order to observe effects and causes of variability. The goal is to have a compre-
hensive overview to address the problem of process variability in online examination
processes at German universities and show the necessity of managing it through an
appropriate business process model. To achieve this goal, we set out the state of the art
in research regarding the process variability of online examinations from different
perspectives. This could be the basis for developing a process model to manage
existing variability in this field. We evaluate existing approaches and concepts in the
context of e-assessment in the literature and clarify current accreditation processes
in educational fields. This will help to identify to what extent existing examination
procedures reflect variability and demonstrate the necessity of developing a unified
e-assessment model to cover all variability in the learning-teaching process. The paper is organized as follows: After illustrating motivation through existing
studies in the following section, the research method is explained. 1
Introduction After exploring
the literature and data collected in the identified domains, the results are evaluated. Finally, the need for further work is explained in the conclusion. 2
Motivation In this section, we have a close look at process variability and its challenges, iden-
tifying the importance of variability management in the organizations. Basically,
process models capture an organization’s activities in achieving certain business
goals. The aim is to better understand the process, its implementation, and its execu-
tion in a workflow (Becker et al. 2013). However, there are a lot of possible variants
for one process. Such business process variability creates considerable challenges in
process modeling and execution: • the variants may be modeled in a highly redundant way, so there are many identical
or similar parts; • the variants may be modeled in a highly redundant way, so there are many identical
or similar parts; • there is no strong relation between the variants, so there is no support for
automatically combining existing variants; • there is no strong relation between the variants, so there is no support for
automatically combining existing variants; Toward Process Variability Management … Toward Process Variability Management … 113 • manual modeling in every single process variant would be time-consuming and
error-prone. • manual modeling in every single process variant would be time-consuming and
error-prone. • manual modeling in every single process variant would be time-consuming and
error-prone. In recent years, the proper management of business process variability has been
the subject of numerous scientific studies. A very comprehensive survey article about
business process variability can be found in Valenca et al. (2013), which describes
more than 80 primary sources. Based on this study, significant numbers of variability
approaches exist, where each one addresses different issues in terms of process vari-
ability. Valenca and colleagues observed 57 new approaches to different aspects
of variability in processes (Valenca et al. 2013). They divided these references into
five categories: business process configuration, to capture an instance of the reference
model;businessprocesscorrectness,tosemanticallysupportcorrectionoftheprocess
model; business process flexibility, to change process models fast and easily; busi-
ness process modeling, to visualize variability in process models; business process
similarities, to investigate differentiations between business process models. It is
argued that only 30% of solutions are practically evaluated through case studies and
surveys, especially of industry: The lack of empirical studies in process variability
is considerable, with implications for executing process variability (Valenca et al. 2013). 2
Motivation In the public sector, as in business, processes have a lot in common, but signif-
icant differences due to the local conditions and legal regulations are considerable. Vogelaar and colleagues analyze and compare the different processes of ten Dutch
municipalities which are found to vary in terms of classical standardization processes
(Vogelaar et al. 2012). In education, Arnold and Laue studied controllability of variability in examination
process models (Arnold and Laue 2014). They investigated six different courses
at three different universities in the German Federal State of Saxony, to achieve
better comparability. Based on this research, considerable variability in examination
processes exists, even in one university between different fields of study. The authors
triedtoprovideasolutionbasedonexistingvariabilityapproaches,inordertomanage
examination processes. They argued that appropriate process variability modeling
requires modeling skills and significant experience in the identified domain (Arnold
and Laue 2014). We focus on online examination processes in higher education, presenting the state
of the art in three different domains and observing existing process variability in order
to gain a comprehensive overview of process variability in this field, highlighting the
need for this to be managed. 3
Research Method • We reviewed the state of the art in three identified domains within e-assessment • IT-related approaches; • designing study courses and e-assessment concepts; • accreditation process. In the following, the results of our literature review and data collection in each
domain are explained separately. 3
Research Method The purpose is to evaluate the existing variability in higher educational e-assessment
processes, as a basis for further research into variability management in this field. The state of the art is identified in five phases (Cooper 1998): The purpose is to evaluate the existing variability in higher educational e-assessment
processes, as a basis for further research into variability management in this field. The state of the art is identified in five phases (Cooper 1998): 114 M. Heidari and O. Arnold M. Heidari and O. Arnold 1. Problem formulation: The academic goal and research relevance are defined; 1. Problem formulation: The academic goal and research relevance are defined 2. Literature search and data collection: Literature and data related to the problem
formulation are identified; 2. Literature search and data collection: Literature and data related to the problem
formulation are identified; 3. Literature evaluation: The acquired literature is assessed for relevance and
categorized; 3. Literature evaluation: The acquired literature is assessed for relevance and
categorized; 4. Interpretation: The results are analyzed and interpreted; 5. Presentation: The results are presented in a suitable fashion. Assessments are an important part of the educational cycle (Ferrão 2010) and have
a great impact on the learning process. They provide valuable information about the
effectiveness of a study course in increasing the students’ knowledge (Primiano
et al. 2004). An appropriate assessment process is not only important in terms of
teaching and learning, but also for accreditation processes and educational standards
(Ferrão 2010). Recent developments in e-learning can be seen as an accelerator to
developing e-assessment alternatives. It is therefore becoming more important to
develop methods for e-assessment and to gain feedback on learning and teaching
(Sangi and Malik 2007). Furthermore, Dermo has shown that e-assessment can offer
different forms of assessment with immediate feedback to both students and lecturers,
so it can be recognized as a complementary tool in the learning framework (Dermo
2009). Exam regulation documents, which are the basis for accreditation processes
in higher educational institutions, have a lot in common. But in some points, they
differ from one university to another or even from one course to another within the
same institution. Therefore, there is variability in assessment processes, which is an
obstacle to developing a unified process model for e-assessment. 1Numbers in brackets refer to the references in Appendix 1. 3.1.1
Domain: IT Approaches Data sources: AISel and EBSCO
Research period: 2000–2013
Search terms and keywords: e-assessment, education, online examination, e-test,
computer-based exam (in abstract and title)
Number of related articles:
AISel: 51 after reviewing and removing doublets and non-related articles: 14
AISel: 51 after reviewing and removing doublets and non-related articles: 14 Data sources: AISel and EBSCO
Research period: 2000–2013 Data sources: AISel and EBSCO
Research period: 2000–2013 Search terms and keywords: e-assessment, education, online examination, e-test,
computer-based exam (in abstract and title) Number of related articles: Number of related articles: AISel: 51 after reviewing and removing doublets and non-related articles: 14 AISel: 51 after reviewing and removing doublets and non-related articles: 14 AISel: 51 after reviewing and removing doublets and non-related articles: 14 115 Toward Process Variability Management … Toward Process Variability Management … Toward Process Variability Management …
115
Table 1 Pedagogical aspects of e-assessment
Pedagogical issues
References
Evaluation of the impact of e-assessment on
learning processes (strengths and weaknesses)
Becker et al. (2008, 2013), Braun (1998),
Coyle (2009), Dermo (2009), Dittman and
Deokar (2008), Ferrão (2010), Gruhn and Laue
(2007), Hodgson and Pang (2012),
Impagliazzo et al. (2002), Johnson-Glenberg
(2010), and Jordan and Mitchell (2009)
Formative e-assessment (feedback)
Charoen (2009), Davis et al. (2001), El-Ashy
(2006), Hall et al. (2010), Hallerbach et al. (2010), Hallerbach et al. (2008), Hodgson and
Pang (2012), and Irani et al. (2000)
Collaborative e-assessment
Ayora Esteras (2012), Boyle (2010), and Davis
et al. (2001)
Different types of e-assessment and questions
Coyle (2009), Gorgone (2006), Gruhn and
Laue (2007), and Jordan and Mitchell (2009)
Table 2 Technical aspects of e-assessment
Technical issues
References
E-assessment tool evaluation (strengths and
weaknesses)
Accountants find e-assessment … (2011), Boyle
and Hutchison (2009), Braun (1998), Charoen
(2009), Cooper (1998), Dascalu and Bodea
(2010), Davis et al. (2001), Davis (2007), Dermo
(2009), Gorgone (2006), and Impagliazzo and
Gorgone (2002)
E-assessment implementation (challenges:
validity, security, task assessment, adoption,
etc.)
Attali and Burstein (2006), Braun (1998),
Campbell (2008), Daly et al. (2010), Ferrão
(2010), Impagliazzo and Gorgone (2002), Irani
et al. (2000), Jacob et al. 3.1.1
Domain: IT Approaches (2006), Johannsen and
Leist (2012), Johnson-Glenberg (2010), and
Jordan and Mitchell (2009) EBSCO: 62 after reviewing and removing doublets and non-related articles: 18
Based on the reviewed articles, a main classification can be recognized in the EBSCO: 62 after reviewing and removing doublets and non-related articles: 18
B
d
h
i
d
i l
i
l
ifi
i
b
i
d i
h EBSCO: 62 after reviewing and removing doublets and non-related articles: 18
Based on the reviewed articles, a main classification can be recognized in the
context of e-assessment in higher education: EBSCO: 62 after reviewing and removing doublets and non-related articles: 18
Based on the reviewed articles, a main classification can be recognized in the
context of e-assessment in higher education: • pedagogical issues (educational view) • pedagogical issues (educational view) • technical issues Different kinds of terms and concepts are used, based on pedagogical and technical
approaches: Each one addresses one or more aspects of e-assessment. These issues
are summarized in the following Tables 1 and 2.1 Most of these references include multiple issues from the technical and pedagog-
ical perspectives. These issues are connected and cannot be separated. 116 M. Heidari and O. Arnold Jacob and colleagues deploy an e-assessment tool, the Black Board Learning
System (BBLS), as a comprehensive e-learning software to facilitate continuous
assessment and evaluate its effects on learning processes (Jacob et al. 2006). It reveals
that the biggest advantage of e-assessment in this system is immediate feedback,
which bolsters the formative assessment.2 One weakness of the system is the lack
of the automatic evaluation of essay-writing exams. Kehily analyzed the impact of a
Web-based e-learning platform that can support effective teaching (a course manage-
ment system for lecturers) and formative assessment (a computer-assisted learning
tool for students) in a case study (Kehily 2011). Venkatraman developed a four-step
student-centered approach to an effective e-learning process and, in a case study
of information system (IS) courses, evaluated this approach for different assessment
methods including individual, group, peer, and self-assessment (Venkatraman 2007). These four steps are: 1. understanding the students’ learning style and their learning expectations; 2. identifying suitable assessment models; 3. designing a set of assessments; 4. evaluating the impact of the assessment on the learning process. 3.1.1
Domain: IT Approaches Dermo evaluates the possible risks in planning e-assessments such as computer
stress, fairness of choosing questions randomly from a bank, accessibility, and the
contribution of e-assessment to students’ learning, through six dimensions in a case
study (Dermo 2009). These six dimensions are: affective factors, reliability and
fairness, validity, security, practical issues, and teaching and learning terms, which
are a mixture of pedagogical and technical issues. Daly and colleagues argue that
existing e-assessment solutions focus on developing technical and infrastructural
issues more than educational aspects (Daly et al. 2010). McCann identifies different
factors which affect real implementations of e-assessment systems based on two IS
theories: Roger’s theory3 and Eckel and Kezar’s theory4 (McCann 2010). 2Formative assessment encourages deeper engagement with learning and is a motivation and
progressive force in learning. The key element of formative assessment is feedback.
3It identifies five variables to demonstrate how and why new ideas are adopted: relative advantage,
compatibility, trialability, observability, and complexity (McCann 2010).
4It identifies five core strategies that explain change across institutions: senior administrative
support, collaborative leadership, flexible vision, staff development, and visible actions (McCann
2010). 3It identifies five variables to demonstrate how and why new ideas are adopted: relative advantage
compatibility, trialability, observability, and complexity (McCann 2010). 2Formative assessment encourages deeper engagement with learning and is a motivation and
progressive force in learning. The key element of formative assessment is feedback. 4It identifies five core strategies that explain change across institutions: senior administrativ
support, collaborative leadership, flexible vision, staff development, and visible actions (McCann
2010). Toward Process Variability Management … Toward Process Variability Management … In this domain, we began by finding some case studies of e-assessment or online
examination at German universities. In order to have an appropriate sample, we
selected universities which conducted online examinations or had a project to recog-
nize a unified approach or process regarding e-assessment in Germany. Different
kindsofprojectsintermsofcomputer-basedexaminationshavebeeninprogressfrom
the year 2000 onward. Table 3 summarizes all these projects with their functionality
and their relation with exam regulation documents. Of all the universities studied, only the University of Duisburg-Essen proposes
a process model for implementing online examination. Proposing such a process
model for online exams has the following advantages: • improves the speed of feedback to students; • motivates students and lecturers to increase computer skills through the integra-
tion of multimedia elements such as audio and video, and using complex digital
systems; • motivates students and lecturers to increase computer skills through the integra-
tion of multimedia elements such as audio and video, and using complex digital
systems; • significant time saving for lecturers by automatic correcting process. By reviewing the exam regulations and conditions, it becomes obvious that there
is no identified exam process model in the administrative processes at different
universities. A process model not only supports understanding the complexities
of processes properly, but also contributes to advancing and improving defined
processes (Irani et al. 2000). Therefore, in order to understand the examination
workflows carried in the universities, a process model is required to analyze exam
processes comprehensively. 5Association for Information Systems eLibrary. 3.1.2
Domain: Designing Study Courses and E-Assessment Concepts Data sources: German university homepages
Research period: 2000–2013
Search terms and keywords: e-assessment, online examination, project, computer-
based exam, e-exam, e-test Search terms and keywords: e-assessment, online examination, project, computer-
based exam, e-exam, e-test 2Formative assessment encourages deeper engagement with learning and is a motivation and
progressive force in learning. The key element of formative assessment is feedback. 117 3.1.3
Domain: Accreditation Process Data sources: Accreditation agencies authorized by AISel5 and EBSCO
Research period: 2000–2013
Search terms and keywords: e-assessment, education, online examination,
computer-based exam, accreditation process, accreditation criteria (in abstract
and title) Data sources: Accreditation agencies authorized by AISel5 and EBSCO
Research period: 2000–2013 Data sources: Accreditation agencies authorized by AISel5 and EBSCO
Research period: 2000–2013
Search terms and keywords: e-assessment, education, online examination,
computer-based exam, accreditation process, accreditation criteria (in abstract
and title) Search terms and keywords: e-assessment, education, online examination,
computer-based exam, accreditation process, accreditation criteria (in abstract
and title) As a definition, accreditation is a criteria-based procedure to assess and evaluate
the admissibility of an educational program in terms of quality (Gorgone 2006;
Impagliazzo and Gorgone 2002; Reichgelt and Yaverbaum 2007). The main goal of
accreditation is to assess the educational quality of an academic program to ensure
that it meets certain quality standards, called accreditation criteria (Reichgelt 2007). Based on the European Network for Quality (ENQA), each educational program
should fulfill the minimum in the following set of requirements to be accredited: • requirements and objectives; • teaching–learning process; • learning resources; M. Heidari and O. Arnold M. Heidari and O. 3.1.3
Domain: Accreditation Process Arnold 118 Table 3 E-assessment projects in German universities
University
Description of e-assessment
projects
Relation to exam regulation
documents
Free University of Berlin
• Since 2005
• Run by the center for digital
systems (CeDiS)
• Software: LPLUS Test
Studio
• 407 spaces for
e-examinations
• Not used for all study
courses
Not mentioned
University of Duisburg-Essen
• Since 2007 (in progress)
• Software: LPLUS
• Faculties: human science,
social science, biology and
geography, chemistry,
engineering, and
mathematics
• Implementation of e-exams
based on a process model
e-exams are mentioned in
some study courses as one of
the exam methods beside other
traditional forms
Details of the e-exam process
are not mentioned in these
documents
University of Bremen
• Since 2004
• Software: LPLUS
• 7500 e-exams per semester
Since 2010, performing the
electronic examinations as one
of the examination forms is
admissible in the examination
rules and regulation documents
University of Giessen
• Since 2007
• Software: open-source
learning platform (ILIAS)
• Offers many opportunities
such as learning modules for
units, online glossary, import
of SCORM and HTML
tutorials, e-assessment
module for online tests,
survey module for user
surveys, user management in
courses and groups
• This system is limited due to
the lack of appropriate space
to increase efficiency of
e-examinations
Not mentioned
University of Mainz
• Since 2007
• Software: open-source
learning platform (ILIAS)
• Exam regulation documents
mention that e-exams should
be carried out under the
same conditions as
traditional examinations
• The details of the e-exam
process are not mentioned in
these documents
(continued) Table 3 E-assessment projects in German universities • The details of the e-exam
process are not mentioned in
these documents (continued) 119 Toward Process Variability Management … Table 3 (continued)
University
Description of e-assessment
projects
Relation to exam regulation
documents
University of Koblenz-Landau • Since 2013
• Software: open-source
learning platform (ILIAS)
• Two years for pilot and
evaluation phase
• Online exam submission
through electronic exam
schedule service (eKLAPS)
Not mentioned because the
project is new and in the pilot
phase
University of Regensburg
• Since 2010 (in progress)
• Road map defined which
consists of different tasks
and stages
Legal conditions and e-exam
framework during the whole
process are stages of the
e-assessment road map
University of Leipzig
• Since 2005
• Software: open-source
platform (elateXam)
• Around 1000 students per
semester
• Next step: develop the
project as a pilot within the
project iAssess.Sax in the
universities of Dresden and
Zwickau
Not mentioned 3.2
Accreditation Processes in Germany In Germany, the federal states are responsible for accreditation processes and at least
11 authorized accreditation agencies in different fields of education (medical, natural
science, engineering, economics, etc.) are in operation at present.6 Educational
accreditation in Germany is based on two issues: 1. standards of study courses and degrees, which are based on regulations for study
and examinations; 2. accreditation in teaching, which is based on quality improvement measures. The requirements in the examination accreditation process are as follows: • examinations are coordinated so that students have sufficient time to prepare
themselves; • it must be possible to move directly from the bachelor’s degree to the master’
degree without loss of time; • the form of examination is laid down in the description of each module; • the form of examination is laid down in the description of each mod
• examinations should not cause extensions to the period of study; • examinations should not cause extensions to the period of study; • the evaluation criteria are transparent for both lecturers and students; • the degree program ends with a final thesis; • it is checked whether students are capable of oral discussion in their specialis
area; • the supervision of the final thesis is subject to precise regulations in the curriculum The archived documents in the accreditation process are test results, drop-ou
rates, any quantity results of examinations, as well as feedbacks from the courses. This survey of three domains indicates that multiple perspectives exist, which
cause variability in performing and evaluating e-assessment processes. It is therefore
essential to develop an appropriate model to account for this variability in online
examination processes. • monitoring, analysis, and overview. • monitoring, analysis, and overview. The assessment or examinations are placed in the teaching–learning process,
which is the most complex aspect of this model because it includes a mixture of
technical, pedagogical, and social competences and, furthermore, there is a great
freedom to manage courses in order to achieve identified objectives. According to Reichgelt and colleagues, there are two accreditation types: – institutional accreditation is applied to an academic institution, like an entire
university; – institutional accreditation is applied to an academic institution, like an entire
university; – specialized accreditation is applied to a subunit in an institution and includes two
levels: program accreditation focuses on the content of the program, while admin-
istrative accreditation concentrates on the administrative process in a subunit of
an institution (Reichgelt and Yaverbaum 2007). The authors explain that there are two main approaches to accreditation processes. The first one is the input-based approach which measures various minimal stan-
dards through a checklist based on the learning-input processes such as curriculum,
teaching resources, library, laboratory, and other facilities. The second is the
outcomes-based approach, which considers the program’s outcomes, such as the
institution’s educational objectives and student learning. Reichgelt and colleagues
argue that a significant shift from the input-based to the outcomes-based approach 120 M. Heidari and O. Arnold has occurred in recent years and academic institutions attempt to conform themselves
with outcome criteria (Reichgelt and Yaverbaum 2007). has occurred in recent years and academic institutions attempt to conform themselves
with outcome criteria (Reichgelt and Yaverbaum 2007). 6December 2013. 7All these studies are summarized in a table in Appendix 1.
8These universities are listed in Appendix 2. 4.1
Evaluation of IT Approaches Based on reviewed IT approaches, it can be argued that due to the great advantages
of and positive impacts of online exams on learning processes, there is a considerable
movement from traditional to electronic assessment in academia today. Furthermore,
studies7 show that different issues, from pedagogical to technical and even social
matters, cause process variability in higher education examinations. To identify a way
of managing this inherent variability and to construct unified e-assessment proce-
dures, it seems necessary to have a cross-functional view of e-assessment projects. Someoftheissuesrelatedtoe-assessmentare:theimpactsonstudentlearning;effects
on the teaching method; formative and collaborative e-assessment; immediate feed-
back and legal issues; evaluating possible risks in planning such as computer stress or
fairness impression; developing infrastructural issues, such as security and question
banks. 4
Literature and Results This literature review was performed in order to demonstrate existing process vari-
ability in e-assessment in different domains of higher education, which occurs for
different reasons. The results of each domain and its relations to process variability
are analyzed and presented in the following. Toward Process Variability Management … 121 Table 4 Summary of e-assessment projects in German universities
Number of studied universities
30
Number of universities which have e-assessment projects (in progress)
18
Number of universities which perform online examination practically in some fields
9
Number of universities which have a paragraph about online examinations in exam
regulation documents
3
Number of e-assessment projects in universities in Saxony
2 8These universities are listed in Appendix 2. 4.3
Evaluation of Accreditation The results revealed that accredited educational programs are subject to a variety of
quality criteria. These criteria depend on the level and the goals of the courses. Based
on the Information Model from the European Network for Quality (ENQA), assess-
ment and examination processes are placed within the teaching–learning process,
which is one of the complex parts of accreditation. It involves different aspects such
as pedagogical, technical, legal, and even social issues. p
g g
g
No framework for examination forms (traditional or computer-based) was identi-
fied in this study of the German accreditation process. In exam regulation documents,
assessments were only described in the terms listed at the end of Sect. 3.3 above. The form of examinations is not restricted by the accreditation process, but is under
the authority of the educational systems and based on the identified objectives of
courses. This causes process variability from one educational institution to another. 4.2
Evaluation of Study Courses Thirty German universities from different federal states and different study courses
were reviewed.8 The results show that e-assessment or online examination projects
are currently in progress in 18 universities, but just nine are performing such assess-
ments in practice. It should be noted that although online examinations are in use at
some universities, there exists considerable process variability, too, which makes it
difficult to extract a unified platform in this area. Furthermore, legal conditions in regulation documents create practical limitations
on performing online examinations. In order to make it an acceptable form of assess-
ment,electronicexaminationshouldbereferredtoinaparagraphorevenasentencein
the corresponding exam regulation document. Based on reviewing examination rules
documents in all these universities, Table 4 reveals that only three German universi-
ties have a paragraph stating that online examination is an admissible examination
form. 122 M. Heidari and O. Arnold 4.4
Summary of the Results For clarity, we summarize the results of the three domains in Table 5. In sum, exam processes show variability for the following reasons: • variability in legal restrictions and regulations in different educational institutions;
• variability in exam framework, not only in different universities but also in one
university between different courses; • variability in legal restrictions and regulations in different educational institutions;
• variability in exam framework, not only in different universities but also in one
university between different courses; Table 5 Summary of the results
Domain
E-assessment limits on PVa
Why PV management is
necessary
IT approach
Different perspectives:
– teaching–learning issues;
– legal issues;
– technical issues;
– social issues
To have a cross-functional and
integrated view
Course and assessment design
Legal conditions are not
mentioned in exam
regulation documents
Different processes are used
to perform online
examination
To develop an appropriate
approach to support legal
conditions in exam documents
Accreditation
The form of the exam is not
restricted by accreditation
criteria, which leads to
variability
To develop a business process
model for clear e-assessment
criteria
aPV = process variability Toward Process Variability Management … 123 • variability in study course design; • variability in study course design; • variability in technical infrastructure for online examination processes. • variability in technical infrastructure for online examination processes. Based on the obtained results, it can be argued that an appropriate design for
variability management has to be aligned with the specified domain of projects and
conditions to cover all variability within the identified domain. There is only one
process model for performing online examinations in some study courses at Univer-
sity of Duisburg-Essen, which could be an appropriate model for conducting online
examinations at German universities. We studied existing process variability (effects and causes) in online examination
processes from different perspectives. We found that to manage process variability, an
appropriate business process model is necessary to cover all examination processes
and features of educational institutions. According to the existing literature, one approach to process variability manage-
ment is the single model approach, which models all known variants of the process in
one common model (Hallerbach et al. 2010; Kumar and Yao 2012). The alternative is
to model every variant of a single model, which is called the multi-model approach. The latter models will have a simpler structure (Hallerbach et al. 2010; Kumar and
Yao 2012). 4.4
Summary of the Results Some advanced modeling approaches explicitly deal with families of
process models, such as configurable event-driven process chains (C-EPCs) (Rose-
mann and van der Aalst 2007), PROcess Variants by OPtions (PROVOP) (Hallerbach
et al. 2010), ConDec (Pesic and Aalst 2006), and feature modeling, which is normally
used in software engineering. Each of these approaches has their own advantages and
drawbacks but there is a lack of adaptability between different approaches (Valenca
et al. 2013). The next step in this research is to conduct a comprehensive overview of available
variability approaches, to identify which of them are more appropriate for online
examinations in higher education. Further research is needed to evaluate how existing
process variability approaches can be compatible with exam processes, and to what
extent existing process variability in this field can be controlled and managed. 5
Conclusion and Further Work The aim of this research is to demonstrate existing variability in examination
processes and emphasize the need for variability management. This could be the
basis for developing a new approach to business process variability, or extending an
existing one. To reach this goal, we concentrated on online examination processes
in higher education. As a preliminary stage, we performed a literature review in three different
domains: IT approaches; concepts; course design and the accreditation process. This
paper demonstrates the important role of business process management in improving
and promoting the design of e-assessment processes. 124 M. Heidari and O. Arnold M. Heidari and O. Arnold Combined with this literature review, an analysis of current e-assessment case
studies and projects in German universities yielded the following results. Although
different kinds of projects under the name of e-assessment or online examination are
in progress in German universities, the variability in these processes is recognizable. In other words, similar processes exist, but distinctions and variability are observable
as well. Furthermore, the review of the exam regulation documents for various study
courses at different universities revealed that these regulations do not yet mention an
acceptable framework for performing e-assessments. Process variability exists in e-assessment at German universities. It is necessary
to manage this variability through an appropriate business process model to support
online examination procedures. This paper describes research in progress which clarifies and identifies the neces-
sity of developing an existing approach to manage and control the process variability
in university e-assessment. The next step is to study process variability manage-
ment to identify an appropriate model in the context of e-assessment. This could be
followed by the development of a prototype for the identified approach and finally
the validation of the developed method. Appendix 1: Summary of IT Approaches to e-Assessment Appendix 1: Summary of IT Approaches to e-Assessment
No. Reference (author, year)
Summary
1
F. Braun, 1998
It introduces some web-based tools for
online assessment such as Learning space,
Web forms, Microtest, and Quizmaker. 2
Charoen, 2007
It indicates the benefits and limitations of
implementing an e-learning system in an
educational institution in Thailand based on
expert interviews. 3
Dittman, 2008
It introduces a structure, the collaborative
e-learning template (CET), to improve
collaborative activities in the learning
process such as collaborative assessments
through a course. 4
Papp, 2000
It indicates different critical factors in
distance learning. 5
Squires et al., 2004
It is about education policy analysis in
Arizona University. 6
Shen et al., 2000
It analyzes the effectiveness of an online
collaborative examina-tion process through a
questionnaire. 7
D. Hall, 2010
It introduces some tools to assess teachers. (continued) 125 Toward Process Variability Management … (continued)
No. Reference (author, year)
Summary
8
Jacob et al., 2006
It reveals the importance of assessments in
the learning process through different
learning approaches. The Black Board
Learning System (BBLS) is used as a
comprehensive e-learning software platform
in the context of continuous assessments. 9
Campbell, 2008
It proposes an application called the
Electronic Performance Support System
(EPSS) to enhance the performance of
assess-ment tasks. 10
Kehily, 2011
It uses a web-based platform, DIT learning
teaching and technol-ogy center, as a course
management system for lecturers and as a
computer-assisted learning tool for students. It is a case study in the Dublin Institute. 11
Attali and Burstein, 2006
It proposes a flexible modeling procedure
which can be used to as a basis for expert
judgment. 12
Venkatraman, 2007
It is a case study which develops a four-step
student-centered approach to increase
positive impacts on the learning process. It
analyzes the strengths and weaknesses of
assessments in IS courses through a survey. 13
Maheswari, 1998
It is an empirical study of technical problems
in web-based sys-tems for assisting
education. 14
Sybol, 2005
It investigates how use of an online
assessment tool, the Com-puter-Assisted
Personalized Approach (CAPA), helps
achieve teacher and students learning goals. It is a case study of urban courses in Florida
University. 15
Webb, 2010
It evaluates how digital technologies such as
tablet PCs, wireless technology, and Web
2.0, can facilitate formative and
collabora-tive assessment effectively. Appendix 1: Summary of IT Approaches to e-Assessment 16
e-learning age magazine, 2011
It is a case study of The Association of
Chartered Certified Ac-countants (ACCA),
which wants to deliver all accounting
examina-tions electronically through an
e-assessment program. 17
Miller, 2011
It is a case study of the positive role of
aesthetics design on learner perceptions and
task performance in an e-assessment
environment. (continued) M. Heidari and O. Arnold M. Heidari and O. Arnold 126 (continued)
No. Reference (author, year)
Summary
18
Dascalu and Bodea, 2010
It proposes a qualitative analysis of an
e-assessment and its role to increase
knowledge creation and knowledge
management. 19
Sainburg and Benton, 2010
It is a case study of the importance of
formative assessment in the learning process
in schools. 20
Dermo, 2009
It evaluates the possible risks in planning
e-assessment through six identified
dimensions in a case study. 21
Jordan and Mitchell, 2009
It explains some methods to facilitate answer
and assessment of free-text questions in
e-assessment. It examines its model (IAT) in
the UK Open University, using information
extraction tech-niques and NLP. 22
Ferrao, 2010
It shows that an e-assessment system can be
a good alternative to encourage students and
has positive effects on the learning process. 23
British Journal of educational studies, 2009
It summarizes different works which all
encourage educational institutes to use
e-assessment technologies to support the
learn-ing process, with emphasis on
feedback from e-assessments. 24
Hodgson and Y. C. Pang, 2012
It is a study of statistics students to evaluate
the advantage of formative assessment. 25
Glenberg, 2010
It examines the impact of formative quizzes
on knowledge con-struction. 26
Daly et al., 2010
It argues that existing assessment solutions
focus on developing technical and
infrastructure issues more than educational
as-pects of assessment through different
educational ases. 27
McCann, 2010
It is a case study of a US campus to explore
how a new e-assessment system is
implemented and to identify factors which
affect how it is adopted. 28
Nicol, 2007
It suggests a set of principles for the effective
design and evalua-tion of a formative
assessment and feedback process through
two different case studies. 29
Boyle, 2010
It is about forecasting models like the Bass
model, used to evalu-ate how educational
systems can adopt themselves to
e-assessment methods. (continued) (continued) 127 Toward Process Variability Management … (continued)
No. Appendix 1: Summary of IT Approaches to e-Assessment Reference (author, year)
Summary
30
Boyle and Hutchison, 2009
It makes the case for the substantial effects
of e-assessment on the assessing process and
the technical difficulties involved in
developing sophisticated assessment tasks. 31
McNeil et al., 2011
It looks at e-assessment from both sides:
educational and tech-nical. It develops a
model for analyzing the life cycle of
institu-tional assessments. 32
Sangi and Malik, 2007
It reviews existing e-assessment models and
practices and identi-fies the challenges
facing developers in South Asia. Appendix 2: List of German universities reviewed
1. Freie Universität Berlin
2. Universität Bremen
3. Universität Duisburg-Essen
4. Justus-Liebig-Universität Gießen
5. Philipps-Universität Marburg
6. Johannes Gutenberg-Universität Mainz
7. Karlsruher Institut für Technologie
8. Rheinisch-Westfälische Technische Hochschule Aachen
9. Hochschule Koblenz
10. Leibniz Universität Hannover
11. Westfälische Wilhelms-Universität Münster
12. Universität Koblenz-Landau
13. Universität Regensburg
14. Universität Kassel
15. Technische Hochschule Ostwestfalen-Lippe
16. Technische Hochschule Wildau
17. Hochschule Fulda
18. Universität Trier
19. Universität zu Köln
20. Albert-Ludwigs-Universität Freiburg
21. Universität Düsseldorf
22. Hochschule Wismar
23. Universität Ulm
24. Eberhard Karls Universität Tübingen
25. Georg-August-Universität Göttingen
26. Rheinische Friedrich-Wilhelms-Universität Bonn Appendix 2: List of German universities reviewed
1. Freie Universität Berlin
2. Universität Bremen
3. Universität Duisburg-Essen
4. Justus-Liebig-Universität Gießen
5. Philipps-Universität Marburg
6. Johannes Gutenberg-Universität Mainz
7. Karlsruher Institut für Technologie
8. Rheinisch-Westfälische Technische Hochschule Aachen
9. Hochschule Koblenz
10. Leibniz Universität Hannover
11. Westfälische Wilhelms-Universität Münster
12. Universität Koblenz-Landau
13. Universität Regensburg
14. Universität Kassel
15. Technische Hochschule Ostwestfalen-Lippe
16. Technische Hochschule Wildau
17. Hochschule Fulda
18. Universität Trier
19. Universität zu Köln
20. Albert-Ludwigs-Universität Freiburg
21. Universität Düsseldorf
22. Hochschule Wismar
23. Universität Ulm
24. Eberhard Karls Universität Tübingen
25. Georg-August-Universität Göttingen
26. Rheinische Friedrich-Wilhelms-Universität Bonn Appendix 2: List of German universities reviewed 12. Universität Koblenz-Landau 15. Technische Hochschule Ostwestfalen-Lippe 16. Technische Hochschule Wildau 17. Hochschule Fulda 18. Universität Trier 20. Albert-Ludwigs-Universität Freiburg 21. Universität Düsseldorf 22. Hochschule Wismar 23. Universität Ulm 24. Eberhard Karls Universität Tübingen 25. Georg-August-Universität Göttingen 26. Rheinische Friedrich-Wilhelms-Universität Bonn M. Heidari and O. Arnold M. Heidari and O. Arnold M. Heidari and O. Arnold 128 27. Otto-von-Guericke-Universität Magdeburg
28. Technische Universität Dresden
29. Universität Leipzig
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International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate
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Commons license, unless indicated otherwise in a credit line to the material. If material is not
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statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. 1
Background: Theory and Project The results presented in the article are developed in the context of funding measures
of the German Ministry of Education and Research (Sustainable Land Manage-
ment FKZ 033L004, Agricultural Systems of the Future - ZenKO FKZ 031B736,
Urban–Rural Stadt-Land-plus ReGerecht FKZ 033L205) as well as a research and
qualification project of TU Dresden. Selected parts of the article base on former work
published as Zscheischler et al. (2012) as well as Härtel et al. (2015). Designing External Knowledge
Communication in a Research Network
The Case of Sustainable Land
Management Thomas Köhler, Thomas Weith, Sabrina Herbst, and Nadin Gaasch Abstract Designing knowledge communication with external partners is a core
activity of research networks. In science, such communication has been addressed
only recently and is still considered as non-academic activity. Successful commu-
nication with practitioners, that is knowledge transfer, is a crucial factor for effec-
tive research. In the age of online communication, this requires special attention
and skills, for example related to social media communication. Based on our own
empirical results derived from interviews, the authors identify what factors affect
the communication process and how the design of communication content may be
influenced. To do so, successful examples of communication with external stakeholders are
presented. For the theoretical basis, science communication, knowledge communi-
cation, knowledge management, and knowledge transfer were selected and consol-
idated. Although the findings stem from a research network specializing in sustain-
able land management, they can be transferred to other academic collaborations. Our
results indicate that external communication is effective when knowledge has been
transferred between academics and practitioners. Keywords Research network · Knowledge management · Open science ·
Qualitative research · Land management Keywords Research network · Knowledge management · Open science ·
Qualitative research · Land management T. Köhler
Faculty of Education/Institute for Vocational Education, TU Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de
T. Weith
Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
e-mail: thomas.weith@zalf.de
S. Herbst (B)
Media Centre, TU Dresden, Dresden, Germany
e-mail: sabrina.herbst@tu-dresden.de
N. Gaasch
TU Berlin, Office of the First Vice President for Research, Appointment Strategy, Knowledge &
Technology Transfer, Berlin, Germany
e-mail: nadin.gaasch@tu-berlin.de
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_9
131 T. Köhler
Faculty of Education/Institute for Vocational Education, TU Dresden, Dresden, Germany
e-mail: thomas.koehler@tu-dresden.de T. Weith
Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
e-mail: thomas.weith@zalf.de S. Herbst (B)
Media Centre, TU Dresden, Dresden, Germany
e-mail: sabrina.herbst@tu-dresden.de 131 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_9 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_9 T. Köhler et al. 132 T. Köhler et al. 1https://www.umweltbundesamt.de/themen/boden-landwirtschaft/flaechensparen-boeden-landsc
haften-erhalten#flachenverbrauch-in-deutschland-und-strategien-zum-flachensparen. 1.1
Sustainable Communication in the Sciences Attention-grabbing activi-
ties must be taken rather frequently in efforts to change land use, because long-
term changes do not have the direct “media marketing value” of disasters like the
Fukushima tsunami in 2012. Against all communication efforts, discussion of topics
such as soil conservation, land management, or the establishment of regional material
cycles remains largely restricted to professional circles. Despite comprehensive knowledge about communication theories and models,
and especially about the concept of a sustainability communication, it can be stated
that communication processes are not always effectively implemented. Today we
may observe a pronounced awareness of sustainability in general and environmental
issues in particular; in Germany, 64% of the population consider environmental and
climate protection as an important challenge (BMU and UBA 2019) and the German
Parliament may state in its 2019 Environmental Report that a “demanding envi-
ronmental policy with effective environmental laws and competent environmental
administrations is widely accepted by the population” (Deutscher Bundestag 2019,
p. 4). Still there is a discrepancy between this awareness and individual behavior
in Germany. For example, correlations of affect and cognition with environmental
behavior are not particularly strong, but still substantial (r_aff = 0.51 and r_cog =
0.48). This means that people who agree with the affective and cognitive statements
generally act more environmentally conscious (BMU 2019, p. 68). In the view of the authors, this is due to the fact that the variety of existing means of
communication are not used strategically and thus not exploited to their full potential
(Kriese and Schulte 2009; Leipziger 2007). This is especially true in the “bulky” field
of sustainability. The Sustainable Land Management (SLM) funding program of the
German Federal Ministry of Education and Research (BMBF), described below, is
used to critically investigate current practices in research and planning and to identify
options for future activity. From 2008 to 2017, the BMBF initiated the SLM program
tocreateaknowledgeanddecision-makingbasisforsustainableuseoflandresources. Already in designing the program the funder considered communication efforts as
a central requirement for a successful implementation of this objective. This is only
possible if all actors are willing to actually apply the new knowledge gained as a result
of the program (Hinzen 2009). Targeted communication efforts played a central role
in the management of inter- and transdisciplinary research networks of that funding
scheme: It was a condition of information exchange, successful collaboration, and
collaborative learning. 1.1
Sustainable Communication in the Sciences Information and communication processes and the related content form an impor-
tant basis for defining the principles of sustainable spatial development, at least since
the 1992 United Nations Conference on Environment and Development in Rio de
Janeiro. While forms of information provision and strategic use of communication
arefundamental,renewedmediatedinformationandcommunicativeapproacheshave
become widespread since the 1990s (Lievrouw et al. 2000). These can be applied
fruitfully in different academic disciplines such as education or engineering, or in
spatial planning and development processes (Weith et al. 2020). Respective infor-
mation and communication technologies are now seen as part of different gover-
nance forms and are recommended for tackling various problems. For example, in
2003 the German Council for Sustainable Development initiated a “dialogue area”
to strengthen understanding of processes of changing land use. Also the German
federal government, whose goal was to reduce land use by settlement and infrastruc-
ture by 2020 to 30 hectares per day, began using such new communication instru-
ments and triggered activity of further groups (even though the original timeline has
meanwhile been extended to 20301). While in a first step tools such as education
material, brochures, cartoons, and computer games were produced to sensitize the
relevant actors (Bock et al. 2009), in the almost two and a half decades toward the
Sustainable Development Goals (SDGs) the focus has changed from information to
knowledge management (Weith and Köhler 2019). Specifically knowledge manage-
ment is addressed in three of the SDGs (4, 16 and 17) and at the same time linked
to education and lifelong learning. Digitization, although relevant for many goals, is
explicitly addressed in sub-goal 9c (Industry, Innovation, and Infrastructure): “Sig-
nificantly improve access to information and communication technology and ensure
universal and affordable access to the Internet in the least developed countries by
2020” (United Nations 2015). Non-governmental organizations (NGOs) such as the Nature Conservation Feder-
ation of Germany (Naturschutzbund Deutschland NABU), the Federation for the
Environment and Nature Conservation Germany (Bund für Umwelt und Naturschutz Designing External Knowledge Communication … 133 Deutschland BUND), or the international World Wide Fund For Nature WWF now
develop targeted campaigns to raise awareness and promote more sustainable use of
natural resources. Initiatives such as the International Year of Biodiversity 2010, the
International Year of Forests 2011, or the International Year Plant Health 2020 share
mainly attempts to do this on an (inter)national level. 1.1
Sustainable Communication in the Sciences Successful communication not only creates awareness of new challenges, but also
acceptance for new options, and may initiate behavioral change. It thus contributes
significantly to the successful transfer and implementation of scientific findings into
practice, in this case regarding the SLM program. But how can communication
processes be designed in a targeted and successful way? How can existing knowledge
of strategic communication sciences be linked to communicative requirements? How 134 T. Köhler et al. T. Köhler et al. can means of communication be used strategically in such a complex field? What
specific challenges have to be considered? And where are the limits of professional
communication? This paper presents some initial answers to these questions which were developed
by one of the scientific projects accompanying the BMBF-funded SLM network. To
achieve better insight, the authors first present the core topics of the network and then
explain the role of communication in this context. Subsequently, specific challenges
and influencing factors are discussed in order to finally outline a strategic approach. 1.2
Theoretical and Conceptual Considerations
for the Design of Communication Processes Human communication is a constant, every day, yet highly complex process that
predominantly occurs unconsciously. It is social behavior at a time determined by
many factors which accompany the message intendedly sent by a person. These
factors include emotions, situational circumstances, and the knowledge and cognition
abilities of the communication partners involved and its variety makes the communi-
cation process complex. In designing effective communication, it is therefore essen-
tial to be aware of the most important factors for the sender and the receiver; the latter
include attention, the everyday ecology, and the personal and situational capacity
(Kuckartz and Schack 2002). Moreover, communication is expected producing a
social exchange of constructions, orientations, ideas, etc., about the world, exclu-
sively created in social discourse and checked for their suitability (Frindte and
Geschke 2019, p. 107). By social interaction those individual communications form
entities of organizational character (Köhler 2014), which lead to an inter-institutional,
i.e., external communication and exchange of knowledge, for example in networks. i.e., external communication and exchange of knowledge, for example in networks. Designing knowledge communication with external partners is a core activity of
all research, especially of research networks. In science, such communication has
been addressed only recently and is still considered as non-academic activity. In the
age of online communication, this requires further special attention and skills (Köhler
et al. 2019). With Web 2.0, communication technology shifts to a new social form in
which content is produced jointly, incorporating all those interested in a certain topic
even if they do not have scientific backgrounds. In a society defined by mass media,
rivalry for the attention of various target groups is intense, so attracting attention to an
issue may need to be the first step. To be perceived is a basic condition for successful
communication. But this attention has consequences: Those who create attention
must also create content. The term “everyday ecology” takes the real life of the
recipient into account. Information may only have an impact if it has a meaning for the
recipient, that is, if it can be linked to their real life. Strategic communications utilize
this relationship to their advantage by considering the consequences, benefits, and
options for the recipient, and presenting them consciously. Basically, a subject should
not overwhelm a recipient or a target group. 1.2
Theoretical and Conceptual Considerations
for the Design of Communication Processes If they do not have the capacity to process Designing External Knowledge Communication … 135 a topic intellectually or emotionally, they may reject or avoid the information. All of
these factors need to be analyzed and adapted to specific audiences. A communication
strategy must therefore be adapted to the needs of the intended recipient. Senders have
more options, which are determined by variables like authenticity, professionalism,
and the available financial resources (ibid.). The authenticity of a source is relevant to its visibility (Köhler 2016). Commu-
nication functions less on the level of the actual content than in terms of the type
and way it is communicated. Credibility, competence, and empathy are the central
determinants here. Increasingly, the communicator needs to be professional in order
to compete for the “scarce resource” that is the attention of each target group. This
professionalism includes organizational and technical know-how, knowledge about
methodology, that is, how to address specific target groups, and practical experience. This can be achieved with further training and the help of external communications
consultants or agencies. Experience has shown that too often the only aspect of communication to be
considered was the means, and that this was hardly ever strategically communi-
cated (Kriese and Schulte 2009; Leipziger 2007). Recent findings focus on the
need for human and financial resources as key to planning, designing, and imple-
menting communication of innovations successfully (Pscheida et al. 2013). This
means scheduling appropriate resources and setting goals for communication activ-
ities right from the beginning, at the initial planning stage of a research project. Yet, before the actual communicative tasks and related objectives are formulated,
the means are often already fixed, usually without any consideration of whether they
meet the purpose. Researchers and communicators need to consider the following
questions: Is the chosen means useful in view of the objective? Which channel should
be designed to address the target audience? What must be communicated and what
must not? What steps need to be taken and in what order to achieve the goal? 1.3
Knowledge Management in the Sustainable Land
Management Program as a Challenge for External
Communication The Sustainable Land Management program (SLM) had to meet a number of specific
challenges toward developing an integrative communication approach. First, the
organizational structure of the program was very complex (cf. Fig. 1). In more than
two dozen collaborative projects and its 120 subprojects, scientists and practitioners
from over 170 organizations were involved. The scientific disciplines involved in
SLM brought very different perspectives, methods, and understandings to the overall
SLM program. Unsurprisingly, science and practice often have different preferences,
and thus communicative goals could be very heterogeneous. It is therefore obligatory
to develop a comprehensive communication strategy that is accepted by the parties. 136 T. Köhler et al. Fig. 1 Schematic representation of the network representing the funding program “Sustainable
Land Management” (cf. Härtel et al. 2015; translated by authors) Fig. 1 Schematic representation of the network representing the funding program “Sustainable
Land Management” (cf. Härtel et al. 2015; translated by authors) Another challenge was to establish communication structures at the beginning
of the program. In our case, a new organizational context with new communication
channelsneededtobedefinedandthenperpetuatedinthenewSLMresearchnetwork. This was time consuming and required resources, as individual experience from
completed projects could not have been reused one to one. But this is a general
challenge in science as nowadays, research is often project-based and short-term,
that is, the organizational structures are frequently terminated and re-established
again. Although bilateral or multilateral research and practice networks remain, the
topic-overarching management structure, which includes integrated communication,
usually dissolves. This is one reason why it is difficult to implement and perpetuate
the results, knowledge, and experiences obtained. In addition, when research starts,
the results are not yet available and cannot be presented quickly. But media products
to be communicated must be developed first, i.e., cannot be finalized only when
advertising needs to begin. At this stage, researchers are still developing models,
principles, strategies, and combinations of instruments, which are complex and may
be highly abstract. Accordingly, the “new” knowledge is owned only by a small
group of experts only but has not been transferred to the target audience yet. g
p
p
y
g
y
Further, SLM is an overarching term, so its actions are not clearly defined. 1.3
Knowledge Management in the Sustainable Land
Management Program as a Challenge for External
Communication Communications had to clarify what is meant by all three ambiguous and much-
debated parts of the term, “sustainability,” “land,” and “management.” This means
that all participants of the program had to deal with a high complexity and enormous
variety of subjects. In fact SLM combined many issues which embody enormous
communicative challenges. The collaborative projects, for example, were dedicated
to sustainable water management, regional material and energy cycles, renewable
resources, ecosystem services, sustainable urban development, and urban–rural link-
ages. The actors, interests, and target groups were also numerous. Thus, from a scien-
tific point of view SLM is a highly complex field, which is typical for many research
networks, especially for those that link research with its application in practice. 137 Designing External Knowledge Communication … Yet, mass media requires a high level of simplification, which is contrary to the
claims of many scientists. They often have difficulty handling active (non-technical)
media and do not want their highly complex topics to be reduced to simple, striking
stories. This resonates with a common concern about losing their reputation in the
scientific community. Scientists feel that they eventually lose control and sovereignty
of interpreting their results through publication in the mass media. Black-and-
white arguments such as “renewable energy is positive” or “nuclear energy is bad”
contradict not only the scientific, but also the communicative self-understanding of
science. Due to that fear, scientists begin stepping into public in order to engage
for their research, i.e., start acting as lobbyists. Respectively, they become aware to
generate findings which may be associated with social consequences—what calls
for a renewed consideration of research ethics (Dobrick et al. 2017) and can only be
achieved with assessment based on normative values. Roose (2006) therefore speaks
of an increasing politicization of science while Weingart (2001) points out the danger
of its political exploitation. Altogether, an intelligent communication strategy is required that centers on
targeted but achievable action, even though very limited financial resources are avail-
able. Indeed communication for a typical research network like SLM cannot follow
the rules of classic advertising because of the special funding conditions for such
non-commercial topics. Yet, knowledgeof thediscussedkeydeterminants of commu-
nication is essential. Therefore, in the following, the methodology for evaluating the
most significant factors empirically is briefly introduced. 2.1
Data Collection Social science research objects and their stakeholders, as in the present case of
the SLM funding program, are characterized through a complex and procedural
context (Witzel 1985, p. 227). Following the research question, it was necessary to
identify exemplary information transfer and implementation strategies within SLM
funding program represented by the collaborative projects. The problem-centered
interview was selected as the survey method to investigate the communication struc-
tures of the individual projects (Kaiser et al. 2012). We were interested in both
internal and external transfer and implementation strategies. Twelve typical stake-
holders concerned were interviewed, in order to collect their experiences and estab-
lish a systematic knowledge base. Following a qualitative approach, there was an
equivalent consideration of both researchers and practitioners, covering all types
of projects. In the course of the investigation, a research guide was developed as
a basis for discussion, including aspects related to both content and communica-
tion. All researchers of the collaborative projects contributed to the guide, which
covered all subject areas of interest regarding transfer and implementation. For the 138 T. Köhler et al. present analysis, the authors focused on the concept of transfer, and especially on
communication-related aspects. present analysis, the authors focused on the concept of transfer, and especially on
communication-related aspects. 2.2
Evaluation Method To analyze the interviews, the authors applied the qualitative method of content
analysis developed by Mayring (2010), which can be used for communication text
data. To cope with the length of the text and to serve the purpose of the problem-
centered interviews, the authors decided to complete a structured content analysis. Guided by theory-based main categories, we systematically worked through the
transcribed material and passages assigned to the categories. By focusing on the transfer and implementation of knowledge in the project
network and the resulting questions, main forms of practice can be concluded along
the theory in a deductive way, forming main and sub-categories (see Härtel and Hoff-
mann 2013). In order to address the criterion of openness of the research process, the
authors created an inductive category using the summary content analysis. Overall,
the focus was on structured content analysis, in particular on structuring the content:
“to filter out certain topics, content, aspects of the material and to summarize it”
(Mayring 2010, p. 98). The evaluation was conducted using the software MAXQDA. Specifically devel-
oped for structured content analysis, the software allows for the definition and use
of codes and sub-codes which reflect the categories in an orderly manner (Kuckartz
2010, p. 114). Methodologically controlled compression of the material was used to
work out cross-case statements on regularities in the terms of the research question
(ibid., p. 110ff.). 3
Results 3.1
Practitioners and Civil Society as Target Groups
of External Knowledge Communication 3.1
Practitioners and Civil Society as Target Groups
of External Knowledge Communication In the course of the interview analysis, we identified the target groups of external
knowledge communication: These were practitioners in the economy, society, poli-
tics, and administration. Addressed economists often represented the agricultural and
forestry sector; the former included the food manufacturing, and the latter the wood
processing industry. Other practitioners were at the interface between the public and
private sectors such as health care (doctors, health insurance), mobility and trans-
port (transport networks), the energy sector, and the private education and research
sector. Administrative practitioners covered a variety of responsibilities (municipal
and state level) and subject matter including conservation, transport infrastructure, Designing External Knowledge Communication … 139 and health. Civil society actors, in a broader sense, included voluntary clubs and
NGOs, such as nature conservation associations, support groups, and interest groups
such as farmers’ organizations. 3.2
Effects and Interactions of Factors Influencing External
Knowledge Communication Various aspects of inter-institutional, i.e., external knowledge communication (which
we find in networks as well, going beyond bilateral exchanges) can be derived from
the interviews, in terms of both content and process. First, the means of commu-
nication are selected with different intentions. Content includes project content and
results usually developed for two reasons: to transfer knowledge from science to prac-
tice, and to provide feedback from actors during the research process. At the process
level, it was observed that region and theme often influenced whether communicated
content was picked up. Further, different practitioners often have different expecta-
tions onknowledgetransfer. Intheinterviewanalysis, authors identifiedthefollowing
dimensions:efficiencyindevelopingsolutionsandeconomyoftheprovidedsolutions
(project results, scientific knowledge); practicability of the developed solutions to
concrete problems or at least not making such problems worse (positive and negative
movement between actors and researched problems); and the meaning of personal
attitudes (in form of expectations regarding the research topic). These dimensions
influence perception, acceptance of, and willingness for further communication in
networks. The success of external knowledge communication is also affected by
legal and statutory conditions, such as funding and copyright, the available human
and financial resources, and scientists’ capacity for such communication. 3.3
Selecting a Suitable Means of Communication The available financial and human resources often limited the choices regarding
meansofcommunicationinthecollaborativeprojects.Forexample,limitedresources
hindered knowledge transfer between science and practice: “And then it was evalu-
ated how expensive it is (…) and then it was determined that well that would surely
exceed the budget” (Interview 1.1). Legal and statutory conditions had a similar
effect: Privacy policies impeded access to the target group and restricted the means
of communication. External communication needed to be adapted to the concerns of
target groups, seasonal or other variations. “[W]e have always started public relations
work in May, June, and not before, because […] this is a seasonal theme, and you
can’t kindle a fire which keeps [burning] year round” (Interview 1.3). The general
attitude of stakeholders, key players, and the audience to the project problem and
results (e.g., environmentally sustainable agriculture and renewable energies) could 140 T. Köhler et al. T. Köhler et al. T. Köhler et al. impede or even prevent access to the target group, regardless of the means of commu-
nication used: “Of what avail is it, if the owner [of an agricultural land] tells you
at the end (…): ‘No, I don’t like it because I have something against renewables
anyway.’ (…) There are some, very flat opinions” (Interview 2.9). Obstacles related to the character of the actors have been found to be surmountable
using appropriate means of communication. “And it takes a long time for these
introverted groups. You can’t hope at this moment. I have just spoken with one of
them: ‘Yes, yes, mhm, yes it’s good’. And he didn’t even say goodbye. And then
you sit on the phone and think, ‘What just happened?’” (Interview 2.5). It was in
particular difficult to access practitioners who demonstrated a lack of trust. Reasons
may include negative experiences in the past: “[T]his is certainly the downside we
have in East [Germany], that people had pretty big security needs from the political
system of the GDR […] And today it is different and therefore people are sometimes
overwhelmed and in certain places have been, I’d say, fooled, and that’s why they
tend to be careful” (Interview 2.9). 3.3
Selecting a Suitable Means of Communication To reach as many people as possible and to give actors an insight into the status
of the project, open-access publications were recommended: “You have to say that
very clearly, this is a public [research] project, (…) so that we also see our obligation
to make all our results publicly available. (…) [W]e want [the results] to actually
be disseminated and accepted and we will then make the best possible information
available to the public” (Interview 1.6). Direct face-to-face contact with the target
audience could help too to identify representatives who could spread the message:
“We went to the event and just talked with people. And at the agricultural fair you
get very direct contact with the people. And, in fact, an assumption that I had proved
to be correct. Namely, that a well-defined type of farmer […] is the first who we can
connect with” (Interview 2.5). 3.4
Selecting and Preparing the Communications Content The content to be communicated has to meet the expectations of the target audience. In the course of the interviews, it came out that certain scientific project content,
despite its practical relevance, was too complex and abstract for industry partners to
see its relevance. Indeed, the wish was expressed that “the topic is somehow prepared
either for the target group or scientifically […] But, do not tell the whole world. Such
a claim can only go wrong” (Interview 2.8). For scientists, this means “that science
must speak increasingly in the language of the local partner when initiating contacts. So, not the language of science. […] they need to translate for ‘the average Joe’”
(Interview 2.9). Content prepared without a target group in mind, such as an exclusive scientific
publication of project results, could “not reach all who work in practice” (Inter-
view 1.6). For many actors, cost-effectiveness and efficiency are key criteria for the
measure which is communicated. This may be a precondition for any dialogue with Designing External Knowledge Communication … 141 actors outside the scientific community. If project content or results are not consid-
ered economically or efficiently, it will be very difficult to communicate them to
stakeholders. Certain topics in the field of SLM are perceived as “unattractive” or
cannot be communicated easily to the wider public per se, such as the issue of short
rotation coppice or biodiversity. This is often due to general attitudes of actors in the
field of environmental sustainability. If the impact of the project on a target group is expected to be negative, it is
necessary to reflect on when and what content can be communicated: “The word
‘re-watering’, that’s what you say after a half-hour conversation. When people know
that they will not be inundated. […] You cannot come in with that” (Interview 2.5). Nevertheless, direct involvement can have positive effects, especially in the case of
problems that would otherwise enjoy little attention or which create little incentive
to generate scientific knowledge. This is true of non-tradable areas in the health
sector: “My concern is conducive for health projects […] if they are not able to
be commercialized. I’m not talking about pharmaceutical development, where big
profits attract attention but where it actually comes to service” (Interview 1.4). This
partly precluded the need to prepare the project content, resulting in rather low
commitment from scientists. 3.5
Addressing the Attitude of Stakeholders Market conditions and industry policy often influence the attitude of stakeholders to
problems, such as climate change adaptation in the food sector. It required special
treatment of the content—differences and similarities must have been disclosed and
potentials illustrated (see Interview 1.1). Some actors doubt whether the problem
exists: “Is the climate really changing? So, are they telling us the right thing? And
if they are not telling us the right thing, can I still do what I’ve been doing so far? Yes, they are easy and economic decisions … decisions of habit: I have done it this
way before, so why should I do it differently now? And you cannot answer that,
you can just say, ‘From OUR perspective if you do it, this and this will happen, and
that and that will not happen, and you will have this and that risk’” (Interview 1.5). Another important factor in acceptance of research results and policy implications
is vividness: “once it has something presentable. It is precisely what you can show
this clientele—the farmers—something that is useful” (Interview 2.5). This may
be “something photogenic” (Interview 2.5), but may also include specific transfer
measures such as “field days.” Events must specifically be relevant to the practi-
tioners who attend, “but this being-on-site feeling and talking about it is what makes
something. On that level I can facilitate the transfer easily when I create environments
that are unusual” (Interview 2.5). The extent to which communication activities can
be institutionalized successfully often depended on the available financial and human
resources (Interviews 1.5 and 2.2). The degree of concerns of target audience about the problem addressed in project
has partly affected the communication with actors in a positive and negative way. Existing networks could simplify the access to the actors: “facing the transport sector
was […] in many respects beneficial that they knew each other and that communica-
tion then took place without problems” and “it was always a very good basis to get
in contact with these target groups” (Interview 1.2). The means of communication
thus became less relevant: “if now by email or […] the better the connection is, the
less important the communication means becomes and the more likely the success of
communication” (Interview 1.2). Actors in a network make networking work: “if we
have three, four who really want it in the county or district, that’s enough. 3.4
Selecting and Preparing the Communications Content “We collect the messages, see what is framed by this and
then make a nice communication profile. What was the result? After two reminders
came nothing at all. Only after a third, relatively nasty email […], then came the
usual suspects […] the ones that had always made them anyways. And then we have
with very full, very, very, very petty, very painstaking work somehow collected the
messages. But now looking back, they were not really new messages. There were
the usual messages” (Interview 2.8). When project outcomes have been prepared
properly, focused on the target group by integrating a science journalist, the message
reached people who can pass it on, such as journalists (Interview 1.5). Thecontentofexternalknowledgecommunicationmustbetargetedtoitsaudience
to ensure successful knowledge transfer. In order for recommendations to be adopted
in practice, it is important that “you very strongly address […] the participants and
pick them up thematically where they are anchored, that is, when I talk to a farmer
who might not necessarily be interested in the depth of the bird world, but who cares
more about the agricultural effects” (Interview 1.6). Legal frameworks, such as copyright and intellectual property, can hinder knowl-
edge transfer between science and practice, as certain technologies cannot be readily
used by the practitioner: “There is a little problem: This is patented. One cannot
simply be reconstructed, there are costs. But […] it works, if constructed properly”
(Interview 2.4). Another hurdle for knowledge transfer was the profitability and efficiency expec-
tations of practitioners. The cost of project results is even described as “the most
inhibitory factor” (Interview 2.7) for successful knowledge transfer. This applies not
only to economic practitioners but also local governmental ones, such as mayors. The latter could be encouraged to support and potentially pass the message on if
they could identify potential for regional development: “because a small community
in rural areas has to simply see what options are there to generate added value”
(Interview 2.9). T. Köhler et al. 142 T. Köhler et al. 3.5
Addressing the Attitude of Stakeholders We don’t
need much more” (Interview 2.5). If it was in the interest of certain groups of actors
to process a problem, this could encourage their commitment to successful knowl-
edge transfer: “the local players participated because they also partly had a personal
interest” (Interview 2.3). At the same time, actors did not give their support when
a scientific problem has been considered irrelevant in practice: “without personal
involvement, you may encounter limited interest. Because many other things are
more important in the view of the people” (Interview 1.4). “Due to the positive
development for farmers on the world market and also here in Germany for agricul-
tural products, they are not dependent on this new product […]. Everything is going
well for him in the field. Why should he tackle these uncertainties?” (Interview 2.4). Designing External Knowledge Communication … 143 In general, different communication tools and channels, and how the content is
revised, influence the potential for interacting with external knowledge communica-
tion. The analysis shows, the more specific and relevant to practice the content was,
the more likely it was to get feedback from the addressed actors, because “people
ask only if they know that they can ask. […] You can only communicate that. Or I
have a basket full of messages and can precisely position the target and target group”
(Interview 2.8). For successful knowledge transfer to a wider public, acceptance and
civil society participation was important: “you just involve people that are really
objectively confronted with the background information. And people can simply
decide what they, as it were, want. And then people can decide” (Interview 2.1). The potential for interaction was increased by extending the interfaces between the
project researchers and the target audience, for example by including opinion leaders
and key players on external project advisory boards. In general, different communication tools and channels, and how the content is
revised, influence the potential for interacting with external knowledge communica-
ti
Th
l
i
h
th
ifi
d
l
t t
ti
th
t
t Online media could increase the potential for interaction and facilitate target group
feedback: “On our website we also get questions, requests for information. And so
the messages that are received they have recorded. And […] we hear, for example,
that rental charges are a problem at the moment. 3.5
Addressing the Attitude of Stakeholders And we take a look: so, does this
really have an economic impact on this calculation, cost calculation, or is this actually
a side issue, perhaps with a psychological effect, but has no economic meaning? And
we grab the topics and try to then integrate them within our considerations and in our
presentations” (Interview 2.4). Mere marketing efforts in external communication
were not conducive, but rather direct exchange and regular contact with practitioners
and key players: “We just don’t do marketing. Instead we explain to them, we tell the
tale. From our experience, from the first research results come conversations with
practitioners. And then they share something” (Interview 2.5). 4.1
Background and Communicative Tasks Sustainability communication is about to become a topic in scholarly publications at
the intersection to citizen science practices (Weith and Köhler 2019), specifically, the
influence of digitization on the genesis of knowledge in the context of a sustainable,
fair development as discussed. In the context of land management, there is an overall
strong focus on specific branches like tourism (Tiago et al. 2020). In any case that
process begins with the collection of information describing the initial communi-
cation problem. As it is important to identify the significant data, this includes the
consideration of relevant target groups and goals from the very beginning. Initially,
only those facts relevant to communication problems are included. This process will
identify communicative tasks that derive from the description of the initial situation
and the necessity to modify or enhance communication actions. Its interpretation
explores the problems to be solved, but does not yet offer solutions. In the specific
case addressed here, the task is to identify how land users can most effectively acquire
knowledge and develop a decision-making basis for SLM. 4
Conclusions In order to cope with the variety of factors in communication processes and to
keep a clear head, theorists from marketing and communication studies recommend
a systematic approach with a specified sequence of operations, especially with a
clear concept of how social media communication is embedded (cf. Leipziger 2007;
Hansen and Schmidt 2010; Kreutzer 2018). Respective steps usually include an anal-
ysis of the current situation, the definition of the communicative tasks, the develop-
ment of communication goals, the identification of target groups, the development
of messages, and the designation of a strategy to implement the selected communi-
cation approach. To some extent such an approach matches the generic idea about
implementing communication technologies into an organizational configuration in
an ideal manner as developed by Munkvold (2003), who divides into four sub-areas
of implementing collaboration technologies: Organizational context;
Implementation project; 144 T. Köhler et al. Technological context;
Implementation phase. Technological context; Implementation phase. Authors did previously explain how such can be transferred easily to the context
of information exchange, learning and education (Köhler et al. 2010). 4.4
Formulating Messages Messages are content to be communicated to representatives of a target audience. The larger the target group selected, the simpler the messages should be. Such simple
messages should consist only of models for everyday use. Complicated theoretical
concepts have no place in the mass media, which presents a major challenge for
scientists. It should be clear which effect model shall be implemented and why—if
there is a marketing communication or an educational communication addressed. In
a complex topic such as SLM with very different target groups and representatives
on different levels of influence, it is also advisable to limit the selection of subjects
and to focus on key contents. Such contents should contain only the most relevant
information and consequences for the selected audience and the respective recipient. If the aim is behavioral change, the messages should present options for action. 4.2
Definition of Communication Objectives After analyzing the current situation and defining the communicative tasks, commu-
nication objectives should be formulated in a communication strategy. Objectives
describe the desired end state of a process. Those are measurable and thus represent
a kind of commitment. However, goals can change over the course of a project and
then need to be adjusted. Goal setters must ask whether the objectives can be reached at all. As well certain
practices like the sustainability digital communication relationships are especially
effective (Tiago et al. 2020). Of course unrealistic goals may not serve as appro-
priate, reliable basis for a successful communication concept. For example, including
expensive measures within a modest budget will jeopardize the objectives. 145 Designing External Knowledge Communication … 4.3
Definition of Target Groups The more precisely a target group is defined, the better it can be addressed. This
definition determines the communication tools and approach to be used. When iden-
tifying target groups, it can help to be guided by demographic, lifestyle-related, or
functional factors (Hansen and Schmidt 2010). In some cases, target audiences may
be divided into subgroups with different patterns of media reception (Fischer 2012). This information is used to decide how to access the target group. It should be noted
that people play different roles, at work or at home, with family or friends. A survey of collaborative projects in a workshop of the SLM network revealed
that due to the wide range of actors relevant to the topic of land use, a variety of target
groups exist. Some target groups could be clearly identified, such as stakeholders
from management, agriculture, associations, academia, and research. Other target
groups were described only very generally and imprecisely, such as “local people.”
This is problematic, in terms of selecting both the communication tools and content
to be communicated. 4.6
Activity Planning and Scheduling (“Concerted Activity”) Only when the strategy has been defined does the implementation begin. Now is
the time to clarify what measures will be taken when, where, and how often? An
appropriate mix of measures is in line with the strategy and aims to attain the objec-
tives set. Not every interesting idea is to become an appropriate measure. The results
are an action and a schedule that represent all the measures in chronological order,
the so-called communication plan. This becomes a management tool, provides an
overview of all parties, and allows accurate budgeting. However well thought out a plan may be, its implementation depends on many
events which are not clearly predictable. There is the momentum of cross media
communication as well as specific preferences of single stakeholders, especially in
science, who are eventually not skilled for supporting social media communications
(Pscheida et al. 2015; Albrecht et al. 2020). Resulting, delays can occur or journalists
may suddenly no longer be interested in the subject because breaking stories take
priority. Subsequently, deviations between plan and reality arise and one needs to
respond promptly and derive new action consequences. 4.5
Definition of Communication Strategies The next step is to determine how to achieve the designated goals with the resources
available. This means looking for the cheapest “lever” with which the target can be
achieved most efficiently and effectively. The strategy combines all the resources for
a specific parent maxim (Leipziger 2007). More recently, it is suggested that when
analyzing sustainability communication a typology of three different communication
modeswouldbeappropriate:communicationof,about,andforsustainability(Fischer 146 T. Köhler et al. T. Köhler et al. T. Köhler et al. et al. 2016). Obviously the SLM network applied all three dimensions simultaneously
as these have been components of the developmental approach. Well-known and frequently used approaches include the piggyback, testimonial,
and provocation strategies (see Hansen and Schmidt 2010; Leipziger 2007). The
aim of the piggyback strategy (also known as issue management) is to attach the
desired message to a consistent public relations action or to current media issues. The testimonial strategy generates attention through celebrity ambassadors, and the
provocation strategy seeks to attract attention by breaking taboos or challenging
competitors. So far, our network has favored a piggyback strategy. 4.7
Limitations of the Study The empirical data used for the study is limited to just one research network, in
which stakeholders often share a single focus, embedded into a single domain. Even
though the configuration of the network is overarching sectors and includes research
as well as public administration as well as stakeholders from industry, its outreach
is limited. Mainly representativity is hindered by the missing link to the individual
citizen as well as the missing direct link to the media sector. Additionally, the role of project advisory boards has not been addressed in detail,
that is, political influence may overlap with other effects described. In this case, the
direct involvement of the target group also increased the potential for interaction
in the communication process. It would also have been possible to assess external
knowledge communication needs by questioning the target group directly. Finally, Designing External Knowledge Communication … 147 authorsdidnotexplicitlyaddressthepresumablyhighpotentialforinteractionoffered
by the concept of citizen science. authorsdidnotexplicitlyaddressthepresumablyhighpotentialforinteractionoffered
by the concept of citizen science. 4.8
Lessons Learned The study demonstrated that sustainable land management is a case which does
have specific communicative affordances due to its complex, multi-actor character
that brings together different perspectives. Still communication in and for research
networks is not consequently addressed, literature both on practice and research is
rather limited. Not only with the increasing meaningfulness of digital formats there
is an increasing need for a well thought, analytically proven approach in designing
communication of and within research networks strategically. Obviously scientists
are not easily capable of developing such and are hindered first by their individual
characteristics (limited competences skills, etc.) but as well by the ecological condi-
tions (economic and structural deficits). In that sense the paper has collected theoret-
ical and empirical evidence of how research may deal with the expectations toward
the influence of (mainly digital) communications on the genesis of knowledge in the
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the copyright holder. Researching Scientific Structures
via Joint Authorships—The Case
of Virtual 3D Modelling
in the Humanities Sander Münster Abstract One of the topics addressed by e-science research is the measurement of
academic knowledge production based on electronic data and its relevance in defining
the academic landscape. The author employs e-science methods to research coop-
erative authorships and scientific structures in a specific area of applied e-sciences:
virtual 3D modelling in the humanities. Based on the findings, possibilities for cross-
disciplinary and international cooperation are discussed. The number of international
publications and average number of authors involved in each publication are lower
than those found in other scientific fields. Moreover, research indicates that in the
humanities, 3D modelling is relatively new and still emergent. Besides such general
indications, several key players as people and institutions which interconnect groups
of researchers could be identified on a structural level. Keywords Cooperative authorships · 3D modelling · Humanities 1This article reflects the state of my research in 2015. a more recent state was presented in:
Münster, S.: Digital cultural heritage as scholarly field—topics, researchers and perspectives
from a bibliometric point of view. J. Comput. Cult. Heritage 12, 22–49 (2019). S. Münster (B)
Friedrich-Schiller-Universität, Jena, Germany
e-mail: sander.muenster@uni-jena.de © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_10 1
Introduction1 A major issue related to the measurement of academic knowledge production is the
distinction between disciplines and the mapping of scientific structures. The vast and
heterogeneous variety of possible indicators result in a lack of standardisation and
homogenisation. Joint standards to measure academic performance—as intended by
the German Research Council (Wissenschaftsrat: Empfehlungen zu einem Kern-
datensatz Forschung Berlin 2013)—are still being established. Our field of research
is a specific area of applied e-sciences: virtual 3D modelling in the humanities. The
research started with selecting a sample of publications in order to investigate current
trends, scenarios and workflows in this field, and to quantify the scholarly field. The 1This article reflects the state of my research in 2015. a more recent state was presented in:
Münster, S.: Digital cultural heritage as scholarly field—topics, researchers and perspectives
from a bibliometric point of view. J. Comput. Cult. Heritage 12, 22–49 (2019). 151 151 152 S. Münster initial challenges were to (a) develop a suitable research instrument and to (b) perform
an investigation. Due to the limitations of the included information and the magni-
tude of the data sample, many potentially interesting research approaches—such as
a quantification of current topics, standard references and citation networks—are not
applicable. The author examines the scientific community involved in this specific
area and their level of cross-disciplinary and international cooperation. Furthermore,
we identify the key people and institutions, which interconnect groups of researchers. 1.1
Defining Disciplines To start, a definition: disciplines are characterised by common methods and theories
and have similar “reference systems, disciplinary ways of thinking, quality criteria,
publication habits and bodies” (Schophaus et al. 2003) as well as similar institutional-
isation. Likewise, Knorr-Cetina thought that each discipline has its own “epistemic
culture” in the sense of different “architectures of empirical approaches, specific
constructions of the referent, particular ontologies of instruments, and different
social machines” (Knorr-Cetina 1999). Although disciplines and their boundaries
are results of social construction processes (Weingart 1987), a number of phenotypic
fields can be identified (Knorr-Cetina 2002). One basic classification scheme is the
distinction between humanities and sciences. In a more elaborate classification, the
OECD distinguishes between six scientific fields containing about 40 disciplines
(OECD 2002, 2007). Furthermore, especially library classification delivers highly
sophisticated distinction categorisation schemes (Semenova and Stricker 2007). 2Originally published in: Münster, S., Köhler, T., Hoppe, S.: 3D modeling technologies as tools
for the reconstruction and visualization of historic items in humanities. A literature-based survey.
In: Traviglia, A. (ed.) Across Space and Time. Papers from the 41st Conference on Computer
Applications and Quantitative Methods in Archaeology, Perth, 25–28 March 2013, pp. 430–441.
Amsterdam University Press, Amsterdam (2015). 2
The Case of Virtual 3D Modelling in the Humanities 2.1
Field of Research 1.2
Defining Cross-Disciplinarity Cross-disciplinarity refers to a “confrontation of several disciplines with a [joint]
topic or issue” (Schophaus et al. 2003). In regard to this, Schelsky speaks of a
“partial scientific development unit at the empirical object” (Schelsky 1966). Cross-
disciplinary collaboration is characterised by developing a multidisciplinary termi-
nology and a joint methodology (Gibbons 1994; Münster et al. 2014). The degree of
institutionalisation of cross-disciplinary fields ranges from temporary collaborations
to the creation of new “hybrid” research disciplines (Klein 2000) such as the digital
humanities, in which computing is applied to foster humanities research. 153 Researching Scientific Structures … 2.1
Field of Research 3D models and visualisation have always been an important medium for teaching,
illustratingandresearchinghistorical facts anditems. Whilehistorical picturesources
usually provide elusive and fragmentary impressions, digital three-dimensional
models of historical objects and their depictions offer the chance to convey holistic
and easily accessible impressions. Until 2000, virtual 3D modelling technologies and
computer-generated images of cultural heritage objects were used merely as a digital
substitute of physical models (Novitski 1998). Nowadays, 3D models are widely used
to present historic items and structures to the public (Greengrass and Hughes 2008)
as well as in research (Favro 2004) and education (El Darwich 2005). In addition,
3D technologies can obviously serve cultural heritage management and conservation
tasks, and even their advertising. An important distinction needs to be drawn between
still extant, no longer extant, and never realised objects. 3D modelling technologies
make it possible not only to digitise historic objects which are still extant, but even
to virtually reconstruct objects that are no longer extant physically and only known
from descriptions.2 Research design This investigation of scientific structures related to the usage of 3D modelling
techniques for both extant and no longer extant types of historical objects is based
on an analysis of published project reports and presentations. An upstream problem
was the identification of relevant publications. Unlike, for example, in medicine,
there are no comprehensive publication databases extant for cultural studies and
humanities. Prior to creating the database, three experts—chairholders in the fields
of archaeology, art history and geomatics—were queried to identify relevant journals
and conferences. This yielded the following findings: • On the one hand, in the field of cultural and history studies, no multidisciplinary,
periodically held international conferences are known that deal specifically with
3D modelling. However, there are a number of local or non-periodic conferences
and workshops that deal with specific questions or topics. • On the other hand, there are four major conferences on the topic in the
fields of archaeology and cultural heritage: The International Workshop for 3D
Virtual Reconstruction and Visualization of Complex Architectures (3DARCH);
the Computer Applications and Quantitative Methods in Archaeology Confer-
ence (CAA); the International Symposium on Virtual Reality, Archaeology and
Cultural Heritage (VAST); and the Visualisation in Archaeology workshop (VIA). 154 S. Münster S. Münster • The Journal for Digital Heritage represents an overarching publication organ for
digital content on all humanities. • The Journal for Digital Heritage represents an overarching publication organ for
digital content on all humanities. 2.2
Data Sample These findings formed the basis for collecting the data sample presented in Table 1. As a scope for conference proceedings, entire volumes were included and relevant
journal articles were identified via keyword search. A sample of 452 journal articles
and conference proceedings was included during the first stage of the analysis. The
articles selected were written in English and, for practical reasons, had to be available
electronically. Especially the latter selection criterion meant that no publications of
the VIA conference and only single volumes of CAA and VAST could be included. In addition to these conference papers, relevant articles from the Journal for Digital
Heritage and other periodicals were included using a keyword-based search. One major obstacle to building a research database was the fact that most of the
included conferences and journals were not listed in citation repositories or in publi-
cation databases such as ISI Web of Science, Scopus, or Google Scholar in 2012 when
the database was compiled. This made it necessary to retrieve metadata by crawling
data from each single contribution. For each article, the following information was
obtained: • names and affiliations of contributing authors
• names and addresses of affiliated institutions
• source data (conference and publication name, year, type of document)
• title of publication. • names and affiliations of contributing authors mes and addresses of affiliated institutions Moreover, conference contributions were classified based on their content. As
pointed out in (Münster et al. 2013), one-third (37%) of these articles deal with
neither 3D modelling nor historical objects. Nearly the same number of articles report
about single projects. This means that they describe workflows for rebuilding certain
historicitemsas3Dmodels.Anothergroupofcontributionsdealswithcertainaspects Table 1 Sample (n = 452)
Publication
Volume
No. 3DArch Conf. 2005–2009
112
CAA Conf. 2007, 2009
130
VAST Conf. 2003–2007, 2010
105
J. Digital Heritage
From 2000a
52
Various project reports and publications dealing with no longer extant
objects
1999–2011
79
aImportant articles were selected via a keyword-based search Table 1 Sample (n = 452)
Publication
Volume
No. 3DArch Conf. 2005–2009
112
CAA Conf. 2007, 2009
130
VAST Conf. 2003–2007, 2010
105
J. 2.2
Data Sample Digital Heritage
From 2000a
52
Various project reports and publications dealing with no longer extant
objects
1999–2011
79
aImportant articles were selected via a keyword-based search Researching Scientific Structures … 155 of 3D modelling for historical purposes, such as presentation and modelling strate-
gies, data acquisition methods, or handling and classification of 3D data. Focussing
on project reports only, a further investigation takes into consideration whether an
original object is still extant. To quantify, more than 2/3 of project reports deal with
extant objects or their fragments, while another 1/3 focus on non-extant objects. While digitisation of extant objects is mostly based on acquired data and uses widely
automated algorithms, reconstruction of no longer extant or never realised objects
usually involves manual model creation using CAD or VR software tools. For each
type of object, the model creation processes are very different. For this reason, one
aim here is to investigate whether both topics might attract different contributors and
build slightly different sub-communities. 2.3
Scientific Approach: Analysis of Scientific Authorship
Relations One
approach is to calculate key numbers in various ways, such as an average count
of authors per publication or a rate of publications authored by single individuals. As one example, the cutting-edge analyses of De Solla Price (1963) in the early
1960s employed key numbers to investigate the transformation processes of scien-
tificproduction.Asecondapproachistoclusterauthors,forexamplebynationality,to
study preferences for international joint authorships (Glänzel 2001). Both research
approaches are employed in our study to investigate cooperative authorship. A
third approach uses author data to measure disciplinary characteristics such as disci-
plinary productivity, used in this article by employing the Lotka Coefficient (Egghe
2009; Lotka 1926). Furthermore, Schubert and Glänzel studied preference patterns
of cross-national authorships (Schubert and Glänzel 2006) and stated that there was a
“major influence [of] historical, cultural and linguistic proximities” (p. 426). Such an
approach is not applicable to this investigation due to the small number of samples. Several investigational approaches focus on topics described in researched arti-
cles. As one example, a topic graph structure classifies current research topics in a
certain scientific area (Glenisson et al. 2005; Schoepflin and Glänzel 2001). More-
over, approaches like epidemiology of ideas (Goffman and Newill 1964) or scien-
tograms focus on predicting emergent trends based on an evolution of the importance
of topics. Over the last few years, citations have become a very popular object of research
into scientific performance. This includes measuring individual impact factors via
indexes, most popularly the h-index invented by Hirsch (2005), or the total impact
of certain journals via the Garfield index (Vinkler 2012). Furthermore, co-citation
analysis provides clues about the evolution of a scientific area over time and its
standard works (Bellis 2009). Neither citations nor topics are covered by the available
data, so these objects of study are not included in our investigation. Scientific communities as a “group of scientists […] agreed on accepting one
paradigm” (Jacobs 2006) are another research object of bibliometrics. One partic-
ular approach, the study of co-authorship networks, focusses on detecting structures
of scientific cooperation employing graph analysis methods (Vargas-Quesada and
Moya-Anegón 2007). Although such research approaches are limited to a structure
representation (Hardeman 2013) and include a number of potential sources of error
and limitations, computer-based analysis and evaluation of co-authorships fosters
several new insights related to scientific cooperation (De Stefano et al. 2011; Lu
and Feng 2009). 2.3
Scientific Approach: Analysis of Scientific Authorship
Relations From a disciplinary point of view, an investigation of “laws governing the production,
flow and application of information in science” (Vinkler 1996) by a numerical anal-
ysis of publications is part of bibliometrics. This discipline contains a wide spectre
of measures and methods to investigate scientific structures and output. Based on
former categorisation and formalisation attempts (Vinkler 2001; Egghe 2009; Gauf-
friau et al. 2007), several bibliometric approaches are distinguishable, according to
their objects of study (Table 2). Not all research approaches are applicable to the
described data sample. The limiting factors are the low number of samples and the
types of information collected. The metadata of publications are a major object of study. Related approaches
include classification of various attributes, like publication type, journal, disciplinary Table 2 Brief overview of bibliometric approaches
Object of study
Approach (example)
Publications
Classification (i.e. De Solla Price 1963)
Scaling laws (i.e. Bettencourt et al. 2008)
Authors
Key numbers (i.e. De Solla Price 1963)
Clustering of authors (i.e. Glänzel 2001)
Disciplinary productivity (i.e. Lotka 1926)
Topics
Topic graphs (i.e. Schoepflin and Glänzel 2001)
Scientograms (i.e. Vargas-Quesada and Moya-Anegón 2007)
Epidemiology of ideas (i.e. Garfield 1980)
Citations
Impact (i.e. Hirsch 2005; Smith 2012)
Co-citation analysis (i.e. Bellis 2009)
Communities
Structures (i.e. Newman 2001a; Glänzel and de Lange 2002)
Protagonists (i.e. Otte and Rousseau 2002; Newman and Girvan 2004;
Kretschmer and Aguillo 2004) Table 2 Brief overview of bibliometric approaches
Object of study
Approach (example)
Publications
Classification (i.e. De Solla Price 1963)
Scaling laws (i.e. Bettencourt et al. 2008)
Authors
Key numbers (i.e. De Solla Price 1963)
Clustering of authors (i.e. Glänzel 2001)
Disciplinary productivity (i.e. Lotka 1926)
Topics
Topic graphs (i.e. Schoepflin and Glänzel 2001)
Scientograms (i.e. Vargas-Quesada and Moya-Anegón 2007)
Epidemiology of ideas (i.e. Garfield 1980)
Citations
Impact (i.e. Hirsch 2005; Smith 2012)
Co-citation analysis (i.e. Bellis 2009)
Communities
Structures (i.e. Newman 2001a; Glänzel and de Lange 2002)
Protagonists (i.e. Otte and Rousseau 2002; Newman and Girvan 2004;
Kretschmer and Aguillo 2004) 156 S. Münster S. Münster backgrounds or dates. These classes allow for comparison and evaluation of distri-
bution functions, as well as monitoring of trends and prediction of emergent fields of
research based on time rows (Bettencourt et al. 2008). While the latter approach in
particular relies on plenty of lossless data, it does not seem applicable to our research. Another important object of study is related to authors of publications. 2.3
Scientific Approach: Analysis of Scientific Authorship
Relations For example, a comprehensive investigation of publications in the
fields of medicine, science and computing (Newman 2001a, b, c) reveals that the
“small-world phenomenon” (Milgram 1967) (i.e. any two authors are connected in a
chain of on average five to six parties) could be identified for these scientific commu-
nities. A number of smaller studies also deal with co-authorship within individual
disciplines (Aleixandre-Benavent et al. 2012), or for individual countries or regions 157 Researching Scientific Structures … (Abramo et al. 2010; Morelli 1997; Gaillard 1992). Besides describing scientific
networks, another issue is to identify important players as protagonists of scientific
communities (Kretschmer and Aguillo 2004; Hou et al. 2007). This latter aspect is
of interest regarding the community dealing with 3D modelling in the humanities. 3.1
Indication 1: Cooperative Authorship One of the essential characteristics of modern research is the large number of authors
involved in a single publication. In 1962, De Solla Price pointed out that in 1900,
more than 80% of publications had a single author (De Solla Price 1963). In 2000, a
study of scientific articles listed in the Science Citation Index (Glänzel et al. 2004)
revealed an average contribution of 4.2 authors per article, wherein the proportion
of articles written by individual authors was only 11%. Within our research sample,
an average of 3.4 authors was involved in each publication. From the perspective
of cross-disciplinary and international cooperation, the disciplinary affiliation of the
author collectives seems especially interesting. As shown in Fig. 1, the majority of
the studied publications were written by authors or author collectives belonging to
the same area of research and only a limited number of publications were cross-
disciplinary. The author’s disciplinary affiliation was identified from the correspon-
dence addresses noted in publications. However, such data only provides informa-
tion about the disciplinary focus of an employing institution and not on the author
himself. To overcome this potential flaw, an alternative method which takes personal
disciplinary backgrounds into account—self-sorting by authors via questionnaire—
is intended for the next stage of the research, but not yet realised for this set of data. In this data, for 21% of authors the respective disciplines at affiliated institutions
could not be identified or distinguished precisely. Fig. 1 Number of participating disciplines Fig. 1 Number of participating disciplines 158 S. Münster S. Münster With regard to the distinction between types of modelling, the number of cross-
disciplinary publications describing the digitisation of extant objects is significantly
higher than for reconstruction projects. With regard to the distinction between types of modelling, the number of cross-
disciplinary publications describing the digitisation of extant objects is significantly
higher than for reconstruction projects. Another interesting aspect is the disciplinary background of the authors’
employing institutions depending on the type of object modelled. In the table
shown in Fig. 2, cross-disciplinary collaborations were included proportionately and
each cross-disciplinary publication has been counted with 1, while for publications
including two disciplines, each of them has been counted with 0.5. 3.1
Indication 1: Cooperative Authorship It seems remark-
able that a large number of articles describing reconstruction projects of unrealised
or non-extant objects were written by authors affiliated with institutions in the field
of architecture, while publications for digitisation projects were often written by
authors with a background in engineering and geosciences. A plausible explanation
is provided by the competence profiles of these departments. For example, automated
data acquisition via remote sensing techniques is a focus of the geosciences, while
architectural studies incorporate extensive know-how about both architectural history
and CAD modelling. Figure 3 shows cross-disciplinary authorships in the researched
publications. Each node stands for a single publication and each edge represents the
disciplinary assignment of the participating authors. The graph shows that authors
from institutions in the digital humanities are especially frequently involved in cross-
disciplinary cooperative authorships. Preferred partners are authors from institu-
tions in the field of computer science, while joint publication with authors from the
humanities tends to occur rarely. As shown in Fig. 4, a significant number of publications were written by authors
whose employing institutions are in the same nation. Compared to findings related to
other scientific domains, which estimate an overall rate of international publications
at 35% (Acosta et al. 2010), the number of international publications in the sample is Fig. 2 Disciplinary affiliation of publication authors Fig. 2 Disciplinary affiliation of publication authors 159 Researching Scientific Structures … Fig. 3 Cross-disciplinary authorship Fig. 3 Cross-disciplinary authorship significantlylower.Analogoustothefindingsrelatedtointerdisciplinarycooperation,
the number of international publications describing digitisation projects is above
average, while only 8% of the publications describing reconstruction projects were
written by international teams. significantlylower.Analogoustothefindingsrelatedtointerdisciplinarycooperation,
the number of international publications describing digitisation projects is above
average, while only 8% of the publications describing reconstruction projects were
written by international teams. The findings of a below average rate of international and cross-disciplinary author-
ships in combination with a large variety of involved disciplines indicate the fuzzy 160 S. Münster S. Münster demarcation of the field. This assumption is supported by the finding that only 30% of
authorsareemployedininstitutionswhichprioritisehumanitiesordigitalhumanities. 3Originally published in: Münster, S., Köhler, T., Hoppe, S.: 3D modeling technologies as tools
for the reconstruction and visualization of historic items in humanities. a literature-based survey.
In: Traviglia, A. (ed.) Across Space and Time. Papers from the 41st Conference on Computer
Applications and Quantitative Methods in Archaeology, Perth, 25–28 March 2013, 430–441.
Amsterdam University Press, Amsterdam (2015). 3.2
Indication 2: Lotka Coefficient One of the most common indicators is the number of publications per author. Relat-
edly, Lotka (1926) developed a distribution function for the publication frequency of
individual authors which covers a wide range of disciplines and their publications. The distribution curve shows that a large number of authors with only one publication
are contrasted by a very small number of authors with multiple publications. y
y
p
p
Related to the investigated publication data, a classical Lotka distribution already
revealed an extensive congruence (Fig. 5). This follows the formula Y = C/Xn
Fig. 4 Cross-national publications
Fig. 5 Frequency distribution curves for publications Y = C/Xn
Fig. 4 Cross-national publications Y = C/Xn
Fig. 4 Cross-national publications Y = C/Xn Fig. 4 Cross-national publications Fig. 5 Frequency distribution curves for publications Fig. 5 Frequency distribution curves for publications Fig. 5 Frequency distribution curves for publications Researching Scientific Structures … 161 where C is the total number of authors included (n = 1120) and X indicates the
number of publications of each cohort (authors with 1, 2 or more publications). The
exponent n is a constant. From his studies, Lotka postulated an average exponent of
n = 2, which varies significantly depending on the investigated discipline (Egghe
and Rousseau1990; Egghe 2000), while recent studies assumed an average value of
2.3 to 2.5 (Chung and Kolbe 1992; Pulgarín 2012). In the empirical findings, the
distribution function of the investigated publications coincides with n = 2.8 … 2.9. Any further interpretation of these values must be estimated in the context of the
relatively small and potentially flawed sample. Compared to the lower mean values
of the exponent mostly cited in literature, the above-average exponent found here
indicates low publication productivity with a disproportionate number of authors
who are only occasionally involved. There are several studies on scientific communities and inherent social interaction, i.e. Stützer, C.:
Knowledge transfer in web-based collaborative learning systems (PhD-Thesis), Dresden 2013. 3.3
Indication 3: Key Players3 Another hypothesis is that collaborative publications establish knowledge commu-
nication between authors. The basic idea is that, in most cases, common author-
ship would be related to a personal connection and interaction between all included
authors. Depending on sociological role theory, such a connection between people—
regardless of its strength (Granovetter 1973)—could foster sharing and exchange of
ideas and information. Regarding structure, connections between people across disci-
plinary and national borders play a key role in disseminating information in social
communities.4 Nevertheless, information transfer in the context of joint publications
is just assumed and intensity or even information transfer between authors cannot be
reconstructed based on empirical data. The sample publications were authored by 1500 individuals who were connected
by over 3000 links (Fig. 6). Most of the publications were written by authors
belonging to institutions of the same discipline and nationality. All the individuals
at each institution were incorporated into Fig. 7. Key players were highlighted in the
graphs: these were the people and institutions that were in the top ten in the cate-
gories of (a) number of connections to other authors (degree), (b) the relevance as a
connecting factor between author groups (betweenness centrality) or (c) the number
of publications. (Wasserman and Faust 1994) But there are also several interna-
tional or cross-disciplinary networks visible whose members have written more than
just one joint publication. It was possible to identify some important key players 162 S. Münster Fig. 6 Author—co-author relations—individuals (key players highlighted) Fig. 6 Author—co-author relations—individuals (key players highlighted) who connect groups of researchers. From an institutional perspective, the coopera-
tion between the University of Leuven and the technical universities of Vienna and
Zürich has produced a particularly large number of cross-disciplinary and interna-
tional publications. A further, if smaller, cluster includes mostly French and Italian
institutions, but also encompasses authors from Japan and Germany. Generally, there
is a high level of networking and number of publications from people and institutions
workingondata-basedvisualisation.Finally,thekeyplayersaremostconnected,both
internationally and cross-disciplinarily. To validate this, the results were discussed
with experts. Generally, these key players are not only active publishers, but often Researching Scientific Structures …
163
Fig. 7 Author—co-author relations—institutions (key institutions highlighted) 163 Researching Scientific Structures … Fig. 7 Author—co-author relations—institutions (key institutions highlighted) also play key roles in the community in other ways, too, whether as members of
scientific committees, conference chairs, and initiators or leaders of projects. 3.3
Indication 3: Key Players3 We also investigated the connection between theory and practice in the field of
3D modelling in the humanities. We compared, for each institution, the number of
participating digitisation and reconstruction projects described in articles and the
number of publications. The results show that institutions with a high publication
output are usually also involved in an exceptionally large number of projects. A
significant difference between ranks of publication activity and project participation
was identified in just a few institutions, such as the TU Wien or the Istituto di Scienza
e Tecnologie dell’Informazione (Table 3). This leads to the assumption that a scientific community is primarily a community
of practice (Lave and Wenger 1991), with a close link between practical project work
and theory, while specific think tanks as theory building institutions are currently not
visible for this field of research. 164 S. Münster Table 3 Ranks of project and publication participation by institution Table 3 Ranks of project and publication participation by institution
Institution
Projects (Rank)
Publications (Rank)
Politecnico di Milano
10 (1)
14 (1)
ETH Zürich
8 (2)
12 (4)
National Research Council Canada
7 (3)
11 (5)
University of Florence
7 (4)
12 (3)
Istituto di Scienza e Tecnologie dell’Informazione
6 (5)
13 (2)
Centre for Scientific and Technological Research
6 (6)
7 (7)
University of Virginia
5 (7)
6 (14)
Tokyo Denki University
4 (8)
6 (12)
CNR Institute of Technology Applied to Cult. Heritage
4 (9)
6 (15)
TU Wien
4 (10)
11 (6) 4
Conclusion With regard to the aim of identifying scientific structures via co-authorships, it was
found that the field of 3D modelling in the humanities at an international level
is widely dominated by research interests and approaches from archaeology and
cultural heritage research. However, the authors involved come from a large variety
of disciplinary backgrounds. Another finding is that the number of publications written by international
teams and average number of authors involved in each publication are lower than
in other scientific fields. It seems remarkable that publications about digitisation
projects which deal with extant objects are significantly more often written by cross-
disciplinary and international teams than publications describing a reconstruction of
no longer extant or never realised objects. This may be caused by the slightly different
disciplinary constitutions and uses of publications in digitisation and reconstruction
projects. Taking the relatively small and potentially flawed sample into account,
further investigations and additional data are required for a valid evaluation. 3D modelling in the humanities is relatively new and emergent field of research. This is indicated by the above-average coefficient for a Lotka distribution describing
the frequency of publications per author. Nevertheless, contributors from various
disciplines were involved in the researched publications, which may indicate a
currently blurry demarcation of the scientific field. Even if these findings are endorsed
by other studies (Albrecht 2013), both indications provide only a hint that the field
is becoming established. Whataretheimplicationsforresearchone-sciences?Thisarticledescribedseveral
strategies for investigating scientific structures in the field of 3D modelling in the
humanities, based on electronic data and using software tools for graph analysis and
QDA software for qualitative content analysis. Information was retrieved about struc-
tures and publication practices in the field. It was found that the investigated publi-
cations were mostly about archaeology and cultural heritage, while other research Researching Scientific Structures … 165 interestslikeaspectsofculturalorarthistoryweretreatedmostlyvianationalcommu-
nities and published in offline media. While the research objects and issues are closely
related to the humanities, just a minority of authors are affiliated with (digital) human-
ities, and authors with a background in computing are very prominent in the publica-
tions. Even though these findings require further investigation, they may indicate that
an international community in digital humanities is less influenced by practitioners
whose competence relates to the research questions and objects than by those who
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Wissenschaftsrat: Empfehlungen zu einem Kerndatensatz Forschung Berlin (2013) Wissenschaftsrat: Empfehlungen zu einem Kerndatensatz Forschung Berlin (2013) 168 S. Münster S. Münster Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0
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the copyright holder. A. M. J. Skulimowski (B)
Department of Automatic Control and Robotics, AGH University of Science and Technology,
Kraków 30-059, Poland
e-mail: ams@agh.edu.pl International Centre for Decision Sciences and Forecasting, Progress & Business Foundation,
Kraków 30-048, Poland A. M. J. Skulimowski (B)
Department of Automatic Control and Robotics, AGH University of Science and Technology,
Kraków 30-059, Poland
e-mail: ams@agh.edu.pl
International Centre for Decision Sciences and Forecasting, Progress & Business Foundation,
Kraków 30-048, Poland
© The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_11
16 A. M. J. Skulimowski (B)
Department of Automatic Control and Robotics, AGH University of Science and Technology,
Kraków 30-059, Poland
e-mail: ams@agh.edu.pl
International Centre for Decision Sciences and Forecasting, Progress & Business Foundation,
Kraków 30-048, Poland 1
Introduction Based on the results of the foresight project, SCETIST (Skulimowski 2013), and
a Delphi study on future development trends of knowledge platforms performed
within the recent Horizon 2020 project MOVING (Köhler and Skulimowski 2019),
this paper aims to provide an insight into the future of e-science. The focus is on
three specific aspects of this perspective: the emergence of new research tools related
to global expert systems (GESs), researcher communication with computers through
brain–computer interfaces (BCIs), and the role of researchers in shaping holistic
knowledge development systems that will emerge over the next few decades. The aims of the aforementioned foresight projects include making recommenda-
tions to R&D and ICT policymakers, while pointing out prospective ICT develop-
ment and research trends relevant to individual researchers and research teams. The
time horizon of foresight was 2025, with an impact analysis of selected anticipated
technological breakthroughs up to 2030. Some of the project results related to e-
science are presented in Skulimowski (2016b); the results on the emergence of GESs
are published in Skulimowski (2013), while the relation to artificial autonomous
decision systems (AADSs) is discussed in Skulimowski (2014b, 2016b). A diverse spectrum of methods was applied to elaborate on technological and
social scenarios and forecasts. Those used predominantly included bibliometric anal-
yses, extrapolation Delphi surveys (Skulimowski 2019), group building of a hierar-
chical state-space model of information society evolution (Skulimowski et al. 2013)
and anticipatory networks (Skulimowski 2014a). For the purposes of e-science foresight, the computer-assisted multi-round expert
Delphi questionnaire retrieval (cf. e.g. Skulimowski et al. 2013, 2019), combined
with expert panel meetings and outcomes of bibliometric and patentometric research
proved most useful within the overall project. The analysis of expert responses was
combined with an information retrieval strategy from the open Web and from major
bibliographic databases. Different procedures were elaborated for fusing quantitative
and qualitative knowledge and providing recommendations to the ICT industry and
policymakers. A trust and competence factor system was used to compensate for
the impact of diverse expert biases and competences. Each survey respondent was
assigned a vector with trustworthiness coefficients of this expert in the particular
subject areas of the Delphi exercise. A weighted combination of individual responses
with coordinates of the trustworthiness vector was applied, wherever appropriate, to
take account of the difference in respondents’ credibility. Section 2 outlines certain basic ICT/AI development trends that may influence
future research tools. Visions of a Future Research Workplace
Arising from Recent Foresight Exercises Andrzej M. J. Skulimowski Abstract The results of recent foresight projects reveal the impact of future ICT
tools on the practice of scientific research. This paper presents several aspects of
the process of building scenarios and trends of selected advanced ICT technologies. We point out the implications of emerging global expert systems (GESs) and AI-
based learning platforms (AILPs). GESs will be capable of using and processing
global knowledge from all available sources, such as databases, repositories, video
streams, interactions with other researchers and knowledge processing units. In many
scientific disciplines, the high volume, density and increasing level of interconnection
of data have already exhausted the capacities of any individual researcher. Three
trends may dominate the development of scientific methodology. Collective research
is one possible coping strategy: Group intellectual capacity makes it possible to
tackle complex problems. Recent data flow forecasts indicate that even in the few
areas, which still resist ICT domination, research based on data gathered in non-ICT
supported collections will soon reach its performance limits due to the ever-growing
amountofknowledgetobeacquired,verified,exchangedandcommunicatedbetween
researchers. Growing automation of research is the second option: Automated expert
systems will be capable of selecting and processing knowledge to the level of a
professionally edited scientific paper, with only minor human involvement. The third
trend is intensive development and deployment of brain–computer interfaces (BCIs)
toquicklyaccessandprocessdata.Specifically,GESsandAILPscanbeusedtogether
with BCIs. The above approaches may eventually merge, forming a few AI-related
technological scenarios, as discussed to conclude the paper. Keywords ICT foresight · E-science · Technological development trends · Global
expert systems · Brain–computer interfaces · Artificial intelligence (AI) scenarios © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_11 169 © The Author(s) 2021
C. Koschtial et al. (eds.), e-Science, Progress in IS,
https://doi.org/10.1007/978-3-030-66262-2_11 A. M. J. Skulimowski A. M. J. Skulimowski 170 1
Introduction The roles played by AI-based learning platforms (AILPs) and
GESs will gain importance when fusing ever-growing information flows, culmi-
nating in deeper automatic data refinery before presenting them to researchers. GESs will be capable of processing “big data” to “big knowledge”. New knowledge
fusion methods will be developed, such as hybrid and scenario-based anticipatory
networks (Skulimowski 2014a), e-science foresight (Skulimowski 2016b), including
combinations of forecasts (Elliott and Timmermann 2004) or recommendations 171 Visions of a Future Research Workplace … (Skulimowski 2017a). Finally, Sect. 3 presents the results of the Delphi surveys on
information systems prospects, which were conducted for SCETIST and MOVING
projects (Skulimowski et al. 2013; Köhler and Skulimowski 2019). We show that
different technological trends will have a synergetic impact on e-science. Artificial
intelligence-based (AI) tools and approaches will play a major role. New tools will
make the research conducted by humans more efficient by reaching predefined goals
faster and more accurately. Recommendations that may be useful to R&D policymakers, artificial intelligence
researchers, and innovative companies will be presented in Sect. 4. We will also
explore the relationship between BCIs and the future methodology of storing and
processing scientific information in GESs and AILPs. Moreover, Sect. 4 discusses
the opportunities, challenges, and threats posed by the development of AI tools and
how BCIs could be used to quickly overcome the problem of accessing big data
streams and knowledge repositories. 1https://www.statista.com/statistics/267202/global-data-volume-of-consumer-ip-traffic/
[access
Jan 10, 2020].
2An estimate after http://en.wikipedia.org/wiki/Exabyte [access Jan 10, 2020].
3https://www.millforbusiness.com/how-many-websites-are-there/ [access Jan 10, 2020].
4https://www.verisign.com/en_US/domain-names/dnib/index.xhtml [access Jan 10, 2020]. 2
Integration of Future Research Tools in Global
Expert Systems GESs were originally intended as a generalization of large-scale expert surveys and
intelligent digital libraries (Leidig and Fox 2014), capable of merging heterogeneous
information. They were defined in Skulimowski (2013, p. 582) as “all knowledge
sources, sensors, databases, repositories, and processing units, regardless of whether
they are human, artificial, animal, or hybrid, provided that they are all mutually
connected and endowed with … the usual expert system functionalities.” Nodes of
a GES are marked as “users” and each GES has a specific user hierarchy. Moreover,
a GES must offer each user an efficient information management system providing
“knowledge transfer on immediate demand” (ibid.). The growing coverage of scientific information by search engines, with an
increasing share of open access resources, further enhances the capabilities of
autonomous information retrieval, which is the base of the GES paradigm. In the
e-science context, the rationale justifying the introduction of GESs is to determine
rules and principles for the design of knowledge-based systems capable of gathering
and processing big scientific data, information and knowledge at different stages of
verification and refinery. The access of autonomous webcrawlers and other GES tools
to paid or sensitive information sources may be ensured with automatic subscription
passwords or automatic micropayments and may be facilitated by distributed ledger
technologies such as Linux Foundation’s Hyperledger Fabric blockchain (Thakkar
et al. 2018). It is also assumed that the researchers will pursue the trend to upload
the results of their work to public open access repositories such as researchgate.net,
zenodo.org, or academia.edu. The development of GES and the simultaneous emergence of AILPs will ensure
similar progress in learning approaches (Skulimowski 2019). It has also been 172 A. M. J. Skulimowski argued (Skulimowski 2013) that GESs may play an important role in solving the
human–computer convergence problem, which touches upon the AILPs as well. The
following Internet development trends that support the above claims were identified
in Skulimowski (2013, 2014b): • growing integration of heterogeneous information sources (ISs); • increasing interconnection of knowledge units, online and offline; • increasing sophistication of information processing within each knowledge unit;
• growing availability of sensor and other scientific measurement data, including
information from Internet of things (IoT); • growing need to apply big data technologies in scientific information processing
driven by the overall growth of the amount of information available online; • the emergence of common standards for scientific information management
(Jeffery et al. 2014). 2
Integration of Future Research Tools in Global
Expert Systems Google and Bing rose to 6.27 × 1012 in January 2020.5 When the tools offered by
search engines become sufficiently sophisticated, this system of interconnected Web
sites may become a real GES with strong analytic capacities. Another salient trend shaping the future of e-science is the emergence of a new
form of collaborative learning (Köhler and Skulimowski 2019) that is facilitated
and made more efficient with AILPs. This trend supports collaborative research,
the overall growth of collective intelligence of research teams (Mohamed et al. 2013) and their fusion in GESs. Although in the mid-term future, the intellec-
tual capacity of scientists can be outperformed by autonomous “global brain” type
analytic engines (Heylighen 2017), using GESs and AILPs as the composite tools for
learning and research will keep them aligned to the recent progress of autonomously
performed research. In addition, the “explainable AI” paradigm (Xu et al. 2019),
when commonly applied, can use combined GESs and AIPLs as tools to make avail-
able the results of any kind of autonomous research in a comprehensible form for
any GES/AILP user. Internet-based information supply chains of constantly growing size and
complexity necessitate new approaches to designing search-and-survey procedures
and to delegating more of this design work to autonomous agents. In a creative deci-
sion process (Skulimowski 2011), the user defines an initial subset of ISs according
to some criteria, assigns them trust or credibility coefficients (Gligor and Wing 2011)
and activates the procedure that transforms selected IS to autonomous agents with
capabilities similar to those of the user. The procedure runs recursively from the
initial IS, so that second-stage ISs are selected and activated. This allows the agents
to pursue the search autonomously and simultaneously, until a prescribed stack level
or thedesiredretrieval goal is achieved. Acreativity-stimulatingcontent-basedsearch
and recommendation has been investigated within the recent Horizon 2020 project
(Skulimowski 2017a). The design of GES knowledge provision procedures must
ensure that the reply to each query is given at a specified level of trust. When trust
coefficients ϕi, 0 ≤ϕi ≤1, are assigned to each source of information available to
this GES, the resulting trust τ(q) in the information retrieved in reply to a query q
can be higher than any of its individual sources. Autonomous management of complex queries processed by a GES is a multicri-
teria combinatorial optimization problem (Skulimowski 1994). 2
Integration of Future Research Tools in Global
Expert Systems • the emergence of common standards for scientific information management
(Jeffery et al. 2014). The above trends are amplified by qualitative and quantitative refinement of the
information stored and processed online as well as by the growing availability of the
learning content. The latter is fed to AILPs and boosts their development. The usability of online information for scientific purposes depends upon how well
it is structured and accessible via search engines. For instance, the percentage of all
data stored on the open Web and indexed by the search engine Google rose from 1%
in January 2007 to 6% in January 2010 and exceeded 10% in January 2012. This
estimated ratio has been preserved until at least 2019. At the same time, the estimated
amount of information available online rose to 800 exabytes (1018 B) in 2009 and 1.3
zettabytes (1021 B) in 2013. According to the Delphi survey in Skulimowski et al. (2013), question [I.8], it is expected to rise to 1.6 zettabytes in 2020 and to reach the
value of 3.5 zettabytes in 2025 and about 7 zettabytes in 2030. The recent Internet
metrics data1 yield the value of 2 zettabytes of information contained in indexed Web
sites as of 2019, which does not deviate much from the Delphi forecasts from 2012
to 2013 (Skulimowski et al. 2013). The same survey provided replies to the question
of whether the information available online is really useful to scientists. The results
are presented in Sect. 3. The number of Web sites exceeded 1700 million in 2016,2 then slightly declined
and rose again to 1730 million in 2019 (Mill provides the value of 1.27 × 109
as of December 2019). Only 15% of all Web sites are active.3 They are hosted in
about 360 million top-level domains.4 Forecasts of a further increase until 2025 and
beyond diverge considerably depending on whether exclusively machine-operated
and used (M2M) sites in the Internet of things are considered or not. Estimations
vary between 3 and 50 billion sites in 2025. The number of Web pages indexed by Visions of a Future Research Workplace … 173 Google and Bing rose to 6.27 × 1012 in January 2020.5 When the tools offered by
search engines become sufficiently sophisticated, this system of interconnected Web
sites may become a real GES with strong analytic capacities. 5https://www.worldwidewebsize.com/ [access Jan 10, 2020]. 2
Integration of Future Research Tools in Global
Expert Systems All activated units are deactivated after the information requested in qij
is gathered. As previously mentioned, the above procedure is a special case of a multicriteria
search strategy optimization problem, where the resulting strategy maximizes the
amount of information, which is to be gathered in the least amount of time, at a
minimum effort of all activated units, and at minimum cost for the initial unit. Such a
search strategy may be endowed with a certain level of free will and may be designed
to fulfill the definition of a creative decision process (cf. Skulimowski 2011). The natural question of whether science is capable of accommodating any kind
of future AI technology for research purposes and how it can be achieved appears
when projecting the GES future. From a purely economic standpoint, the role of
AADSs in e-science will grow, encompassing new areas of intellectual activity and
the replacement of human researchers. Performing a complex Web search strategy by
an intelligent autonomous web crawler is a real-life example of such empowerment. The development of GESs will challenge users with a growing complexity of queries,
a growing amount of gathered information, and with a need to comprehend the search
workflow. Rejecting useful information due to the lack of an appropriate explanation
of its provenance (Malaverri et al. 2013) may cause the recipients to lose the reply,
but they may prefer to proceed so as to avoid infringing cybersecurity rules. 2
Integration of Future Research Tools in Global
Expert Systems The order of queries
from different users and the sequence of information sources to be contacted can be
assessed from the point of view of precision, recall, and other information retrieval
measures, such as timeliness. The GES functioning proposed in Skulimowski (2013)
is based on a snowball principle: The node that generated a query activates other units
until the desired information is found. The following principles of query processing
in a GES have been defined in Skulimowski (2013). (a)
Each knowledge unit K activated by another one, Ki with a query qij returns the
information specified by qij to Ki or passes to (b). (a)
Each knowledge unit K activated by another one, Ki with a query qij returns the
information specified by qij to Ki or passes to (b). j
(b) If the query qij can be only partly responded by Kj, the latter unit modifies it
to qjk to ask for the missing information. Thus Kj activates further knowledge j
(b) If the query qij can be only partly responded by Kj, the latter unit modifies it
to qjk to ask for the missing information. Thus Kj activates further knowledge 174 A. M. J. Skulimowski A. M. J. Skulimowski units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the
search optimization problem as proposed in Skulimowski (1994). The resulting
information search strategy minimizes the number of repeated activations of the
same knowledge unit. units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the
search optimization problem as proposed in Skulimowski (1994). The resulting
information search strategy minimizes the number of repeated activations of the
same knowledge unit. units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the
search optimization problem as proposed in Skulimowski (1994). The resulting
information search strategy minimizes the number of repeated activations of the
same knowledge unit. (c) (c)
The procedure (b) activates recursively further units. Each unit Kj activated by
Ki fuses the information received from units activated by itself and returns them
to Ki. All activated units are deactivated after the information requested in qij
is gathered. (c)
The procedure (b) activates recursively further units. Each unit Kj activated by
Ki fuses the information received from units activated by itself and returns them
to Ki. 3
Results of the Delphi Survey on e-Science Tools
and Factors This section highlights a sample of the Delphi survey results (Skulimowski
et al. 2013). This survey based on the novel “Extrapolation Delphi” principle was
performed twice, the first time within the above-cited project and once during its
durability period. Specifically, we present the results concerning the future devel-
opment of advanced expert systems, heading toward advanced GESs, which were
the subject of questions contained in survey Section 11 titled “Future prospects of
knowledge base, expert systems, information streams and decision support systems
integration” (Skulimowski et al. 2013). The replies to five questions most relevant
to this article’s topics are presented out of 36 questions in the above mentioned
survey section. Visions of a Future Research Workplace … 175 Table 1 Estimated share ϕ1 [in %] of researchers considering the online information widely
available through browsers and search engines as fully representative in their areas of scientific
research. Analysis of the replies to question No. 11.1a in (Skulimowski et al. 2013) weighted with
combined trust/competence coefficients of respondents
Specification of
results
Estimates for
2015
Forecasts for
2020
Forecasts for
2025
Forecasts for
2030
No. of replies
47
47
47
47
Shapiro–Wilk test
negative
negative
positive
negative
Unimodality test
positive
positive
positive
positive
Mean weighted
value
25,519
28,73
40,146
47,337
Weighted standard
deviation
18,006
16,737
21,449
22,66
Weighted left
semideviation
15,27
16,906
18,867
22,7
Weighted right
semideviation
22,93
17,18
25,806
23,373
Weighted median
value:
20
25
35
45
1st weighted
quintile
5
10
15
20
2nd weighted
quintile
10
20
30
40
3rd weighted
quintile
20
30
35
50
4th weighted
quintile
50
50
50
60
Interquintile range
IQVR
45
40
35
40
Interquartile range
IQR
30
30
30
25
No. of reply
clusters
1
1
1
1 Table 1 Estimated share ϕ1 [in %] of researchers considering the online information widely
available through browsers and search engines as fully representative in their areas of scientific
research. Analysis of the replies to question No. 11.1a in (Skulimowski et al. 2013) weighted with
bi
d t
t/
t
ffii
t
f
d
t 3.1
Delphi Survey Background and Scope The survey results are presented in tables, which provide the basic statistical char-
acteristics of replies, together with Delphi-specific consensus measures of experts
and a cluster analysis (von der Gracht 2012). The latter is then used to construct
the development scenarios of investigated information systems. The survey respon-
dents were requested to define certain numerical development indicators for four
time horizons: 2015 (as forecast in 2013 and an estimate in 2016), 2020, 2025, and
2030 (forecasts). The following indicators have been calculated for all replies and
for all time horizons: A. M. J. Skulimowski 176 – the average value, standard deviation, left and right semideviations, – the median, 1st and 3rd quartile and four quintiles, – the median, 1st and 3rd quartile and four quintiles, – the interquartile range (IQR), defined as the difference between the third and first
quartile, – the interquartile range (IQR), defined as the difference between the third and first
quartile, – the interquintile range (IQVR), defined as the difference between the fourth and
first quintile, – the interquintile range (IQVR), defined as the difference between the fourth and
first quintile, q
– Hartigans’ dip test of unimodality (Hartigan and Hartigan 1985); if negative, it
was followed by a clustering of replies and the number of clusters of replies was
determined, – Hartigans’ dip test of unimodality (Hartigan and Hartigan 1985); if negative, it
was followed by a clustering of replies and the number of clusters of replies was
determined, – the Shapiro–Wilk (log) normality test, applied to replies either directly or to their
logarithms when the question touched upon growth ratios. The consensus indicators IQR and IQVR should be normalized, for example by
dividing them by the maximum data range R: = rmax −rmin after eliminating the
outliers. Then, the consensus is defined by one or both inequalities IQR/R ≤η1, IQVR/R ≤η2, where ηk, k = 1, 2, are certain threshold values and η1 ≤η2. We can clearly see
that given the same threshold value, the IQVR provides a stronger consensus test. A
positive result of the Shapiro–Wilk normality test indicates a potentially unimodal
distribution of replies and rejects the hypothesis that there is more than one cluster
of replies. 6The current version of the system is available at www.forgnosis.eu. 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey The first of the above-mentioned survey outcomes presented in this paper is a basic
statistical analysis of question 11.1a pointing out the forecasted shares of scientists
that consider online information to be accurately representative of their research. It
is shown in Table 1. The above question did not distinguish between the research areas, so the replies
only provide a rough estimate by merging humanities, engineering, etc. However,
it shows the average value of online researchers’ share almost doubling between
2015 and 2030, while the mean square ex-ante forecast error rose only by about
20%, and the relative error decreased considerably. All but one (2025) reply sets for
the estimation (2015) or forecasting (2020, 2025, 2030) horizons were considerably
irregular and did not pass the weighted Shapiro–Wilk normality test. However, all
value distributions were unimodal and concentrated in one cluster. Let us note that all quantiles (quartiles, quintiles, median) and consequently, the
consensus measures, are integers because the respondents select their replies from
the standard integer pick list [0:100]. The same list was used for all questions in
Section 11 of the survey where the replies were to be provided in %. Table 2 shows the breakdown of the verified and raw quantitative information
available on the Web for the same estimation/forecasting. The respondents estimated the amount of trustworthy information (i.e., knowl-
edge) to comprise about one-fifth of all quantitative information available. This
cannot be seen as an optimistic estimate. The forecast for 2030—about 40% of
refined information—presumes the emergence of a new data refinery mechanism. This share is almost double in comparison with the estimate for the present state of
the Internet. Nevertheless, the share of unverified Web information will still be close
to the larger part of the golden proportion, which is an indication of the power of
disinformation and fake data. The question in the first two rounds just touched upon
the knowledge, irrespective of whether it was quantifiable or not. Based upon the
respondents’ postulates, the question for the follow-up round was formulated more
precisely, but without a statistically essential impact on outcomes. 3.1
Delphi Survey Background and Scope The statistical analysis was first performed under the hypothesis that the replies be
weighted according to a self-assessment of certainty by the respondents’ survey, in
combination with a self-assessed credibility coefficient of individual replies, and an
automatically assigned individual expert competence score. This score was computed
by the Delphi support system6 (Skulimowski 2017), based on previous survey partic-
ipation, the record of publications, research projects, and other achievements in
the question-related area. It has been observed (Skulimowski 2016a) that for most
survey questions, there was no significant difference between the statistical indica-
tors for weighted and non-weighted responses. This observation also touches upon
the consensus measures and indicates that the expert group’s ability to estimate the
future evolution of indicator values was homogeneous. Therefore, in this section we
concluded that the resultant analysis variant yields a smaller statistical error (in terms
of the standard deviation) for a majority of forecasting horizons. The sum of errors
was a decisive factor, for an equal number of dominating values at different hori-
zons. Out of five questions selected for this section, only the replies to question 11.8
(Table 4) exhibited smaller errors when analyzed without weighting coefficients. The survey in the project SCETIST (Skulimowski 2013) consisted of two rounds
and was conducted in 2012 and 2013. There was also a post-project update round with
the same participants, questions and Delphi support software. The respondents could
select the questions to answer, according to their competences. Therefore, from over Visions of a Future Research Workplace … 177 100 respondents, the number of those replying to questions in Section 11.1 varied
between 43 and 48 in the first and second rounds. 100 respondents, the number of those replying to questions in Section 11.1 varied
between 43 and 48 in the first and second rounds. 7http://www.wolframalpha.com. 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey A characteristic
feature of the above replies is smaller than the usual difference between the IQR
and IQVR consensus measures, which indicates a relatively large number of equal
replies between the 1st quartile and 1st quintile as well as between the 3rd quartile
and 4th quintile. The next question (11.3) assumed the emergence of a next generation of Wolfram’s
Alpha7—an expert system capable of providing informed replies to virtually any 178 A. M. J. Skulimowski Table 2 Amount of processed and verified quantitative knowledge available online (in % of
all quantitative information available). Replies to question no. 11.2 weighted with combined
trust/competence coefficients Table 2 Amount of processed and verified quantitative knowledge available online (in % of
all quantitative information available). Replies to question no. 11.2 weighted with combined
trust/competence coefficients
Specification of
results
Estimates for
2015
Forecasts for
2020
Forecasts for
2025
Forecasts for
2030
No. of replies
47
47
47
47
Shapiro–Wilk test
negative
negative
negative
positive
Unimodality test
positive
positive
positive
positive
Mean weighted
value
17,186
22,732
27,664
38,079
Weighted standard
deviation
11,66
12,865
16,657
24,339
Weighted left
semideviation
9,363
12,572
18,072
21,447
Weighted right
semideviation
15,135
13,633
16,008
28,604
Weighted median
value:
15
20
30
35
1st weighted
quintile
5
10
10
15
2nd weighted
quintile
10
15
20
25
3rd weighted
quintile
15
25
30
40
4th weighted
quintile
25
30
40
50
Interquintile range
IQVR
20
20
30
35
Interquartile range
IQR
15
20
30
32
No. of reply
clusters
1
1
1
1 query. This question touched upon a quantitative characteristic of a future GES
capabilitytoreachtheexistinginformation,namely,itsmaximumrecallvaluerelative
to the query provided by the system user. Replies equal to “0” were representative of
the disbelief of this particular survey respondent that such software will be created
(Table 3). query. This question touched upon a quantitative characteristic of a future GES
capabilitytoreachtheexistinginformation,namely,itsmaximumrecallvaluerelative
to the query provided by the system user. Replies equal to “0” were representative of
the disbelief of this particular survey respondent that such software will be created
(Table 3). Unlike in the case of the two previous questions, the replies to question 11.3 above
indicate a sharp rise in the GES search range, from an initial estimate of about 2–
27% in 2030, with a high yet relatively decreasing uncertainty, expressed by standard
deviation and semideviations. 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey A symmetrical problem to that shown above was considered in question 11.8
(Skulimowski 2013); namely, we investigated the Internet users’ attitudes to Visions of a Future Research Workplace … 179 Table 3 The share of information available on the Web that can be processed by advanced
expert software (GES) capable of analyzing heterogeneous data (quantitative economic information,
multimedia, publications, video streaming) and providing GES users with informed replies to any
given question (in % of available information used for this purpose) expert software (GES) capable of analyzing heterogeneous data (quantitative economic information,
multimedia, publications, video streaming) and providing GES users with informed replies to any
given question (in % of available information used for this purpose)
Specification of
results
Estimates for
2015
Forecasts for
2020
Forecasts for
2025
Forecasts for
2030
No. of replies
48
47
47
47
Shapiro–Wilk test
positive
positive
positive
negative
Unimodality test
positive
positive
positive
positive
Mean weighted
value
2,156
5,525
14,536
26,926
Weighted standard
deviation
4,928
6,877
14,319
20,797
Weighted left
semideviation
2,091
4,477
10,295
15,467
Weighted right
semideviation
11,713
10,861
18,675
30,245
Weighted median
value:
0
2
10
20
1st weighted
quintile
0
0
2
10
2nd weighted
quintile
0
0
5
15
3rd weighted
quintile
0
3
15
25
4th weighted
quintile
1
10
20
50
Interquintile range
IVQR
1
10
18
40
Interquartile range
IQR
0
10
10
40
No. of reply
clusters
1
1
1
1 searching for solutions to their problems on the Web. The analysis of replies is
given in Table 4. A predominance of solving problems through access to online information is not
a surprise. Actually, the above characteristics may be burdened by a relatively high
share of elderly people who have Internet access via their mobile phones, but use
it sparingly. The most recent research performed within the project (Skulimowski
2019) yields considerably higher estimates for 2025 and 2030, reaching more than
90% of all queries. The last set of results presented in this section touches upon the emergence of
qualitatively new capabilities and phenomena in GESs, manifesting itself through A. M. J. 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey Skulimowski 180 Table 4 Answers to problems, questions, and queries of all kinds (translations, spelling, defini-
tions, geographical information, graphical object finding, legislation, etc.) that will be sought online:
in% of all queries from user with Internet access (mobile or landline); unweighted
Specification of
results
Estimates for
2015
Forecasts for
2020
Forecasts for
2025
Forecasts for
2030
No. of replies
46
45
45
45
Shapiro–Wilk test
negative
negative
negative
negative
Unimodality test
positive
positive
positive
positive
Mean value
38,553
49,189
60,676
71,919
Standard deviation
19,134
18,428
18,64
19,836
Median value:
40
55
65
75
1st quintile
15
25
30
40
2nd quintile
25
40
55
70
3rd quintile
40
55
65
75
4th quintile
50
60
70
85
Interquintile range
35
35
40
45
Interquartile range
32,5
28,75
27,5
20
No. of reply
clusters
1
1
1
1 solving previously intractable problems or answering unresolved questions. Namely,
the integration of knowledge on the Internet will allow for a new level of quality
in resolving problems presented by GES users, specifically those intractable prob-
lems, and providing replies to queries, which are unavailable through contemporary
information processing methods (Table 5). solving previously intractable problems or answering unresolved questions. Namely,
the integration of knowledge on the Internet will allow for a new level of quality
in resolving problems presented by GES users, specifically those intractable prob-
lems, and providing replies to queries, which are unavailable through contemporary
information processing methods (Table 5). Both the uncertainty expressed by the standard deviation and semi-deviations, as
well as the consensus indicators IQR and IQVR for question 11.9, are relatively lower
than in case of the two previous forecasts. Fitting the above replies with the logistic
curve (Skulimowski 2017b), we can calculate the expected time when the majority
of problems and queries can be better solved by GESs, namely the year 2037. This
year can thus be regarded as a kind of a singularity (Skulimowski 2014b); however,
in a limited sense. To conclude this section, let us note that reaching a consensus
need not be the ultimate goal of a Delphi survey. Usually, if the unimodality test is
negative, a lack of consensus indicates the existence of several clusters of replies. 3.2
The Future Use of Information Systems
for e-Science—The Results of the Delphi Survey If
this is not the case and the IQR or IQVR values are rather high, while growing more
slowly than the trend investigated by the survey, it means that there is a common
expectation of a certain trend or event among the survey respondents, with a high
uncertainty regarding its time of occurrence, however. Visions of a Future Research Workplace … 181 Visions of a Future Research Workplace … Table 5 The share in % of problems and queries that will be more adequately solved by GES,
compared to the solutions and replies provided by human experts (question 11.9)
Specification of
results
Estimates for
2015
Forecasts for
2020
Forecasts for
2025
Forecasts for
2030
No. of replies
46
45
45
45
Shapiro–Wilk test
negative
negative
positive
positive
Unimodality test
positive
positive
positive
positive
Mean weighted
value
14,477
23,12
31,653
45,813
Weighted standard
deviation
9,439
9,786
11,459
18,268
Weighted left
semideviation
7
7,436
8,881
16,184
Weighted right
semideviation
12,231
12,634
15,542
21,121
Weighted median
value:
10
20
30
40
1st weighted
quintile
5
15
20
25
2nd weighted
quintile
10
15
30
35
3rd weighted
quintile
10
20
30
40
4th weighted
quintile
20
30
40
60
Interquintile range
IQVR
15
15
20
35
Interquartile range
IQR
15
10
20
25
No. of reply
clusters
1
1
1
1 Table 5 The share in % of problems and queries that will be more adequately solved by GES
compared to the solutions and replies provided by human experts (question 11.9) 4
Discussion and Conclusions The results of the Delphi survey presented in Sect. 3 provide clues, arising from
expert judgments, regarding the amount of information available online and its use
for e-science purposes until 2030. It is expected that by 2030, the corresponding
information retrieval tools will reach sufficient enough levels to provide virtually
all necessary scholarly information to researchers. Furthermore, within a similar
time frame, GESs are expected to outperform human experts in solving complex
knowledge processing tasks. Another AI trend that may have a relevant impact on e-science is the development
of brain–computer interfaces (BCIs) and their deployment in enhancing research,
their joint use with GESs and AILPs, as well as in intelligent decision support 182 A. M. J. Skulimowski systems.TheresultsofaDelphisurveyonBCIsarepresentedinSkulimowski(2014b,
2016b). Here, we briefly discuss a summary of these findings. By definition, in a BCI,
outward information is retrieved by recognizing the brain’s electromagnetic neural
activity, while for the inward transfer direction, a BCI triggers the neural circuits
directly (Brunner et al. 2011; Jiang et al. 2019). The best transmission rates and
qualities were obtained with invasive BCIs, based on intracranial implants, but the
greatest hope in enhancing human capabilities is placed on non-invasive BCIs, such
as wearable devices that are used to retrieve EEG or fMRI signals. They are expected
to facilitate efficient bidirectional communication with GES (Zhang et al. 2013) as
well as direct communication between human brains, called hyperinteraction (Grau
et al. 2014; Jiang et al. 2019). The ability of a BCI to directly connect researchers’
brains with powerful expert systems will speed up progress in global data integra-
tion provided by GESs. It will also increase the efficiency of scientific collaboration
(Leidig and Fox 2014; Shi et al. 2017) and the use of AILPs. The positive effect
of BCIs on researchers who obtain efficient and instant access to big research data
may partly compensate for the negative impact of data explosion. However, the ques-
tion of whether e-science can fully exploit the capabilities of emerging advanced AI
tools and technologies such as AILPs, GESs, and BCIs to increase the quality and
efficiency of scientific research remains to be seen. The analysis of the full set of SCETIST Delphi survey replies resulted in deriving
three human–AI interaction scenarios (cf. Skulimowski 2014b, 2016a, b). Here, we
adjust them slightly to provide conditional responses to the above question. 4
Discussion and Conclusions The full
and beneficial use of AI defines the optimistic scenario of human–AADS interaction,
while the negative response is associated with the pessimistic scenario, often referred
to as the AI threat problem. The foresight results presented in Skulimowski (2014b)
suggest that the main condition triggered between the positive and negative scenarios
is the capability of future BCIs to provide a direct interface to GESs and facilitate
the creative process of GES users. In the optimistic scenario, the growing empowerment of AADSs will be compen-
sated for by the ability of human supervisors and authorized users to control them
directly with BCIs. This scenario is backed by results of the Delphi survey presented
in Sect. 3, which suggest that GESs and AILPs supported by high-performance BCIs
and enhanced reality will ensure control over advanced AI technologies. Further
results of the Delphi survey on the development of artificial creativity and creativity
support systems performed in SCETIST (Skulimowski 2016a) highlight the impor-
tance of coupling human users with GESs and AILPs via BCIs to stimulate their
creative abilities. The pessimistic scenario presumes that a growing share of human creative
activity, specifically in research, will be replaced by AADSs due to the ever-
growing complexity of research and decision problems to be solved along with
increasingly large data volumes. In this scenario, AADSs will specify goals, criteria
and constraints, target quality and the scope of applicability of solutions. Human
researchers will only perform auxiliary and assistive roles. In the third, neutral scenario, technological development is generally slowed down
in the face of various setbacks. In this case, the AADS/human competition problem Visions of a Future Research Workplace … 183 will be deferred to a more distant future, beyond horizon 2030 of the foresight studies
presented here. will be deferred to a more distant future, beyond horizon 2030 of the foresight studies
presented here. In conclusion, the results of recent foresight studies highlight the relevance
of development trends in selected advanced AI technologies for future e-science,
e-learning, and e-research. According to the outcomes of the research projects
(Skulimowski et al. 4
Discussion and Conclusions 2013; Köhler and Skulimowski 2019), the areas of inten-
sive ICT/AI development efforts that can be of utmost relevance for e-science are
GESs driven by autonomous web crawlers and dedicated decision support systems,
creativity support systems capable of stimulating or at least preserving human
creative abilities, and bidirectional non-invasive BCIs providing direct links to GESs
and other researchers to efficiently tackle large amounts of scientific data. Acknowledgements The author is grateful for the support of the research project “Scenarios
and Development Trends of Selected Information Society Technologies until 2025” (acronym
“SCETIST”), financed from the ERDF funds within the Innovative Economy Operational
Programme, contract No. WND-POIG.01.01.01-00-021/09. Some results presented in this paper
have been also verified and extended within the Horizon 2020 research project “Training towards
a society of data-savvy information professionals to enable open leadership Innovation” (acronym
“MOVING”) financed by the EC, contract No. 693092. Finally, the author is grateful for the
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https://openalex.org/W3199588561 | https://www.scielo.br/j/cr/a/wwMkrkX8mpMwBjTKJBH8hhr/?lang=en&format=pdf | Portuguese | null | Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products | Ciência rural | 2,022 | cc-by | 7,937 | Maniçoba para ovinos e caprinos: produção de forragem, estratégias de conservação, desempenho
do animal e qualidade dos produtos RESUMO: Nas regiões secas mundiais, fornecer alimentos para ruminantes tem sido um grande desafio, havendo necessidade de utilizar
plantas que contribuam para a resiliência dos sistemas de produção. A maniçoba é vista como um potencial recurso forrageiro no semiárido
brasileiro, sendo utilizada como feno ou silagem para alimentação de ruminantes. O objetivo desta revisão foi sumarizar os resultados quanto
à produção de forragem da maniçoba, além do consumo de matéria seca (MS), desempenho produtivo e qualidade dos produtos de origem
animal obtidos com dietas à base de maniçoba, quando comparados com dietas compostas por outros volumosos para caprinos e ovinos. Considerando os estudos avaliados, a produtividade média da maniçoba variou de 367 a 1.592 kg de MS ha-1, com aumento da produção
de forragem pela maior fertilização da planta e densidade de plantio. As dietas à base de maniçoba promoveram resultados semelhantes ou
superiores para ingestão de matéria seca e desempenho produtivo de caprinos e ovinos, quando comparadas às dietas compostas por outros
recursos forrageiros. A qualidade dos produtos de origem animal também foi semelhante às proporcionadas por dietas à base de volumosos
tradicionais, como feno Tifton 85 ou palma-forrageira. Portanto, a maniçoba apresenta produção de forragem que pode contribuir com os
sistemas de produção de ruminantes em ambiente semiárido, e promover desempenho produtivo e qualidade dos produtos de origem animal
compatíveis com as proporcionadas pelas forrageiras tradicionais. p
p
p
p
f
g
Palavras-chave: alternativa forrageira, recurso forrageiro, mandioca silvestre, Manihot, planta cianogênica. Ci
Received 12.19.20 Approved 06.03.21 Returned by the author 07.30.21
CR-2020-1096.R2
Editors: Rudi Weiblen Henrique Mendonça Nunes Ribeiro Fiho Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1*
Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1
Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1*
Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1
Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 1Centro de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), 56304-917, Petrolina, PE, Brasil. E-mail: renaldovilar.zootecnia@gmail.com. *Corresponding author. 2Instituto Federal de Educação, Ciência e Tecnologia do Sertão Pernambucano (IFSertãoPE), Santa Maria da Boa Vista,
3Universidade de Pernambuco (UPE), Petrolina, PE, Brasil. (
),
,
,
esa Brasileira de Pesquisa Agropecuária (Embrapa Semiárido), Petrolina, PE, Brasil. (
)
4Empresa Brasileira de Pesquisa Agropecuária (Embrapa Semiárido), Petrolina, PE, Brasil. ABSTRACT: In dry regions worldwide, providing feed for ruminants has been a great challenge, with a need to use plants which contribute
to the resilience of production systems. Maniçoba is seen as a potential forage resource in the Brazilian semiarid, being used as hay or silage
to feed ruminants. This review summarized results regarding forage production of maniçoba, in addition to dry matter (DM) intake, productive
performance, and quality of animal products obtained providing maniçoba based diets, when compared to diets composed by other roughages
for goats and sheep. Considering the evaluated studies, the average yield of maniçoba varied from 367 to 1,592 kg DM ha-1, enhancing the
forage yield by increasing plant fertilization and planting density. Diets based on maniçoba promoted similar or higher intake of DM and
productive performance for goats and sheep, when compared to diets comprising other forage resources. The quality of animal products was
also similar to the ones obtained with diets based on traditional roughages, such as Tifton 85 hay or spineless cactus. Therefore, maniçoba
allows a forage production that may contribute to ruminant production systems in semiarid environment and promote productive performance
and animal product quality compatible to the ones provided by traditional forage plants. Key words: forage alternative forage resource wild cassava Manihot cyanogenic plant Key words: forage alternative, forage resource, wild cassava, Manihot, cyanogenic plant. Maniçoba for sheep and goats - forage yield, conservation strategies, animal
performance and quality of products Maniçoba for sheep and goats - forage yield, conservation strategies, animal
performance and quality of products Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1*
Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1
Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 Maniçoba for sheep and goats - forage yield, conserva
Ciência Rural, Santa Maria, v.52:3, e20201096, 2022 Maniçoba for sheep and goats - forage yield, conserva
Ciência Rural, Santa Maria, v.52:3, e20201096, 2022 ormance and quality of products. 1
ISSNe 1678-4596
http://doi.org/10.1590/0103-8478cr20201096
animal production INTRODUCTION forage plants that are inserted in the socioeconomic
context of the population and contribute to new
strategies for supplying nutrients for ruminants,
reducing production losses and increasing animal
yield and farm income. Food security for herds has been an
important challenge for livestock production in arid
and semiarid regions (MLAMBO & MAPIYE, 2015)
and there is great concern about food production to
meet the demands of the world’s growing population,
with drylands playing a relevant role in this scenario
(TARRASÓN et al., 2016). In this sense livestock
systems need to improve land use by using adapted Maniçoba
comprises
plants
(wild
species) of the genus Manihot, including Manihot
glaziovii Müll. Arg., Manihot catingae Ule and
Manihot carthaginensis (Jacq.) Müll. Arg, all native
to the Brazilian semiarid, showing genetic and Gomes et al. 2 morphoagronomic diversity (CAMPOS et al., 2020). The plants are perennial, tolerant to cuttings and long
periods of drought, with morphological adaptation
related to water retention (NASSAR et al., 2010), and
physiological mechanisms via control of stomatal
aperture to maintain a positive carbon balance even
in drought conditions (MORGANTE et al., 2020). In
ruminant feeding, maniçoba is used exclusively as hay
or silage to reduce the toxicity of hydrocyanic acid,
thus allowing a safe feeding for animals (MATOS et
al., 2005; SOARES, 2000; SOUZA et al., 2006). morphoagronomic diversity (CAMPOS et al., 2020). The plants are perennial, tolerant to cuttings and long
periods of drought, with morphological adaptation
related to water retention (NASSAR et al., 2010), and
physiological mechanisms via control of stomatal
aperture to maintain a positive carbon balance even
in drought conditions (MORGANTE et al., 2020). In
ruminant feeding, maniçoba is used exclusively as hay
or silage to reduce the toxicity of hydrocyanic acid,
thus allowing a safe feeding for animals (MATOS et
al., 2005; SOARES, 2000; SOUZA et al., 2006). Soil management using ridges and the
cutting heights of the plants (MOREIRA FILHO
et al., 2008), the water depths and the nitrogen (N)
fertilization (ARAÚJO FILHO et al., 2013) are also
factors that affect the plant growth and increase the
forage yield. Presumably, the ridges increase the
accumulation and availability of nutrients in the soil,
favoring the development of the plant root system. The increase in productivity with N fertilization
suggested that maniçoba has efficient metabolic
responses to the use of this nutrient. INTRODUCTION Productive and qualitative characteristics
of the plant must be considered, along with its
potential to constitute diets that provide a proper
productive performance to the animal. In this sense
the evaluation of yield and quality of maniçoba
forage, as well as the assessment of dry matter
(DM) intake, productive performance of goats and
sheep, and its influence on animal product quality,
are important aspects to understand the potential of
this plant as an alternative for livestock production
systems in semiarid environments. Beyond the forage yield, BELTRÃO et al. (2008) pointed out the proportion of leaves on the plant,
reporting that approximately 50% of the produced
forage (kg DM-1 ha-1) corresponds to this component,
which may still be incremented by management
practices, as for instance organic fertilization. These results denoted that maniçoba
allows forage yield compatible with the semiarid
environment. Therefore, it contributed to the forage
input for ruminant production systems, while
management factors may increase the productive
efficiency of the crop. The present review summarized the results
of forage yield of maniçoba in the semiarid region
of Brazil, the DM intake and productive performance
of goats and sheep fed maniçoba-based diets, and the
quality of animal products. It is important that there should be a greater
number of studies evaluating this forage resource,
especially including diverse locations in the semiarid
region, thus enlarging the database on crop yield,
above all regarding long-term studies. Forage quality 3 Table 1 – Mean and maximum forage yield (kg DM ha-1) of maniçoba, cutting intervals (days), municipality, and rainfall (mm/period)
from studies carried out in Brazilian semiarid in rainfed condition. Table 1 – Mean and maximum forage yield (kg DM ha-1) of maniçoba, cutting intervals (days), municipality, and rainfall (mm/period)
from studies carried out in Brazilian semiarid in rainfed condition. from studies carried out in Brazilian semiarid in rainfed condition. Mean productivity
---Maximum productivity---
----Cutting interval----
---------Municipality--------
--------Rainfall--------
4561
626
240
Areia-PB
893.5*
4712
1,800
1,095
Cubatí-PB
321
3673
462
152
Campina Grande-PB
765
1,1784
1,746
120-240
Areia-PB
893.5-1,163
1,5925
3,733
365-456
Petrolina-PE
937**
1BELTRÃO et al. (2008) *accumulated rainfall of years 2002 and 2003 in Areia-PB from AESA (2020), 2MOREIRA FILHO et al. (2008), 3VASCONCELOS et al. (2010), 4ARAÚJO FILHO et al. (2011), 5SOARES (1989). **accumulated rainfall of years 1987 and
1988 in Petrolina-PE (Meteorological Station of Embrapa Semiárido). 1BELTRÃO et al. (2008) *accumulated rainfall of years 2002 and 2003 in Areia-PB from AESA (2020), 2MOREIRA FILHO et al. (2008), 3VASCONCELOS et al. (2010), 4ARAÚJO FILHO et al. (2011), 5SOARES (1989). **accumulated rainfall of years 1987 and
1988 in Petrolina-PE (Meteorological Station of Embrapa Semiárido). compatible with or higher than the ones presented by
other forage resources used to feed ruminants in the
Brazilian semiarid. High CP and low NDF are positive
aspects in roughage for feeding ruminants. SANTOS
et al. (2017) evaluated different forages in natura
and observed 208.0 g kg-1 CP and 434.0 g kg-1 NDF plant (MOREIRA FILHO et al., 2009), indicating the
conservation process of maniçoba as an important
tool to maintain the nutrients. compatible with or higher than the ones presented by
other forage resources used to feed ruminants in the
Brazilian semiarid. High CP and low NDF are positive
aspects in roughage for feeding ruminants. SANTOS
et al. (2017) evaluated different forages in natura
and observed 208.0 g kg-1 CP and 434.0 g kg-1 NDF Maniçoba exhibited high lignin levels,
which may reduce the forage digestibility. Conversely,
this forage also showed high CP and low NDF, able 2 – Crude protein (CP), ash, ether extract (EE), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HE
cellulose (CELL) and lignin (LIG) of maniçoba (in natura, hay and silage). Ciência Rural, v.52, n.3, 2022. Forage quality The results of five experimental trials (n
= 50 treatments) in the Brazilian semiarid evaluated
the forage production of maniçoba, considering
single-crop and rainfed conditions. These studies
were carried out in the states of Pernambuco and
Paraíba, with cutting intervals varying from 152 to
1,095 days and accumulated rainfall in the period
varying from 321 to 1,163 mm. The average forage
yield reported for maniçoba ranged from 367 to
1,592 kg DM-1 ha-1 (Table 1), considering different
cutting intervals of the plant, reaching 3,733 kg
DM-1 ha-1 regarding the sum of the production of two
consecutive harvests, performed after up to fifteen
months (SOARES, 1989).l The dry matter content of fresh maniçoba
varied from 204.4 to 289.2 g kg-1 (ARAÚJO FILHO et
al., 2011; SILVA et al., 2011). The chemical composition
of the plant, based on data from 21 articles, reported by
authors as hay, silage or fresh (in natura) maniçoba,
consisted on average of crude protein (CP), ash, ether
extract (EE), neutral and acid detergent fiber (NDF and
ADF), hemicellulose (HEM), cellulose (CELL) and
lignin, at 156.5; 79.4; 43.9; 473.4; 354.9; 125.3; 231.5
and 109.2 g kg-1, respectively (Table 2). Crude protein levels ranged from 90.8 to
227.5 g kg-1, and NDF varied from 355.0 to 586.0 g
kg-1 (Table 2). The offered forms of maniçoba (fresh,
hay or silage) did not result in great differences
on main parameters of chemical composition. On
average, fresh maniçoba showed 173.8 g kg-1 for CP,
while as hay and silage CP levels were 141.1 and
154.7 g kg-1. Additionally, NDF for fresh maniçoba
was 449.8 g kg-1, while as hay and silage it was 475.5
and 494.8 g kg-1, respectively (Table 2). The authors
attributed changes in chemical composition mainly to
the proportion of leaf/stem (FRANÇA et al., 2010),
as well as genotype and development stage of the Several factors influence the production
of maniçoba forage. ARAÚJO FILHO et al. (2011)
verified that organic fertilization increased the yield by
up to 80%, in comparison to non-fertilized maniçoba,
due to the nutrient supply to the crop. The increase
in plant density also increased the forage yield, with
plant densities reaching 6,667 (ARAÚJO FILHO et
al., 2011) or 10,000 plants ha-1 (SOARES, 1989),
indicating that maniçoba can respond favorably to
intensive crop management. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006);
6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017);
11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012);
16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA
FILHO et al. (2012). Ciência Rural, v.52, n.3, 2022. Forage quality In addition, N and K contents differed according to
the municipality of origin of the maniçoba sample,
associated with soil and climatic characteristics. for maniçoba, while Cunhã (Clitorea ternatea L.),
Sabiá (Mimosa caesalpiniifolia Benth.), Gliricídia
(Gliricidia sepium (Jacq.) Steud.) and Mororó
(Bauhinia cheilanta (Bong.) Steud.) presented 148.0;
124.0; 175.0; and 115.0 g kg-1 CP and 604.0, 679.0,
510.0 and 683.0 g kg-1 NDF, respectively. for maniçoba, while Cunhã (Clitorea ternatea L.),
Sabiá (Mimosa caesalpiniifolia Benth.), Gliricídia
(Gliricidia sepium (Jacq.) Steud.) and Mororó
(Bauhinia cheilanta (Bong.) Steud.) presented 148.0;
124.0; 175.0; and 115.0 g kg-1 CP and 604.0, 679.0,
510.0 and 683.0 g kg-1 NDF, respectively. The nutritional value of maniçoba is
influenced by divers factors, such as chemical
fertilization, soil types and management, plant
cutting height and stage of development of the plant
(ANDRADE et al., 2014; MOREIRA FILHO et al.,
2009). In a study carried out by PARENTE et al. (2007), maniçoba in natura showed 13.91% CP when
supplied with 100 kg N ha-1, while without nitrogen
fertilization the CP content was 8.58%, Sodium, iron, zinc, and manganese were
the main microminerals presented by maniçoba
(Table 4). Mineral elements exert an important role in
the plant, including structural functions and metabolic
process, and they are also essential for animals. The
insufficiency of even one element may negatively
affect animal growth, as well as health and reproductive
functions. In the Brazilian semiarid the main source
of minerals for ruminants is forage, and the supply
of minerals through maniçoba forage contributes to
meeting the requirements for these elements. According to MENEZES et al. (2012),
the potential DM degradability of maniçoba hay was
70%, while the effective degradability (5%/h) was
57.4%. The potential degradability of CP was 92.5%
and the effective one (5%/h) was 80%. SOUZA et
al. (2006) reported a potential degradability of NDF
varying from 52.12 to 54.45%, with an effective
degradability (5%/h) varying from 32.41 to 32.55%. Furthermore, the knowledge of mineral
contents in maniçoba enables the comprehension of
extraction and exportation of nutrients by the plant,
and determines the mineral reposition, according to
the forage yield. FRANÇA et al. (2010) observed that the
DM degradability is related to a great participation of
leaves in the produced biomass, presenting tissues with
less thickened walls and lower lignification, promoting
higher degradability than the stem part. Forage quality p
(
),
,
(
),
g
(
),
g
(
),
(
),
cellulose (CELL) and lignin (LIG) of maniçoba (in natura, hay and silage). ---------------------------------------------------------------------Contents (g kg of DM)----------------------------------------------------------------------------
Fractions
---------------in natura-------------
---------------Hay----------------
-------------Silage-------------
----Overall average----
Mean Min. – Max. Mean Min. – Max. Mean Min. – Max. CP
173.8
141.1
154.7
156.5
110.9 – 227.51,2,3,4,5,6,7,8,9,10,11
90.8 – 196.02,12,13,14,15,16,17
125.0 – 188.05,6,18,19,20,21
Ash
76.4
76.9
85.0
79.4
61.0 – 142.8,2,3,4,5,6,8,10,11
61.7 – 99.52,12,13,15,16,17
71.5 - 97.85,6,18,19,20,21
EE
42.1
50.3
39.3
43.9
20.6 – 102.01,2,3,4,5,6,7,9,10,11
22.0 – 99.62,12,13,14,15,17
29.8 – 62.05,6,18,19,20,21
NDF
449.8
475.5
494.8
473.4
359.0 - 557.11,2,3,4,5,6,7,8,9,11
355.0 - 586.02,12,13,14,17
400.2 – 584.5,6,20,21
ADF
337.3
351.8
375.7
354.9
264.5 – 466.51,3,4,5,6,7,8,9,10,11
279.0 – 462.72,12,13,14,15,16,17
264.6 – 473.05,6,20,21
HEM
129.0
113.0
133.9
125.3
95.0 – 189.81,4,8,10
113.0 – 113.012
57.0 – 210.86,19
CELL
197.1
258.7
238.6
231.5
116.2 – 242.01,4,10
230.3 - 287.012,14
191.2 - 286.06,19
LIG
106.6
113.1
108.0
109.2
65.1 – 141.4,2,3,4,6,7
93.0 - 171.02,12,14,15,16,17
78.5 – 182.06,19,20,21
Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006);
6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017);
11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012);
16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA
FILHO et al. (2012). Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006);
6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017);
11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012);
16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA
FILHO et al. (2012). Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Gomes et al. 4 leaf development and the plant location. They observed
N and K differences in the leaves at the beginning of
the senescence process compared with expanding or
completely expanded leaves, attributed to the nutrient
translocation, especially N from old to new leaves. Ciência Rural, v.52, n.3, 2022. Forage quality These
authors also reported that the main factor promoting
low degradability of NDF was the thickening and
lignification of cell walls, especially in stem tissues. As secondary compounds, da SILVA
(2016) reported the presence of steroids, saponins,
tannins and flavonoids in maniçoba leaves, with
differences in concentration among evaluated
accessions and leaf maturation stages. In addition,
BELTRÃO et al. (2015) reported total tannins
varying from 0.2 to 5.3% DM and HCN ranging
from 97.2 to 291.6 mg kg-1 DM in maniçoba, while
FRANÇA et al. (2010) observed tannin levels of
1.58 and 1.87% DM, respectively for maniçoba
in natura or hay, and reported an important anti-
nutritional action when they exceeded 5% DM in Macromineral levels in maniçoba are
shown in table 3. Nitrogen and potassium presented
the greatest contents, followed by calcium and
magnesium. According to ANDRADE et al. (2014), N
and K levels of maniçoba are influenced by the stage of Table 3 – Content of macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Mineral
------------------------------------------------Contents (g kg-1 DM)----------------------------------------------------
----------------Mean---------------
--------------Minimum------------
--------------Maximum---------------
Nitrogen1,2
30.74
17.26
40.30
Phosphorus4
2.54
1.46
4.28
Potassium 4
13.75
4.10
20.48
Calcium3
4.65
3.54
13.50
Magnesium3
4.45
3.60
5.45
Sulfur2
1.85
1.80
1.90
Sources: 1,4ANDRADE et al. (2014); 1,2,3,4ARAÚJO FILHO et al. (2011); 3,4FERREIRA et al. (2009); 3,4PARENTE et al. (2007) . f macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Table 3 – Content of macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Sources: 1,4ANDRADE et al. (2014); 1,2,3,4ARAÚJO FILHO et al. (2011); 3,4FERREIRA et al. (2009); 3,4PARENTE et al. (2007) . Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. 5 Table 4 - Micromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowth. Micromineral
-----------------------------------------------Contents (mg kg-1 DM)----------------------------------------------
----------------Mean--------------- --------------Minimum------------- ---------------Maximum--------------
Boron
14.40
9.46
18.6
Copper
20.40
17.72
22.04
Iron
239.13
125.19
644.10
Manganese
111.00
91.48
146.97
Zinc
129.61
106.15
228.75
Sodium
2,548.33
1,970.00
3,280.00
Source: LIMA (2019). Table 4 - Micromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowt icromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowth. Forage quality diets, indicating there is no negative effect of tannin
levels presented by maniçoba on DM digestibility. are also important to reduce HCN levels in the forage,
providing safe feed. The chemical composition of maniçoba
offers opportunities to perform studies aiming the
evaluation and selection of genotypes with lower
concentrations of hydrocyanic acid and lignin, and
greater degradability of fiber, as well as the evaluation
of crop management practices that increase the
degradability of the fibrous fraction. The high presence of cyanogenic glycosides
in maniçoba, when hydrolyzed, release hydrocyanic
acid (HCN) through the action of enzymes such as
ß-glucosidase (linamarinase), which may be poisonous
to animals, depending on the ingested quantity. Ingestion greater than 2.4 mg of HCN/kg of body
weight may cause several disorders (SOARES, 2000). i SOUZA et al. (2006) verified 972 mg kg-1
of HCN in maniçoba in natura (% DM) and 162 mg
kg-1 in silage (% DM), while SOARES (2000) reported
a reduction in HCN by over 65% in maniçoba silage
after the first 29 days of ensilage, reaching a reduction
of up to 78% after 174 days. According to MATOS
et al. (2005) the enzyme linamarinase is inactivated
by heat and the ensiling process also contributes to
the fermentation of glycosides by anaerobic micro-
organisms, reducing HCN concentration. Ciência Rural, v.52, n.3, 2022. Dry matter intake and productive performance of
goats and sheep (2008)
1,168.5
1,060.11**
Sheep
MACIEL et al. (2019)
1,066.92
1,060.11
Sheep
MACIEL et al. (2019)
1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al.,
2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. Gomes et al. 6 Table 5 – Dry matter intake (DMI) of goats and sheep fed diets based on maniçoba in comparison to diets based on the other roughages. DMI (g animal-1 day-1)
--------Animal specie-------
-------------------------Reference-------------------------
Maniçoba
----Others roughages----
----------------------------------------------------------------------------Hay--------------------------------------------------------------------------------------
839.8
799.041
Sheep
LIMA JÚNIOR et al. (2014)
544.2
415.91
Goat
LIMA JÚNIOR et al. (2015a)
545
5793
Goat
MOREIRA et al. (2008)
545
1784*
Goat
MOREIRA et al. (2008)
1,168.5
1,060.11**
Sheep
MACIEL et al. (2019)
1,066.92
1,060.11
Sheep
MACIEL et al. (2019)
1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al.,
2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al.,
2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al.,
2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. to 5.40% BW (ARAÚJO et al., 2004; CASTRO et al.,
2007; SILVA et al., 2007; MENDONÇA JÚNIOR et al.,
2008; ARAÚJO et al., 2009a; MOURA et al., 2020). performance, seeing that DMI determines the supply
of nutrients. Diets composed of maniçoba provided
up to 290 g day-1 of weight gain for feedlot sheep,
including 20 to 40% DM (CASTRO et al., 2007) or
30% DM of this roughage (CARTAXO et al., 2008). In addition, one study evaluated milk yield of goats
fed increasing levels of maniçoba in diets (30 to 60%
DM) (ARAÚJO et al., 2009b). Dry matter intake and productive performance of
goats and sheep Increasing maniçoba (% DM) in diets
promoted greater DMI (ARAÚJO et al., 2004) or
did not alter the DMI of sheep and goats (Table 6),
indicating this roughage can be included in considerable
proportion in diets, without harming the DMI. The results for productive performance
of sheep and goats fed maniçoba diets demonstrate
weight gain compatible to the one promoted by diets
comprising traditional roughages, and enable the
inclusion of considerable levels of this plant in animal
diets. In addition, other research fronts are important
to be pursued, providing a better understanding of the
maniçoba based diets for ruminants, regarding the
methane emission and the interactions of nutrition
and immunological or reproductive responses. Five studies evaluated the average weight
gain (ADG) (CASTRO et al., 2007; LIMA JÚNIOR
et al., 2014; MACIEL et al., 2019; MOREIRA et al.,
2008) of sheep or goats, comparing maniçoba based
diets to rations comprising other roughages, or assessing
increasing levels of maniçoba in diets (Table 7). In one of those studies, comparing maniçoba
hay with Tifton 85 in diets for Moxotó goats, LIMA
JÚNIOR et al. (2015a) reported that animals fed with
this roughage had -9 g day-1 of body weight variation,
while the Tifton 85 based diet (control diet) promoted
10 g day-1 of weight gain (Table 7), without statistical
difference for diets. The authors attributed the low
ADG promoted by both diets to a lack of adaptation
of the animals to the feedlot management, because
they had come from an extensive production system,
in addition to the advanced age of the animals, and
the low DMI presented by goats. Dry matter intake and productive performance of
goats and sheep Dry matter intake (DMI) data for goats
and sheep fed on maniçoba based diets (hay or silage)
were obtained from 13 studies (n = 46 treatments). In four of them maniçoba was compared to other
roughages (Table 5), while in nine increasing levels
of this forage in diets were evaluated, replacing
roughages (MENDONÇA JÚNIOR et al., 2008;
MOURA et al., 2020) or concentrates (CASTRO et
al., 2007; ARAÚJO et al., 2009a) (Table 6). Maniçoba silage can be made without using
additives promoting a proper fermentation process to
the ensiling mass, showing aerobic stability for up to 14
days after silo opening (SOUZA et al., 2006); although,
the use of additives, such as corn meal, can contribute to
the quality of the silage (BACKES et al., 2014). Maniçoba diets promoted similar DMI
compared to diets composed by others roughages
offered to goats and sheep, and even higher DMI when
compared to feed based on hay from feijão-bravo
(Capparis flexuosa L.) and gliricidia (Table 5), which
might be associated to the presence of anti-nutritional
factors, such as tannins and coumarins, respectively,
impairing the acceptance of the feed by the animals
(LIMA JÚNIOR et al., 2014; MOREIRA et al., 2008). In addition, MACIEL et al. (2019) reported greater
DMI by sheep fed maniçoba hay based diets compared
to a Tifton 85 based diet (Table 5). Similarly, FRANÇA et al. (2010) reported
HCN values of 512.83 and 86.34 mg kg-1 DM for
maniçoba in natura or hay, respectively. During the
haying process, the plant is chopped and dehydrated
promoting the HCN volatilization by the action of
sunlight and wind (ARAÚJO et al., 2004). The use
of maniçoba silage or hay did not affect the DMI
and the average daily gain of sheep (MACIEL et al.,
2019). Therefore, both conservation strategies (hay or
silage) can be offered to ruminants, seeing that they On average, DMI promoted by maniçoba
diets was 4.30% body weight (BW), ranging from 2.85 Ciência Rural, v.52, n.3, 2022. 6
Gomes et al. Table 5 – Dry matter intake (DMI) of goats and sheep fed diets based on maniçoba in comparison to diets based on the other roughages. DMI (g animal-1 day-1)
--------Animal specie-------
-------------------------Reference-------------------------
Maniçoba
----Others roughages----
----------------------------------------------------------------------------Hay--------------------------------------------------------------------------------------
839.8
799.041
Sheep
LIMA JÚNIOR et al. (2014)
544.2
415.91
Goat
LIMA JÚNIOR et al. (2015a)
545
5793
Goat
MOREIRA et al. (2008)
545
1784*
Goat
MOREIRA et al. Ciência Rural, v.52, n.3, 2022. Quality of animal products Using maniçoba for sheep did not result in
changes in carcass traits (LIMA JÚNIOR et al., 2014;
MACIEL et al., 2015) and non-carcass components
yield (MACIEL et al., 2015) when compared to Tifton
85 hay based diets, neither were there changes in the
yield of “buchada” and “panelada” (typical dishes using
organs and viscera) (LIMA JÚNIOR et al., 2015a). The productive performance of animals
receiving maniçoba diets was similar when compared
to the other roughages or increasing levels of this
roughage in diets in all studies, except MOREIRA et
al. (2008), who observed greater ADG for goats fed on
a diet based on maniçoba hay compared to a gliricidia
based diet, due to the greater DMI (Table 7). The
food consumption of animals fed maniçoba diets
is an important factor influencing the productive Increasing maniçoba in diets (35 - 70%) for
Moxotó and Canindé goats did not alter the centesimal
composition, final pH and color of the meat (LISBOA
et al., 2010), evincing proper digestive and metabolic
responses. The replacement of spineless cactus by
maniçoba in sheep diets did not change the physical-
chemical composition of the meat, its color or the
weight loss in cooking (MOURA et al., 2020). Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. 7 Table 6 – Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry
matter). Table 6 – Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry
matter). Levels (% DM)
-----Dry Matter Intake (g day-1)----
-------Animal specie-------
------------------Reference------------------
---------------------------------------------------------------------Maniçoba hay------------------------------------------------------------------
30
591.0
Sheep
ARAÚJO et al. (2004)1*
40
604.0
50
633.0
60
683.0
70
710.0
20
1240.0
Sheep
SILVA et al. (2007)1
40
1240.0
60
1200.0
80
1300.0
20
1160.0
Sheep
CASTRO et al. (2007)1
40
1280.0
60
1220.0
80
1190.0
30
1940.0
Goat
ARAÚJO et al. (2009a)1
40
2060.0
50
1910.0
60
1910.0
0
845.8
Sheep
MENDONÇA JÚNIOR et al. (2008)2
50
912.8
100
960.6
0
1290.0
Sheep
SANTOS et al. (2021)1
10
1270.0
20
1240.0
30
1430.0
0
1022.8
Sheep
MOURA et al. (2020)1
20
1146.0
40
1183.4
60
1134.8
--------------------------------------------------------------------Maniçoba silage---------------------------------------------------------------
60
470.0
Goats
LOIOLA FILHO et al. Quality of animal products (2012)1
70
500.0
80
470.0
90
430.0
25
957.0
Goats
MATIAS et al. (2020)2*
50
1113.0
75
1127.0
100
1220.0
*Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage
portion in diets. *Diet exclusively composed by roughages. Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry
matter) *Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage
portion in diets. *Diet exclusively composed by roughages. *Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage
portion in diets. *Diet exclusively composed by roughages. MOURA et al. (2020), based on sensory
evaluation of lamb meat, reported greater purchase
intention for meat of lambs fed on diets with greater
inclusion of maniçoba in comparison to the spineless
cactus based diets, evincing greater consumer preference,
indicating the meat of lambs fed maniçoba hay diets has
adequate equilibrium in sensory parameters as color, aroma, tenderness, juiciness, and flavor. Additionally,
MADRUGA
et
al. (2006)
reported
adequate
polyunsaturated fatty acid levels and polyunsaturated /
saturated fatty acids for sheep fed maniçoba diets. An inclusion of maniçoba of up to 60%
DM in diets for lactating goats did not modify
the physical-chemical composition (proteins, fat, Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Gomes et al. 8 Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others
roughages or increasing maniçoba levels in diets. Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others
roughages or increasing maniçoba levels in diets. Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others
roughages or increasing maniçoba levels in diets. ------------------------------------------------------------------Average weight gain (g day-1)----------------------------------------------------------------
Animal specie
-----Maniçoba-----
-------Others roughages------
-Inclusion level (% DM)-
--------------Reference---------------
Sheep
122.05
139.01,5
40
LIMA JÚNIOR et al. (2015b)
Sheep
146.18
153.31
30
Sheep
135.3
153.31
30
MACIEL et al. (2019)
Goat
181a
187a2
30
MOREIRA et al. (2008)
181a
60b3
30
181a
50b4
30
Goat
-9.07
10.01
40
LIMA JÚNIOR et al. ACKNOWLEDGEMENTS lactose, dry extract, density and acidity) of the milk
(ARAÚJO et al., 2009b; COSTA et al., 2008), nor
the fatty acid contents (saturated, monounsaturated
and polyunsaturated) (MESQUITA et al., 2008),
or the sensorial parameters (odor, taste and overall
appearance) (COSTA et al., 2008). We thank FACEPE for the scholarship of the first
author IBPG-1424-5.04/18. This study was also financed in part by
the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
(CAPES), Brasil– Finance code 001. Therefore, the use of maniçoba for goats
and sheep has not promoted changes in qualitative
parameters of animal products, especially meat and
milk, compared to traditional roughages. Further
studies are important to increase the database for this
forage plant on quality of animal origin products. CONCLUSION The author M L R Gomes was responsible for structuring
the manuscript. The authors M L R Gomes and L C Souza wrote topic
2 (Productivity and factors that affect the yield). The authors F C
Alves, C M Souza and M N P Silva wrote the topics 3 (Forage quality)
and 4 (Dry matter intake and productive performance of goats and
sheep). The authors J R V Silva Filho and R A Santana Júnior wrote
topic 5 (Quality of animal products). The author T V Voltolini was
responsible for correcting all topics and structuring the manuscript. Maniçoba presents forage productivity
that may contribute to livestock production systems
in the Brazilian semiarid, besides providing forage with
adequate nutritional value. Its use in diets for sheep
and goats has allowed dry matter intake, productive
performance, and quality animal products similar to the
ones provided by traditional forage resources, such as
Tifton 85 or spineless cactus, reinforcing the possibility
of its use in the sheep and goat production systems. Quality of animal products (2015a)
Sheep
290.84
-
20
CASTRO et al. (2007)*
293.62
-
40
253.35
-
60
208.48
-
80
--------------------------------------------------------------------Milk yield, kg day-1--------------------------------------------------------------------------
Goat
1.40
-
30
ARAÚJO et al. (2009b)
1.45
-
40
1.33
-
50
1.36
-
60
1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by
Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at
slaughter – initial body weight) / number of days. 1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by
Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at
slaughter – initial body weight) / number of days. 1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by
Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at
slaughter – initial body weight) / number of days. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. Produção, respostas morfofisiológicas, composição
química e cinética de fermentação de acessos de plantas do gênero
Manihot. 2019. 42f. Dissertação (Mestrado em Ciências Veterinárias
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https://openalex.org/W2086802919 | https://www.scielo.br/j/ref/a/t4CcKRNnRRnrCYLgc5HJRrM/?lang=es&format=pdf, https://periodicos.ufsc.br/index.php/ref/article/download/S0104-026X2007000300003/1084 | es | Los discursos masculinos como dispositivos de control y tensión en la configuración del liderazgo y empoderamiento femenino | Revista Estudos Feministas | 2,007 | cc-by | 9,023 | Paulina Irene Salinas Meruane
Escuela de Periodismo de la Universidad Católica del Norte, Chile
Los discursos masculinos como
dispositivos de control y tensión
en la configuración del liderazgo y
empoderamiento femenino
Resumen
esumen: En el presente artículo se exponen algunos de los antecedentes centrales del proyecto
de investigación “Los Discursos de la Masculinidad”: El Empoderamiento Femenino desde el
Análisis Critico del Discurso.1 Utilizando un enfoque cualitativo, se desarrollaron entrevistas abiertas
con el objetivo de comprender el significado que le asignan los hombres al liderazgo femenino.
Los discursos fueron analizados en base a la Teoría Fundamentada de Anselm Strauss y Juliet
Corbin (2003).2 Los resultados muestran que los varones coinciden en términos generales respecto
a los cambios que ha habido en los roles de género, en que las mujeres tienen y deben tener
más oportunidades, en que hay una mayor incorporación de éstas en el mercado laboral y en
la necesidad de tener relaciones más equitativas al interior de la familia. Así mismo, emergen
tensiones que configuran el malestar de la masculinidad, traspasando la esfera íntima y
cuestionando las relaciones de intergénero actuales. También hay discursos más progresistas
en los varones, que se aventuran hacia un reconocimiento de las capacidades y roles que han
ido asumiendo las mujeres en el espacio público, aunque se trata de un reconocimiento vigilante,
ambivalente, mediatizado por una percepción de confianza/desconfianza, eficiencia/
incompetencia, hacia lo que ellas son capaces de lograr.
Palabras claves
claves: empoderamiento; transformaciones; genero
Copyright ¤ 2007 by Revista
Estudos Feministas.
1
Investigación realizada entre el
2005 y 2006 y que contó con el
financiamiento de la Dirección
General de Investigación y
Postgrado de la Universidad
Católica del Norte, Antofagasta.
2
STRAUSS y CORBIN, 2003.
2
STRAUSS y CORBIN, 2003.
Introducción
En el presente artículo se exponen algunos hallazgos
obtenidos en el proyecto de investigación: Los Discursos
de la Masculinidad: El Empoderamiento Femenino desde
el Análisis Crítico del Discurso, realizado el 2006. Este trabajo
se enmarca en una línea investigativa que se desarrolla
desde el 2003, periodo en el que se abordó la comprensión
del liderazgo de las mujeres en organizaciones de la I y II
región de Chile. Dicho trabajo permitió describir el liderazgo
femenino e identificar fortalezas y debilidades en el ejercicio
Estudos Feministas, Florianópolis, 15(3): 336, setembro-dezembro/2007
541
PAULINA IRENE SALINAS MERUANE
3
Norman FAIRCLOUGH y Ruth
WODAK, 2000.
del mismo. Luego nos plateamos avanzar en la comprensión
de este fenómeno, teniendo en cuenta dos premisas
centrales: la primera, que las preguntas acerca de las
mujeres implica comprender la perspectiva de los varones,
ya que el género es un sistema de interacciones sociales y
no un sistema de compartimientos estancos, es decir, lo
que afecta a unas implica a otros. Y la segunda, referida a
concebir el lenguaje y el habla como una forma de práctica
social, es decir se trata de desentrañar la relación dialéctica
entre un suceso discursivo particular y las situaciones,
instituciones y las estructuras sociales que lo enmarcan.3
En consecuencia, analizar la práctica discursiva de
los hombres sobre el liderazgo y empoderamiento femenino
es un factor significativo en la comprensión subjetiva de
este fenómeno y ayuda a develar el lenguaje como
productor y reproductor de las relaciones de poder
desiguales.
Dicho esto, el artículo se centra en analizar los
significados que le asignan los hombres al empoderamiento
femenino, las tensiones, ambigüedades y mecanismos de
control que tienen respecto a las transformaciones en el
ejercicio del poder femenino. Nos interesó profundizar
desde la perspectiva masculina, ¿cómo perciben los
varones el poder personal que han alcanzado las mujeres?,
¿hay transgresiones y/o reivindicaciones en el empoderamiento femenino?, ¿qué obstáculos reconocen ellos en
este proceso? La perspectiva de análisis desde los discursos
masculinos se centra en la búsqueda de una comprensión
holística del fenómeno del liderazgo y participación
femenina, entendiendo la perspectiva de género como
una categoría relacional de todos los procesos y fenómenos
sociales, y no sólo como un tema que se constriñe a la
configuración de las identidades y roles.
Este estudio presenta algunos adelantos en este
sentido, ya que se plantea la comprensión de los aspectos
subjetivos relacionados a la conformación del liderazgo,
teniendo presente que se han producido transformaciones
significativas, vinculadas con el cuestionamiento que
elaboran los varones acerca de las demandas que se les
hace como hombres, lo que representa una expresión de
malestar o una cierta perplejidad que se extienden más
allá de la esfera íntima y que los interpela en el ejercicio
de roles en tanto hombres, padres, parejas, amigos.
El contexto discursivo
La producción y comprensión del discurso implica
tomar en cuenta el contexto, y particularmente en lo que
respecta al empoderamiento de las mujeres en América
542 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
Ximena MACHICAO Barbery,
2006.
4
5
PNUD, 2004; INE, 2002; OIT, 2000.
6
José OLAVARRÍA, 2001b, p. 31.
latina debe hacerse referencia al elemento sincrónico del
proceso, ya que efectivamente se han producido
transformaciones importantes desde la segunda mitad del
siglo XX en adelante. Tanto en América Latina como el
Caribe se observa una apertura política que se traduce en
una mayor incorporación de las mujeres a los espacios de
poder, en cargos de ministras en Chile, Argentina, Brasil,
Bolivia y Uruguay; en el área legislativa, judicial, en los
gobiernos municipales o proyectándose como candidatas
a la presidencia o vicepresidencia, como fue el caso de
México y Costa Rica, lo que junto a la larga historia que
tienen luchando por una mayor participación y
representación política, dan cuenta de que se han
producido transformaciones en favor de una ruptura de la
hegemonía masculina en el ejercicio del poder político.4
En esta dirección, en marzo 2006 se marca un hito
en la historia política del país: por primera vez una mujer
logra ser elegida presidenta de la república, siendo este
hecho en si mismo un avance sin precedentes para las
mujeres, y que sólo el análisis posterior de la historia podrá
dimensionar en toda su magnitud. Sin embargo, instalado
el gobierno de Michelle Bachelet, es oportuno analizar la
conflictiva relación de las mujeres y el poder y las
reivindicaciones y transgresiones que esta analogía
provoca.
En este sentido, si presentan algunos antecedentes
preliminares para comprender la dimensión de este
fenómeno, y si apuntan a una transformación de los códigos
culturales del país y a una democratización real de la
sociedad, o estamos presenciando algunos cambios para
que todo permanezca igual. Diversos estudios coinciden
favorablemente en que en Chile se ha producido un
aumento gradual tanto de la participación como del
liderazgo femenino en las distintas áreas del quehacer
nacional. Por ejemplo en el ámbito laboral, la incorporación
de las mujeres experimentó, durante la década de los mil
novecientos noventa, un incremento sustantivo desde un
28,06% en 1992 a un 35,5% en el año 2002, lo cual marca
un incremento superior a 7 puntos porcentuales.5
También en la política un enclave eminentemente
masculino ha sido levemente modificado, con la inclusión
de la paridad como principio articulador del poder
ejecutivo – léase ministerios, intendencias, gobernaciones.
En cambio, se constatan resistencias en sectores
como las organizaciones sindicales, las que siguen
controladas por los varones que son quienes articulan los
espacios y redes de homo sociabilidad y, en general, lo
mismo se observa en los puestos de mayor jerarquía
pública.6
Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
543
PAULINA IRENE SALINAS MERUANE
7
Teresa VALDÉS y Mariza
WEINSTEIN, 1993; Olga RUIZ,
Sandra SOLANO y Claudia
Zapata, 1998; SERNAM, 2000;
GIM, 2002; VALDÉS, 2001; Paulina
SALINAS, 2002; PNUD, 2004.
8
PNUD, 2004, p. 87.
9
PNUD, 2004, p. 17.
10
Mala HTUN, 2003.
Otros estudios profundizan las complejidades que
han experimentado las mujeres en su lucha por alcanzar
un mayor protagonismo y reconocimiento en la sociedad.7
Estas investigaciones develan las tensiones que han existido
entre las mujeres y su acceso a los espacios de poder.
Algunos de los argumentos que se arguyen para explicar
este fenómeno se relacionan con pesados lastres y grandes
brechas que caracterizan la distribución de recursos y
derechos existentes en la sociedad chilena.
El quinto Informe sobre Desarrollo Humano identifica
dos elementos que frenan un mayor y mejor aprovechamiento de las oportunidades que el país ofrece, y que
se relacionan con la insuficiente disposición de poder social
y una desigual distribución del poder de acción personal,
ambas afectando la capacidad de los ciudadanos para
aprovechar las oportunidades y levantando barreras a la
asociatividad.8
Otras amenazas más imperceptibles se vinculan a
la permanencia del statu quo de parte de quienes no
quieren ceder poder: el temor a entregar poder a otras
personas, especialmente a las mujeres, y a las
organizaciones. Hay desconfianza en las capacidades de
estos actores para tomar decisiones.9 Otras resistencias son
hacia lo que implica promover la participación ciudadana,
sean estas en iniciativas colectivas o individuales; hay temor
al “desborde”, a los pliegos de peticiones, al aumento de
expectativas, entre otras.
Por lo tanto, analizar los avances y retrocesos en el
proceso de empoderamiento y construcción ciudadana
de las mujeres como sujetos políticos con relevancia social,
facilita la comprensión de los cambios en su verdadera
dimensión como una manera de visualizar los desafíos que
tiene la sociedad chilena en su conjunto, entendiendo que
los avances en la consolidación de la democracia están
entramados al desarrollo sostenible y a un crecimiento
económico equitativo.
Sin embargo, la mayor libertad política y la
promoción de mercados más liberalizados no han
desencadenado directamente avances sustantivos en
cuanto a los derechos ciudadanos, ni respecto al bienestar
económico de la población en su conjunto. De hecho
plantea Mala Htun que en la medida que las brechas
salariales se incrementan, muchas mujeres en
Latinoamérica carecen de las capacidades básicas y
permanecerán excluidas de los sectores elegibles para
ocupar cargos de mando.10
Por ejemplo, no es menor que, no sólo en el país,
sino que en el resto del mundo las mujeres, aunque
representan más de la mitad del electorado, apenas
544 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
11
MACHICAO, 2006, p. 20.
12
PNUD, 2004, p. 21.
13
OLAVARRÍA, 2001b, p. 24.
14
Robert W. CONNEL, 1998, p. 77.
alcanzan al 12,7% del total de bancadas parlamentarias
en el mundo, y que en América Latina no logran el 10%. Si
bien en algunos países como Argentina y Costa Rica
muestran logros importantes, en otras naciones los progresos
han sido relativos o nulos, a pesar de las medidas de
discriminación positiva, que de hecho no tienen un carácter
vinculante a la Constitución Políticas de los Estados. Por lo
tanto, su aplicación se encuentra supeditada a la voluntad
de los gobiernos de turno. 11 En este contexto, cabe
preguntarse para el caso chileno, en qué medida la
pariedad introducida por el gobierno de Bachelet por
ejemplo, ¿es una iniciativa que perdurará en el tiempo?,
¿será que la presencia de las mujeres en el poder ejecutivo
marcará la agenda pública?, ¿cuáles son los obstáculos
que enfrentan en los puestos de poder?, ¿la mayor
presencia de las mujeres en cargos de representación
conlleva modificaciones en los mandatos de género?, es
decir son múltiples los cuestionamientos plausibles de
hacerse y las sospechas que se generan sobre el tipo de
política que se está construyendo en el país. Además, las
alianzas políticas femeninas no siempre han logrado resistir
con éxito las exigencias partidarias con la inclusión de
temas que favorezcan los derechos de las mujeres.
Estas interrogantes permiten abrir la discusión hacia
esferas que hoy día son gravitantes para el desarrollo y la
consolidación del sistema democrático. Chile ha tenido
logros importantes en materia de indicadores sociales, ha
alcanzado un destacado posicionamiento en cuanto al
Desarrollo Humano en el contexto latinoamericano,12 a lo
que se suma un mejoramiento en la búsqueda de un mayor
equilibrio en las relaciones entre hombres y mujeres,
producto de la evolución económica, social y cultural de
la sociedad chilena y del mundo en general.13 Tanto la
globalización como los cambios de la economía han
potenciado demandas de modernización en el espacio
íntimo, cuestionándose las bases de la masculinidad
autoritaria y la familia nuclear patriarcal, por perpetuar esta
última la inequidad, limitar la autonomía, la diversidad y
las relaciones democráticas al interior de la familia.
Asimismo, los debates respecto a las relaciones de género
se están produciendo globalmente. Las relaciones de
género forman parte de la estructura de la sociedad
mundial y es necesario reconsiderar muchos temas a la luz
de este hecho.14
Junto a lo anterior, la sociedad chilena también
presenta irrefutables fracturas, una inequitativa distribución
de los ingresos, insuficiente política de igualdad de
oportunidades, entre otras. En consecuencias, hoy día es
una condición sine qua non del desarrollo humano
Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
545
PAULINA IRENE SALINAS MERUANE
fortalecer la participación ciudadana, entregando más
poder a cada uno y a la sociedad en su conjunto.
Estrategia metodológica y corpus
15
WODAK, 2003, p. 19.
16
Ron SCOLLON, 2003.
17
Teun A. VAN DIJK, 1997, p. 15.
18
Angelika HENNECKE, 2004, p.
107.
19
FAIRCLOUGH y WODAK, 2000.
20
Lupicinio IÑIGUEZ Rueda, 2003,
p. 94.
Como mencionamos anteriormente, la propuesta
investigativa se inscribe dentro del Análisis Critico de Discurso
(en adelante ACD), concebido éste como un enfoque que
se ocupa de develar las relaciones de dominación,
discriminación, poder y control, tal como se manifiesta a
través del lenguaje. En otras palabras plantea Wodak,15 el
ACD se propone investigar de forma crítica la desigualdad
social tal como viene señalada, expresada, constituida,
legitimada por los usos del lenguaje.
El lenguaje acompaña frecuentemente a nuestras
acciones, y las acciones acompañan gran parte de lo que
decimos. 16 Así entonces, el ACD propone analizar
críticamente el discurso como una forma de abordar los
problemas sociales que se van concadenando en los
discursos. Vale decir nos interesó analizar qué y cómo
hablan los hombres respecto a las transformaciones en el
empoderamiento de las mujeres, cómo discursean sobre
los cambios que se han experimentado ellas en la sociedad,
qué tensiones se generan, y cómo viven esta experiencia
tanto en el ámbito público como privado.
El ACD es la denominación genérica que se aplica
a un planteamiento especial dedicado a estudiar los textos
y el habla y que emergen de la crítica lingüística, semiótica,
y, en general, del modo sociopolítico consciente y oposicionista en que se estudia el lenguaje, el discurso y la comunicación.17 La ampliación de la lingüística del texto pragmático – comunicativa por el Análisis Crítico del Discurso –
consiste en que ésta le permite visualizar la relevancia social
y política de los textos, faculta mostrar una dimensión de
significado que sobrepasa el encasillamiento a un marco
situacional, concreto y actual.18 Es una forma de intervenir
en la práctica social y en las relaciones sociales.19 Es
considerado una práctica tridimensional, en el sentido que
la práctica analítica opera en tres dimensiones: a) el
discurso en tanto texto, b) el discurso como práctica discursiva enmarcado en una situación social concreta, y el
c) el discurso como un ejemplo de práctica social, que no
sólo expresa o refleja identidades, prácticas, relaciones,
sino que la constituye y conforma.20
A la luz de esta propuesta analítica se desarrolló un
estudio descriptivo con fines interpretativos, es decir, una
propuesta investigativa eminentemente cualitativa, en la
que se concibe la realidad social como subjetiva, múltiple
y cambiante, como resultado de una construcción de los
546 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
José Ignacio RUIZ, 1999; Miguel
S. VALLES, 2000; María Paz SADÍN
Esteban, 2003.
21
22
STRAUSS y CORBIN, 2002.
23
RUIZ, 1999, p. 64.
24
STRAUSS y CORBIN, 2002.
sujetos participantes que se encuentran en interacción con
otros miembros de la sociedad.21
El corpus del estudio estuvo conformado por los
discursos de 59 hombres. En la primera fase investigativa
se aplicaron 20 entrevistas individuales en profundidad,
durante el 2005. Esta etapa se desarrolló en forma
secuencial (comparación constante),22 de tal manera que
una vez que la primera entrevista fue realizada, se procedió
a su trascripción y análisis preliminar; de este modo la
segunda entrevista incorporó los aportes de la primera y
así sucesivamente. Luego en una segunda fase, durante el
2006, se entrevistaron 39 hombres en cuatro entrevistas
grupales, de tal manera de triangular la información
obtenida en la modalidad individual y así acceder al
discurso social de los varones.
Para seleccionar a los entrevistados se utilizó un
muestreo cualitativo intencional,23 buscando distintos representantes del universo masculino en la región. Se entrevistó
en la modalidad individual a varones, con distintos niveles
socioeducacionales, nueve profesionales universitarios,
cinco con formación técnica, tres estudiantes universitarios
y tres con cuarto año medio rendido. Las edades fluctuaron
entre los 19 y los 63, con edad promedio de 40 años.
En la primera entrevista grupal participaron 10
varones, cuyas edades fluctúan entre 21 y 46, con un
promedio de 30 años, todos tienen cuarto año medio
rendido y se desempeñan como operarios en la empresa
C.S.M, Tecnología Ltda. de Antofagasta. En la segunda,
participaron 14 varones, cuyas edades fluctúan entre 39 y
56 años, y 46 años de edad promedio, el nivel de
escolaridad de los participantes es de enseñanza básica
(5), enseñanza media (6) y algunos tiene formación técnica
(3). En la tercera, participaron 7 varones, cuyas edades
fluctúan entre los 32 y 49 años, y 38 años de edad promedio.
Se desempeñan como auxiliares de servicio en el Liceo
Experimental Artístico de Antofagasta. El nivel de escolaridad
de los entrevistados es enseñanza básica completa (3),
enseñanza media incompleta (3) y completa (1). Y en la
cuarta entrevista participaron 8 varones que se
desempeñan como personal en la Cárcel de Hombres de
la ciudad de Antofagasta (gendarmes y vigilantes), cuyas
edades fluctúan entre 19 y 43 años, con 29 años de edad
promedio. Todos poseen cuarto año medio rendido.
El análisis de los datos complementó dos propuestas:
la primera corresponde a la utilización de una teoría base
de análisis cualitativo como la Teoría Fundamentada, de
Barney Glaser y Anselm Strauss,24 identificando de esta
manera las prácticas sociales de los sujetos; luego para
comprender las prácticas discursivas y textual se hizo una
Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
547
PAULINA IRENE SALINAS MERUANE
25
JÄGER, 2003.
26
Luis Enríque ALONSO, 2003, p.
204.
CONNELL, 1998; OLAVARRÍA,
2001a, 2001b, 2005; María José
MORENO Ruiz, 2001.
27
28
OLAVARRÍA, 2005.
aproximación de acuerdo a la propuesta de ACD de
Siegfried Jäger.25 Esta aproximación implicó rescatar los
elementos más significativos y pertinentes para el estudio.
Por lo tanto, nos centramos en identificar el hilo discursivo,
su caracterización y la combinación de un análisis global
y fino de la textualidad de los discursos de los hombres.
Estas propuestas de análisis fueron apropiadas para
la investigación, ya que generaron resultados que describen
el fenómeno y permiten establecer relaciones teóricas. Se
trató de situar los discursos no sólo en consideración al
marco situacional, sino que también a los propios sujetos y
sus subjetividades.26
Resultados y análisis: hilando los discursos
Casi dos décadas después de los avances
experimentados en las sociedades industrializadas, se
inician los estudios sobre la masculinidad en Chile, sobre
todo los referidos a la construcción de la identidad de
género de los hombres. Sirviéndose de los adelantos ya
alcanzados en otros contextos, ha comenzado un interés
creciente en distintas universidades y centros de estudios
del país por abordar interrogantes sobre sí la masculinidad
se encuentra en crisis, cómo se construye hoy la masculinidad. ¿Hay una nueva masculinidad?
Más que responder estos cuestionamientos
exhaustivamente abordados por diferentes autores 27
concluyen sobre las transformaciones que se han
experimentado en las identidades de género y que están
estrechamente vinculadas a procesos estructurales como
la globalización, la sociedad de la información y el modelo
neoliberal. Asimismo, los estudios realizados en Chile
expresan que, aunque los hombres se muestran proclives
a las demandas de las mujeres, en la vida cotidiana no se
advierten cambios significativos, ya que ellas siguen siendo
las principales responsables de lo doméstico y de la crianza
de los hijos. Igualmente se confirma una cierta fragilidad
en los discursos que hablan de una nueva masculinidad,
ya que no tienen un correlato empírico que los sustente.
Más aún, aspectos como la intensidad del lazo amoroso
tendría un papel preponderante en la relación de pareja,
de manera que facilitaría negociar de mejor manera la
participación del varón en la unidad doméstica.28
A partir de estos hallazgos, nos centramos, en
aquellas transformaciones de la masculinidad que han
provocado una ruptura en la exclusividad de los espacios
de poder que históricamente eran asignados a los hombres,
tanto en el ámbito público como en el privado,
configurándose nuevas formas de relacionarse en el interior
548 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
Kathia ARAUJO y Francisca
ROGERS, 2000, p. 60.
29
de la familia, en el ámbito laboral y en las distintas esferas
de sociabilidad. Estos procesos de fracturas socioculturales
han modificado los equilibrios previos, surgiendo nuevos
órdenes de género en los que se cuestionan algunos valores
como la masculinidad hegemónica, el autoritarismo, la
violencia intrafamiliar, entre otros.
Estas variaciones han sido referidas por algunos
autores como una ruptura de ciertos sustentos estructurales
que se acompañan por la pérdida de los significados de
la masculinidad, develando distintas formas de ser hombre,
ampliando las identidades y las formas de construir lo
masculino.29
Desde aquí se propuso en este estudio hacer un giro
respecto a la tendencia que se ha dado en las
investigaciones de género, en el sentido de abordar estas
temáticas generalmente en forma dicotómica, ya sea lo
femenino o lo masculino. En este sentido buscamos
destacar el carácter relacional de los cambios, ya que han
desencadenado modificaciones en la construcción de
identidades de hombres y mujeres marcadas por las
transgresiones, rupturas resistencias de género, que están
lejos de lograr un acomodo social, por lo tanto, avanzar
en su análisis posibilita su abordaje y comprensión.
Dicho esto, a continuación presentaremos una
síntesis sobre algunos resultados del estudio que se
aproximan a delinear las tensiones en los espacios de poder
y liderazgo femenino, desde la textualidad masculina.
Los caminos zigzagueantes de las mujeres
al poder: entre el control y la tensión
Irene VASILASCHIS DE GIALDINO,
2003.
30
En los discursos analizados, tienen como elemento
transversal la dificultad de los hombres para hablar desde
el yo; la tendencia es que ellos se explayan en un lenguaje
general que no los interpela en sus experiencias individuales. El hilo discursivo que cruza el habla masculina está
marcado por una serie de oposiciones30 personal/impersonal, particular/general afirmativo/negativo, gusto/disgusto,
aceptación /rechazo. Esto queda de manifiesto en formulaciones ambivalentes respecto a las percepciones que
tienen sobre el poder alcanzado por las mujeres en los
ámbitos laborales, políticos y familiares.
Los hombres elaboran un discurso proactivo,
favorable al cambio de roles que se ha experimentado en
la sociedad chilena, que ha impulsado la incorporación
de las mujeres al mercado laboral, pensando en las
transformaciones como un proceso normal de evolución
hacia un mayor protagonismo de las mismas.
Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
549
PAULINA IRENE SALINAS MERUANE
31
Entrevista individual, hombre 62
años.
32
María Asunción GONZÁLEZ DE
CHÁVEZ Fernández, 1998, p. 16.
33
Entrevista individual, hombre 60
años.
34
Entrevista individual, hombre 55
años.
Paulina SALINAS y Susana
ARANCIBIA, 2006.
35
Las mujeres estaban relegadas a la casa y no podían
votar, no tenían ninguna participación ciudadana, no
tenia ningún tipo de decisión cívica, era difícil que ellas
llegaran a acceder al poder, pasan los años y la mujer
se comienza a incorporar a la fuerza laboral, más aún
de manera más formal, accede más a la educación,
antes era muy difícil.31
Los conflictos de las mujeres de hoy están vinculados
con las restricciones impuestas al modelo de mujer/
feminidad vigente, con las dificultades que presentan ellas
para descubrir/aceptar/expresar sus deseos al margen de
dicho modelo, y con la vigencia de una organización social
y una identidad masculina, compartida por las mujeres,
que no permite el cuestionamiento real del statu quo, al no
integrar como responsabilidad y (dis) valores “femenino”,
estigmatizados y/o hiperdemandado a las mujeres que
luchan por un nuevo modelo social y de género.32
Como ejercen el poder hoy día las mujeres… yo creo
que siempre, sin perder su rol femenino y yo creo que
eso les ayuda mucho, yo te diría esa coquetería innata
que tiene la mujer, no puede perderla; aunque pudiera
mandar, porque ya me veo una niña buenamoza te
fijas, y es la jefa más encima.33
Ahora hay mujeres que han alcanzando, cargos que
antiguamente ni siquiera se habían soñado. Pienso que
las mujeres son muy capaces en los puestos son más
metódicas, son, “menos corruptas” que los hombres,
desde mi punto de vista personal, yo creo que están
entrando en una esfera donde ya no deberían haber
muchos distingos de sexo.34
Junto a esta visión proactiva al cambio de roles de
las mujeres en la sociedad se devela en los discursos
también la vigencia de mandatos socioculturales que las
constriñen en un imaginario social masculino de: mujer/
madre/feminidad, configurándose, entonces, un proceso
dinámico, transformador, con elementos de control y
tensión, ruptura y continuidad en las relaciones entre los
géneros. En otras palabras, en los discursos se constata la
vigencia de la perspectiva esencialista en los hombres, y
que circunscribe a estas últimas a una identidad de mujer,
pasiva sensible, femenina, correspondiente con una
identidad homogénea construida desde la estructura
patriarcal y que retrotrae a las mujeres al espacio privado
como principales responsables de las tareas domésticas y
reproductivas, y con una marcada distribución sexual de
los roles.35
Mi esposa hace poco se puso a trabajar, hace poco,
yo creo que hace un año más o menos. La percepción
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LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
36
37
38
39
Entrevista grupal Nº 2.
que tengo de este asunto, personalmente, hemos tenido
algunos problemas por el asunto, por el problema de
que ahora que ella… aparte del dinero que yo le
entrego, ella ahora recibe su dinero cierto, pero ahora
por ejemplo a veces tenemos conversaciones, y ella
como que se pone muy altanera, o sea como que ahora
como que dispara más de lo que se disparaba antes.
Yo creo que como se puede decir vulgarmente, como
que se creen el cuento.36
Entrevista grupal Nº 2.
Tiene su pro y su contra que la mujer trabaje. Yo ahora
estoy teniendo problemas por ese asunto, porque yo
siempre llevé el dinero a la casa, cierto yo, o sea, no es
que ella me pase a llevar, sino como que ella tiene
otra percepción de este asunto; digamos ahora, según,
como que se pone más altanera, así ya, me levanta
más la voz, y uno que es..., yo me considero un hombre
machista, para mi es molesto.37
Entrevista grupal Nº 3.
Por mi parte, no me gustaría que la mujer trabajara o
sea, yo no soy machista, pero yo creo que el hombre
es el que, que las lleva en la casa, uno le da alimento
a ella, porque la mujer cría los hijos.38
SALINAS y ARANCIBIA, 2006.
GONZÁLEZ DE CHÁVEZ, 1998, p.
15.
40
Estas resistencias, como decíamos, se traslapan con
discursos más progresistas en los varones que se aventuran
hacia un reconocimiento de las capacidades y nuevos roles
que han ido asumiendo las mujeres en el espacio público,
aunque se trata de un reconocimiento vigilante,
ambivalente, ya que está mediatizado por una percepción
de confianza/desconfianza, eficiencia/incompetencia,
hacia lo que ellas son capaces de lograr, lo que, muchas
veces, también es autoreferido por las propias mujeres.39
De ello se infiere la actualidad que tiene en la identidad
femenina una construcción en la que preexiste una
naturaleza o una esencia femenina o masculina, subsidiaria
de un orden simbólico dado, también construido, y, por
tanto, no único posible e inmodificable. Tales identidades
van enraizadas a un sistema de representaciones y a
elaboraciones culturales que sirven de base y las
cimentan.40
Estas representaciones ambiguas tienen altos costos
afectivos y emocionales para las mujeres y que redundan
en insatisfactorias relaciones inter género y que por su
naturaleza son de difícil contención. En el ámbito privado
ellas se articulan, ya sea cediendo, traspasando o negando
sus propias aspiraciones. Y en el ámbito público, espacio
de desarrollo en el que se juegan aspiraciones como el
reconocimiento de los otros, el respeto, la valoración, son
logros que alcanzan a costa habitualmente de otros
aspectos de su vida, la familia, la relación con los hijos,
con la pareja, ya que estos últimos y las propias mujeres
Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
551
PAULINA IRENE SALINAS MERUANE
41
42
43
GONZÁLEZ DE CHÁVEZ, 1998.
responden al imaginario social de la mujer como sujeto
capaz de cubrir todas demandas y con alta capacidad,
para estar simultáneamente cubriendo “exitosamente” las
distintas demandas del espacio público y privado.
A pesar de la mayor apertura del campo laboral
para las mujeres, ellas se encuentran en dificultades para
compatibilizar el papel tradicional que de ellas se espera
en el hogar con la inclusión en un medio cultural androcéntrico. Ya que este ámbito altamente competitivo ha sido
organizado por el hombre para cumplir con el nivel de
exigencia acorde con las circunstancias, contando con el
contingente provisto por la mujer para cubrir las necesidades vitales y emocionales de él y de los hijos.
En consecuencia, la tensión que experimentan las
mujeres en la configuración de su identidad y en el proceso
de empoderamiento como mujeres y como madres, es
donde se plasma con mayor énfasis el conflicto y las
resistencias, llenando de sentimientos de culpabilidad e
inadecuación a aquéllas que se desmarcan de él o
comparten duramente diversas tareas intra y extrafamiliares.
Por otra parte, muchas madres, gratificadas a menudo en
detentar el lugar – la fantasía – de la omnipotencia, han
tenido y tienen dificultades internas y sociales para
escaparse al papel y la imagen en que han sido
encerradas.41
Entrevista grupal Nº 2.
Por ejemplo, el cambio también lo que yo me he dado
cuenta también que por ejemplo mis niños cierto y a
veces yo me he levantado y los niños tienen puesta la
mesa digamos, las tacitas todo, la tetera y todo el
asunto, o sea como que ellos también se están
acostumbrando a ese sistema pero también les ha
afectado, por ejemplo la niña no hace tareas hasta
cuando llegue la mamá, el más chiquito también, tiene
que hacer algún trabajo y todo, lo hace, pero está
esperando a su mamá.42
Entrevista grupal Nº 2.
Yo creo que hay dos cosas, que trabaje la mujer es
bueno, porque también tiene derecho igual que el
hombre a estudiar, a desarrollarse profesionalmente
todo el asunto, pero a la vez también es un atentado
contra la familia porque alguien tiene que estar más,
como cerca con los hijos. Son dos cosas, una que la
mujer se pueda desarrollar profesionalmente y otra
¿pero qué pasa con la familia? ¿qué pasa con los hijos?,
y todos estos problemas que se han suscitado ahora.43
El modelo de mujer-madre conserva toda su vigencia
ética, en los discursos masculinos, llenando de sentimientos
contradictorios las existencias femeninas. Hay un deseo de
la maternidad arraigado a la socialización primaria de las
mujeres, y que encuentra un cimiento idealizador en los
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LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN...
hombres. Por lo tanto para aquéllas que desean distanciarse
de esta construcción resulta culpabilizador, complejo
cargado de dificultades internas y sociales, ya que implica
negar un imaginario social que ha sostenido la familia
nuclear patriarcal.
44
45
Entrevista grupal Nº 4.
Aparte que de todo esto del cambio, también la mujer
es… una… parte súper importante, es protagonista,
porque en estos tiempos igual, hay mujeres que dicen,
por ejemplo tú dices ya, voy a lavar, voy a cocinar, voy
a hacer esto otro y la mujer te dice no, yo hago eso,
no, yo plancho, entonces como que la mujer también
se siente amenazada porque tú estay ocupando el rol
que ocupa ella. Entonces ahí la mujer cumple una
función principal y si realmente queremos lograr un
equilibrio y una igualdad la mujer también va a tener
que cambiar la mentalidad .44
Entrevista grupal Nº 4.
Hay bastantes mujeres que aunque trabajen y todo,
tienen una mentalidad machista, o sea al hombre no
lo dejan hacer sus cosas y lo terminan haciendo ellas
dándole en el gusto en todo.45
En los discursos los varones hablan de los nuevos
roles que las mujeres desempeñan en la sociedad actual,
sobre todo en el ámbito laboral y la compatibilidad de
ellos, pues aprueban que las mujeres trabajen y aporten al
sustento de la familia, pero ojalá esto no modifique el orden
familiar y por ende, aunque ellos ya no sean los único
proveedores, sus expectativas se aferran a los mandatos
de género de la familia tradicional, respecto a la crianza y
cuidado de los hijos.
Entrevista individual, técnico, 20
años.
46
Es que antes eran distintos los cambios, la sociedad
era distinta, o sea, con la mujer tenía muchos más hijos
que ahora, y era por la circunstancia, ante se podía
tener más hijos, ahora ya no se puede tener tantos hijos
como antes, entonces la mujer debe tomar otros roles
también más protagónicos en la parte laboral, para
poder mantener un equilibrio económico, porque ya
no alcanza a lo mejor con un sueldo, o simplemente
que la mujer sea dueña de casa, ya no basta con por
la política económica que actualmente estamos
viviendo.46
La participación social igual ha ido en menoscabo un
poco de la participación que las mujeres tenían en la
crianza de los hijos antiguamente. Hoy en día, la mujer
pasa mucho tiempo fuera del hogar como que ha
mermado, en cierta forma las relaciones familiares, pero
igual es positivo que esté trabajando, esté ocupando
cargos, porque igual posee capacidades…que son
bien positivas también, en todas las cosas existen
ventajas y desventajas. Y la desventaja es esa, la crianza
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553
PAULINA IRENE SALINAS MERUANE
47
48
Entrevista grupal Nº 4.
María Elena VALENZUELA, 2000.
Rosalía TODARO, Amália
MAURO y Sonia YAÑEZ, 2000, p.
94.
49
de los hijos ya se le está delegando a la escuela, a los
profesores, a las academias, no sé, a los gimnasios, a
los clubes deportivos… ya no es tanto la casa, la familia,
como el núcleo de la formación de una persona.47
En las últimas décadas han surgido nuevos modelos
productivos que han afectado significativamente el sistema
de relaciones laborales y la calidad de los empleos. Estos
modelos tienen como centro la flexibilidad del empleo y
de la organización de las empresas, y han brotado en
medio de una masiva incorporación .de las mujeres a la
fuerza de trabajo. En el Cono Sur, Chile registró el mayor
incremento en los últimos 30 años, aun cuando el nivel de
participación laboral de las mujeres se sitúa bajo el
promedio regional.48 Sin embargo, la incorporación masiva
de las mujeres al empleo ha sido acompañada de una
notable precarización del mismo. Aspectos de la calidad
del empleo de las mujeres, tales como la regularidad y
estabilidad laboral, los ingresos, las horas de trabajo y su
intensidad, los peligros ocupacionales para la salud, el
ambiente de trabajo, la protección laboral y social, los
contenidos de los empleos y las oportunidades que ofrecen
para el desarrollo personal y las trayectorias laborales, como
el estatus social que proporciona, están siendo fuertemente
permeados por el fenómeno de la segregación de
género.49
Aunque la identidad masculina tradicional sigue
vigente, se aprecian transformaciones en su forma y en su
fondo, ya no se trata del hombre que exige abiertamente
que la mujer permanezca en el espacio doméstico y que
realice las tareas que históricamente se le han asignado al
sexo femenino, vale decir, socialmente se reconoce que
las mujeres deben cumplir un rol más activo en la sociedad,
tener un trabajo y realizarse como persona. Sin embargo,
el histórico machismo se ha camuflado y hoy se basa más
en el control y en la coerción psicológica que en la
discriminación o en las restricciones físicas. Es el dominio
que se ejerce en la clandestinidad, el denominado
neomachismo.
Sabe una cosa yo pienso que cuando, que las mujeres
se ahogan mucho de que cuando se habla mucho de
que se ha incorporado al ámbito laboral. Es cierto si
hay mujeres de que se han superado y han… han
digamos ehh… al hombre lo han superado digamos,
en muchas, en muchas carreras, muchas etapas, pero
si es cierto entra a una empresa y empiezan a
discriminarla, me entiende, a aislarla, o sea siempre el
hombre va por naturaleza, va a tirarla pal lao…Porque
es así, yo lo veo de esa manera, no porque soy machista
ni nada de eso, por naturaleza se da así, se da así, la
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50
51
Entrevista grupal Nº 2.
mujer…llega una jefa y el jefe de al lado y… le hace la
guerra y ella no tiene nada que ver con los empleados
es una guerra de jefatura digamos.50
Entrevista grupal Nº 2.
Me ha afectado bastante esta situación de que la mujer
trabaje, porque como tú siempre dices que tú vas a
aportar siempre y ahora que te sientes con un poco
menos derechos de repente, que tienes que llegar
como de otra manera.51
Si bien la participación de los hombres en el espacio
doméstico ha aumentado, presenta algunas restricciones:
primero los hombres conciben su participación como un
apoyo generoso a la mujer, es decir, está condicionada
por el lazo afectivo que estos tengan con la pareja y el
éxito que logren las mujeres en las negociaciones
cotidianas, vale decir no es el resultado de una convicción
cabal de éstos por hacerse cargo de las tareas domésticas
por el solo hecho que son parte de un grupo familiar.
Segundo, este apoyo también se limita a algunas tareas
dentro de la estructura familiar, de hecho los hombres se
toman la opción de elegir qué hacen y qué no, en cambio
para las mujeres esta opción no existe.
Los hilos discursivos
Al analizar lo discursos en forma longitudinal y
transversal se pueden distinguir tópicos centrales y que se
presentan en oposición respecto al poder alcanzado por
las mujeres, y los obstáculos que visualizan ellos en el
proceso de empoderamiento.
· Observan una transformación social, un cambio
de mentalidad respecto a los roles que desempeñan
actualmente las mujeres en la sociedad.
· La globalización implica el poder tener acceso a
otras culturas distintas donde hay más tolerancia, y así
alejarse del pensamiento religioso y tener más apertura.
· Con la llegada de la democracia se han abierto
más espacios para la mujer, que está adquiriendo cada
vez más poder.
· Los hombres aprueban el discurso oficial respecto
a la igualdad de derechos que tienen hombres y mujeres
en la sociedad.
· El hombre ejerce el poder por el poder, las mujeres
ejercen el poder y le agregan las relaciones humanas y el
trato.
· Las mujeres son las que manejan las relaciones
personales en todos los ámbitos.
· Las mujeres son más capaces, más metódicas,
menos corruptas, más delicadas y meticulosas.
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PAULINA IRENE SALINAS MERUANE
· Son relevantes los ingresos económicos que
generan actualmente las mujeres para el bienestar de la
familia.
· Valoran positivamente que las mujeres sean un par
con la cual se puede conversar y que no deben responder
a las expectativas de lo que se considera “un macho
proveedor”.
· En la familia la mujer ejerce el poder.
· Hay resistencia de parte de las mujeres para ceder
el poder al interior de la familia.
· Las actividades propias del hogar deberían ser
compartidas, no puede seguirse cargando la mano a una
sola persona (mujer).
· Las mujeres se están incorporando en diferentes
áreas y no se sabe si el mercado logrará absorber toda
esa mano de obra.
· La mujer está preparada para hacer lo que quiera,
pero incomoda.
· En los puestos de ministros hay paridad, sin embargo
no se sabe si serán capaces como los hombres en puestos
tan altos.
· Para los hombres que aspiran al poder, consideran
a la mujer como una persona que se le cruza en el camino.
· Las mujeres no deben perder sus características
innatas, ni su rol femenino.
· Las mujeres tienen que demostrar más que los
hombres para poder ejercer liderazgo, tienen que tener
más cuidado, los hombres pueden hacer más cosas, que
a las mujeres no se les perdonaría.
· Los hombres están siendo igual que las mujeres y
por eso surgen problemas en las relaciones de pareja.
· En el norte del país el poder masculino ha sido
emblemático, por ser descendientes de la cultura pampina,
donde la virilidad masculina se medía con el poder
absoluto.
· La asunción de Michelle Bachelet a la presidencia
de la república significo una perdida importante para los
hombres.
· Las mujeres se desenvuelven bien en los centros
de madres, en las juntas de vecinos, son cargos que
debieran llevar ellas por naturaleza, porque es un centro
social que tiene la facultad de ocuparse de la comunidad
y de los niños.
· A las mujeres les cuesta más llegar al poder, no
tienen plataforma, eso hace mucho en el tema del
liderazgo.
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A modo de conclusión
52
FAIRCLOUGH y WODAK, 2000.
53
Jorge LARRAÍN, 2001.
En base a tres de los principios teóricosmetodológicos del ACD 52 analizaremos, a modo de
conclusión, cómo se relaciona cada uno de ellos con el
análisis crítico realizado sobre los discursos masculinos.
· Las relaciones de poder como elementos
discursivos, el ACD subraya el carácter discursivo de las
relaciones sociales de poder en la sociedad contemporánea, carácter que proviene en parte de cómo se
ejerce y negocian las relaciones de poder en el interior del
discurso. Al respecto, el habla de los hombres devela el
malestar e incomodidad que le produce la incorporación
de la mujeres a los espacios de poder que históricamente
han sido ocupados por ellos, sean estos en el mercado
laboral o en los espacios de decisión, ministerios,
presidencia de la república, entre otros. Los hombres
refuerzan en sus discursos la vigencia de las características
esencialistas de las mujeres, la femineidad, la
responsabilidad que se le asigna en la manutención de las
relaciones de pareja y su preocupación por las actividades
de la comunidad y de los niños.
· El discurso modela la sociedad y la cultura, y esto
implica que el lenguaje hace su propia contribución a la
reproducción y/o transformación de la sociedad y la cultura,
incluidas las relaciones de poder. En los hilos discursivos
identificados en las entrevistas se observan con intensidad
elementos de continuidad y de cambio en los discursos
masculinos, es decir, el proceso argumentativo en la
producción del texto evidencia una serie de oposiciones
capacidad/incapacidad, más participación/menos
liderazgo, menos corruptas/sin plataforma política, etc. Hay
ambigüedad y un cierto continuum en las representaciones
que hacen los hombres sobre las mujeres, donde se da
una dialéctica entre características tradicionales y
modernas, estas últimas reconocidas como eminentemente
masculinas.
· El discurso es histórico, y esto implica que se
produce en un contexto, hay convenciones y reglas subyacentes que es necesario reconocer como asimismo los
elementos del pasado que nos remite el discurso. En este
sentido podemos señalar que la ambigüedad y tensión
discursiva analizada es concomitante con el proceso identitario de la sociedad chilena actual, que se caracteriza por
la existencia de profundas transformaciones que conjugan
aspectos tradicionales con otros más modernizadores, es
decir, en el proceso identitario de la sociedad chilena hay
una coexistencia de diversas dimensiones que van conformando un proceso dinámico y en construcción.53 Lo anterior
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557
PAULINA IRENE SALINAS MERUANE
se manifiesta, por ejemplo, en que se mantiene una tradición de autoritarismo en las relaciones junto con una valoración de relaciones más democráticas; hay una mayor
apertura producto de la globalización y el mayor contacto
con el resto del mundo, pero también existe un racismo
más bien oculto, sobre todo con los países vecinos. El
machismo tiene plena vigencia en algunos segmentos de
la sociedad, mientras que en otros se encuentra más camuflado. Cada una de estas dimensiones nos permite visualizar
la ambigüedad y sincretismo presentes en el proceso
modernizador que experimenta la sociedad chilena.
Finalmente, las trayectorias de las mujeres hacia la
autonomía y el posicionamiento en el ámbito público son
zigzagueantes en el sentido que están plasmadas por
tensiones entre las resistencias que provocan en el espacio
intra y extra familia, como por las oportunidades que han
sido capaces de ir generando en la sociedad. Esta
oposición marca el desempeño y posicionamiento de las
mujeres en los distintos planos del quehacer nacional.
En los discursos analizados queda en evidencia las
tensiones que están vivenciando los hombres respecto al
empoderamiento femenino. Hay reconocimiento y temor,
hay seguridad frente al desempeño y capacidades de las
mujeres, pero al mismo tiempo incomodidad y el deseo a
que las mujeres mantengan sus características “naturales”,
de femineidad, sensibilidad, etc.
Los obstáculos que refieren los hombres respecto al
empoderamiento de las mujeres se relacionan con que las
limitantes que se les pueda generar a ellos en aquellos
espacios donde han tenido control, el trabajo o la actividad
política.
Analizar los discursos y el habla, en este caso
masculina ha posibilitado, desmontar las estructuras
esencialistas presentes en el lenguaje que producen y
reproducen prácticas sociales discriminatorias, y que se van
reforzando en el imaginario social de los sujetos.
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Chile: FLACSO-Chile/Universidad Academia de
Humanismo Cristiano/Red de Masculinidades, 2000. p.
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CONNELL, Robert W. “El imperialismo y el cuerpo de los
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561
PAULINA IRENE SALINAS MERUANE
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[Recebido em novembro de 2006
e aceito para publicação em fevereiro de 2007]
Masculine Discourses as Control and TTension
ension Devices in W
omen
’s LLeadership
eadership and Empowering
Women
omen’s
Configuration
Abstract
Abstract: The present contribution deals with the meaning of the feminine leadership from a
masculine perspective. By using a qualitative approach, open interviews were developed to
understand the meaning that men assign to the feminine leadership. The speeches were analyzed
on the basis of the Strauss/Corbin-theory (2003). The results show that men agree with the changes
experienced by the gender roles. In a specific way, men agree that women need to have more
societal-economic opportunities, which are necessary for more equitable relationship inside the
family. However, within this positive framework emerging tensions configure a dissatisfaction of
the masculinity that, in turn, impact the intimate sphere questioning the present day inter-gender
relationship. Finally, there is a men’s group with more progressive speeches which venture towards
a positive evaluation of the women’s capacities and their assumed public space-roles. However
this positive evaluation is vigilant, ambivalent, and influenced by a perception of confidence/
uncertainty, efficiency/inefficiency of the effective societal contribution that women are able to
reach.
Key W
ords
Words
ords: Power; Societal Changes; Gender.
562 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
| |
https://openalex.org/W2753454165 | https://link.springer.com/content/pdf/10.1007%2F978-3-319-58042-5_8.pdf | English | null | New GDP Series and Earlier Estimates for the Pre-national Accounts Era | Springer eBooks | 2,017 | cc-by | 5,855 | © The Author(s) 2017
L. Prados de la Escosura, Spanish Economic Growth, 1850–2015,
Palgrave Studies in Economic History, DOI 10.1007/978-3-319-58042-5_8 New GDP Series and Earlier Estimates
for the Pre-national Accounts Era How do the new GDP series compare to earlier estimates?1 Let us
examine them first. Unlike contemporaries who were interested in
assessing national income levels, early Spanish research has been con-
cerned with trends and fluctuations in real output and expenditure.2 All
available GDP estimates are output indices constructed with a fixed,
single benchmark level whose economic significance tends to decline as
one moves away from the base year.3 Moreover, trends in real gross value
added are proxied by production indices, which imply the unlikely
assumption that total output and input consumption evolve in the same
direction and with the same intensity.4 Three types of yearly GDP
estimates can be distinguished: official estimates by the Consejo de
Economía Nacional, its revisions and extensions, and independent
estimates. 153 © The Author(s) 2017
L. Prados de la Escosura, Spanish Economic Growth, 1850–2015,
Palgrave Studies in Economic History, DOI 10.1007/978-3-319-58042-5_8 L. Prados de la Escosura 154 8
New GDP Series and Earlier Estimates … An index of total production was obtained by combining agricultural
and industrial indices with fixed weights (0.6 and 0.4, respectively, over
1906–1929, and 0.5 each, thereafter). In addition, to allow for short-term
fluctuations over the period 1906–1935, a de-trended nuptiality index
was combined with the total production index. Nuptiality was excluded
after the Civil War (1936–1939) as unsuitable for post-war cycles. In a second stage, the total production index was linked to an estimate
of national income for 1923 in order to derive national income at
constant prices.7 A further step was to obtain national income figures at
current prices by reflating real income with a wholesale price index. Finally, for the years 1957–1964, CEN computed national income
directly. 8.2
Revisions and Extensions of CEN
Estimates Modern national accounts constructed according to OECD rules are
available in Spain since 1954. Attempts to extend them backwards led to
revisions of CEN figures that, occasionally, were expanded to cover the
expenditure side. Three estimates are worth mentioning. 8.1
Consejo de Economía Nacional
Estimates In 1944, the Consejo de Economía Nacional or National Economic
Council (CEN, thereafter) was asked to estimate a set of national
accounts for Spain (CEN 1945, 1965). Three were the main targets: to
provide income figures for the years prior to the Civil War (1936–1939),
to evaluate 1940 GDP on the available, fragile statistical basis, and to
design a direct method to estimate national income for the years to come
(Schwartz 1977: 460). Dearth of data forced CEN to split output indices into two segments
with 1929 as the link year. In each case, independent production indices
for agriculture and industry were obtained, from which an aggregate
index was derived to approximate national income. No regard was paid
to services and was implicitly assumed that output in services evolved as a
weighted average of agricultural and industrial production. For the earlier period, 1906–1929, an agricultural output index was
built up on the basis of eleven products, mostly dry farming crops (while
no livestock output was included), representing half the value of total
output. The index of industrial production included eighteen products,
rendering a good coverage for mining, but insufficient for manufacturing
and construction. Output indices were obtained for agriculture and
industry by weighting each single product with its average price over
1913–1928, and the aggregate results were expressed by taking the
average for 1906–1930 as 100. The composition of agricultural and industrial indices changed from
1929 onwards. Thirteen new crops were added to the agricultural index,
distributed into eight main groups of products, that reached up to 80%
of total production, while the industrial index’s coverage rose to 38
products distributed into ten different groups.5 To derive output indices
for agriculture and industry, quantities were weighted by 1929 farm-gate
prices and unit value added, respectively.6 Improvements in data cov-
erage took place in the 1950s, but the method remained practically
unaltered until 1956. 155 8
New GDP Series and Earlier Estimates … 8.2.1
Comisaría del Plan de Desarrollo A first attempt to revise CEN’s estimates was carried out by Comisaría
del Plan de Desarrollo, the Development Planning Authority (CPD,
thereafter), and covered the period 1942–1954 (CPD 1972).8 CPD
economists were concerned with the high volatility shown by CEN
figures that they attributed to its high dependence on agricultural output
and to the exclusion of services. The alternative proposed by CPD was to
construct a new index of aggregate performance in which services were
added to CEN’s indices of agricultural and industrial output. Services
output was obtained by combining series on transport and communi-
cations and banking.9 A real product index was calculated by weighting
each sectoral index with the shares of agriculture, industry and services in L. Prados de la Escosura 156 1954 GDP at factor cost, as established in official national accounts
(CNE58).10 GDP at constant prices for 1942–1953 was, then, derived
through backward extrapolation of the 1954 GDP level with the real
product index. GDP at current prices was computed, in turn, by reflating
real output with a composite index of wholesale prices (0.3) and the
cost-of-living index (0.7).11 g
GDP was completed with a breakdown of its expenditure components
that included direct estimates of investment, public consumption and net
exports of goods and services. To approximate private non-residential
fixed capital formation, a physical index of private investment was built
up by combining, with 1954 weights (CNE58), steel and cement output,
machinery imports, electric power and registered transport vehicles. An
index of residential investment was proxied by the number of completed
dwellings. Public investment, in turn, resulted from adding up invest-
ment in agriculture and public works and provincial and local public
investment, deflated by a wholesale price index. Levels of each type of
investment for 1954 were taken from the national accounts and pro-
jected backwards with each investment index to derive real capital for-
mation series and, then, reflated with price indices for production goods
and construction materials. Total expenditure of public administration
(central, provincial and local governments) re-scaled to match national
accounts was used for public consumption and, then, deflated with a
wholesale price index. Net exports of goods (at current and constant
prices) were used as a proxy for net exports of goods and services, except
in the case of tourism, in which the number of tourists (and the cost of
living index as deflator) was accepted. 8.2.1
Comisaría del Plan de Desarrollo Private consumption was obtained
as a residual from GDP at market prices (derived by adding indirect taxes
net of subsidies to GDP at factor cost, obtained through the production
approach) and the directly estimated components of expenditure. 8.2.3
Naredo An apparent inconsistency in the CEN series that would have led to
underestimating national income for the post-Civil War years motivated
José Manuel Naredo’s revision of CEN’s national accounts (Naredo
1991). The rationale for the under-registration of economic activity in
official national accounts lies in the response of economic agents to
systematic regulation and intervention of markets under Francoist
autarchy.15 He also noticed that CEN’s implicit income-elasticity of
demand for imports in the 1940s was too low. Naredo proposed, then,
an alternative real GDP series for 1920–1950 based upon the revision of
official national account estimates by hypothesizing higher income-
elasticity of the demand for imports in the 1940s and by assuming a 10%
fall in GDP resulting from the Spanish Civil War (1936–1939). 8
New GDP Series and Earlier Estimates … 157 1976).12 For the period 1901–1935, Alcaide derived an index of
domestic production by combining, with 1906 fixed weights, CEN
indices for agricultural and industrial output, and total employment in
services, as a proxy for its output.13 GDP at current prices was obtained
by reflating real output with a wholesale price index.14 8.2.2
Alcaide A revision of CEN series was also attempted by Julio Alcaide, a pioneer
of Spanish national accounts, who, concerned for its volatility and
cyclical behaviour, attempted to smoothing CEN’s real output (Alcaide 8
New GDP Series and Earlier Estimates … 8.3.1
Información Comercial Española The contribution by the research unit of the Ministry of Commerce and
published in its journal, Información Comercial Española (ICE, there-
after), represented a major improvement over earlier indices of Spanish
aggregate performance (ICE 1962).16 The ‘general index of total pro-
duction’, as its authors named it, covered 1951–1960 and represented a
Laspeyres volume index in which three major sectors, agriculture and
fishing, mining, manufacturing and construction, and trade and services,
were combined with 1958 gross value added as weights. For each sector,
a Laspeyres volume index with 1958 weights was constructed, in which L. Prados de la Escosura 158 L. Prados de la Escosura four branches were included for agriculture, sixteen for industry, and six
for services, the latter appearing for the first time in pre-national accounts
GDP estimates.17 Real product series was complemented with a quantity index for
investment based on construction and public works, afforestation and the
consumption (production plus imports) of machinery and equipment. 8.3.2
Schwartz A major attempt at overcoming CEN’s estimates for the period 1940–
1960 was carried out by Pedro Schwartz, at the Bank of Spain’s research
unit, where he assembled new empirical evidence and used transparent
methods in which indirect methods and regression analysis were com-
bined (Schwartz 1976). In the new series, gross value added for every
major sector in the economy was obtained by regressing their
value-added levels (derived from official national accounts) on a set of
indicators over 1954–1960, and the resulting structural relationship was
applied to the set of variables or indicators to compute sectoral value
added for the earlier pre-national accounts period 1940–1953. Gross
domestic product (nominal and real) was derived by aggregation.18 8
New GDP Series and Earlier Estimates … 159 clothing) are those of lower income-elasticity of demand.22 In addition,
the use of end-year (1958) fixed weights could underestimate GDP
growth since relative prices for capital goods, the fastest growing com-
ponent of expenditure, declined over time rendering, hence, a lower
weight for investment than would have been the case if relative prices of
any previous year were used.23 8.3.3
Carreras The most ambitious attempt to derive historical series of real GDP was
produced by Albert Carreras (1985) who built up an index from the
demand side, covering a longer time span, 1849–1958.19 Weights for the
main aggregates (private and public consumption, investment, net
exports) were derived from the 1958 benchmark from the national
accounts, while the 1958 input–output table allowed the breakdown of
each series into its main components.20 However, a few shortcomings can be observed in an otherwise major
piece of research. For example, the consumption series only cover food,
beverages and tobacco, and clothing while services are neglected.21
Actually, it could be argued that consumption growth may be possibly
biased downwards since the goods included in the series (food and 8
New GDP Series and Earlier Estimates … 8.4
Comparing the New and Earlier GDP
Estimates How does the new GDP series compare to the earlier estimates? There is
a significant agreement about performance over the long run between
Carreras estimates and my new series, although significant discrepancies
emerge in the short term. During the first half of the twentieth century,
the new GDP series present slower growth than those by Alcaide and
CEN (Fig. 8.1). When the focus is placed on specific periods, the variance across
different estimates emerges. World War I years seem to have been of fast Fig. 8.1
Alternative real GDP estimates, 1850–1958 (1958 = 100) (logs) L. Prados de la Escosura 160 growth (CEN, Alcaide and Carreras), in which the economy would have
taken advantage of Spain’s neutrality to cater for the needs of belligerent
nations while domestic industry expanded on the basis of import sub-
stitution. This conventional depiction is challenged by the new GDP
series. Then, the post-war years and especially the 1920s exhibit accel-
erated growth in CEN and Alcaide’s. estimates while Carreras’ suggest
deceleration. The new GDP series provide an even more optimistic
picture than Alcaide’s. The impact of Great Depression in Spain (1929–1933) varies dra-
matically according to different authors. Spain’s economy decelerated but
continued growing in Alcaide’s view, stagnated in Naredo’s, mildly
contracted in Carreras’ computations and definitely shrank in CEN’s
estimates. The new series side along CEN’s but with a less intense decline. Earlier estimates are discontinued between 1936 and 1939, so com-
paring output levels in 1935 and 1940 is the only way to assessing the
impact of the Civil War (Fig. 8.2). A consensus exists about a substantial
contraction in economic activity during the war years, around 6% per
annum, but for Naredo’s mild −2.1%. In my new estimates, the Civil
War represented a milder but still deeper shrinkage than Naredo’s.24 The impact of Great Depression in Spain (1929–1933) varies dra-
matically according to different authors. Spain’s economy decelerated but
continued growing in Alcaide’s view, stagnated in Naredo’s, mildly
contracted in Carreras’ computations and definitely shrank in CEN’s
estimates. The new series side along CEN’s but with a less intense decline. Earlier estimates are discontinued between 1936 and 1939, so com-
paring output levels in 1935 and 1940 is the only way to assessing the
impact of the Civil War (Fig. 8.2). 8.4
Comparing the New and Earlier GDP
Estimates A consensus exists about a substantial
contraction in economic activity during the war years, around 6% per
annum, but for Naredo’s mild −2.1%. In my new estimates, the Civil
War represented a milder but still deeper shrinkage than Naredo’s.24 Fig. 8.2
Alternative real GDP estimates, 1900–1958 (1958 = 100) (logs) Fig. 8.2
Alternative real GDP estimates, 1900–1958 (1958 = 100) (logs) 8
New GDP Series and Earlier Estimates … 8
New GDP Series and Earlier Estimates … 161 Table 8.1 Real
GDP
growth
in
the
pre-national
accounts
era:
alternative
estimates, 1850–1958 (%)
CEN
CPD
Alcaide
Naredo
ICE
Schwartz
Carreras
New series
1850–1958
1.7
1.7
1901–1958
2.6
2.8
1.6
1.8
1850–1883
2.2
1.7
1883–1913
0.6
1.1
1901–1913
1.6
2.3
0.1
1.2
1913–1918
1.4
1.9
2.2
0.3
1918–1929
2.5
2.6
1.6
1.5
3.9
1929–1933
−2.1
1.0
−2.1
−0.6
−1.5
1933–1935
4.3
1.5
4.3
−1.1
3.0
1935–1940
−6.7
−6.0
−2.1
−5.9
−3.5
1940–1944
3.6
0.7
2.6
4.8
2.6
6.5
4.0
1944–1950
0.8
2.8
2.5
2.9
0.6
−1.5
0.2
1950–1958
7.2
6.2
5.8
5.8
5.1
6.0
5.0
5.8
Note ‘New Series’ are GDP estimates at market prices. Sources New Series, see the text. CEN (1945, 1965), ICE (1962), CPD (1972), Alcaide (1976), Naredo (1991), Schwartz (1976),
and Carrerras (1985) 8.1 Real
GDP
growth
in
the
pre-national
accounts
era:
alternative
tes, 1850–1958 (%) Note ‘New Series’ are GDP estimates at market prices. Sources New Series, see the text. CEN (1945, 1965), ICE (1962), CPD (1972), Alcaide (1976), Naredo (1991), Schwartz (1976),
and Carrerras (1985) The post-war recovery was mild (but for Carreras and Naredo esti-
mates) and short-lived (CEN, Carreras and Schwartz), and only resumed
at a fast pace in the 1950s (except for Alcaide) (Table 8.1). The new
GDP estimates concur with the view of a post-Civil War mild and long
recovery, which makes Spanish post-war experience different from
western Europe’s fast return to pre-war output levels (Maddison 2010). 1. Attempts to provide historical GDP at benchmark years have been
carried out by economic historians. Bairoch (1976) and Crafts (1983,
1984) included Spain in their estimates for the nineteenth century
computed along Beckerman and Bacon (1966) indirect approach.
Following Deane (1957), Prados de la Escosura (1982) reconstructed
Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and
derived a set of benchmark estimates for Spanish national income for
1832–1894. In addition, GDP estimates for seven benchmarks over the
period 1800–1930 from the industry of origin approach are provided in
Prados de la Escosura (1988). L. Prados de la Escosura 162 2. It is worth mentioning Mulhall (1880, 1884, 1885, 1896) estimates of
national income for a large number of countries, including Spain, in the
late nineteenth century. The main contemporary attempts to derive levels
of Spain’s national income have been collected in Schwartz (1977). The
literature on Italy, where detailed benchmark estimates have been con-
structed, provides a counterpoint (Rey 1991, 1992, 2000, 2002). 2. It is worth mentioning Mulhall (1880, 1884, 1885, 1896) estimates of
national income for a large number of countries, including Spain, in the
late nineteenth century. The main contemporary attempts to derive levels
of Spain’s national income have been collected in Schwartz (1977). The
literature on Italy, where detailed benchmark estimates have been con-
structed, provides a counterpoint (Rey 1991, 1992, 2000, 2002). p
p
y
3. Unfortunately, the 1958 GDP benchmark is the earliest available in
Spain. New, direct GDP estimates for benchmark years prior to 1958,
e.g. 1910 or 1930, years for which population censuses are available,
would be required to provide a rigorous check on GDP figures derived
by projecting benchmarks backwards with quantity and price indices. p
p
y
3. Unfortunately, the 1958 GDP benchmark is the earliest available in
Spain. New, direct GDP estimates for benchmark years prior to 1958,
e.g. 1910 or 1930, years for which population censuses are available,
would be required to provide a rigorous check on GDP figures derived
by projecting benchmarks backwards with quantity and price indices. 4. The reader should be aware that my own estimates suffered from this
bias (see Section III). Actually, only a double deflation procedure for
inputs and output would provide a correct alternative. By double
deflation is meant independent deflation, with their own price indices,
of final production and intermediate inputs, so real value added is
obtained as a residual. Cf. Cassing (1996). 4. The reader should be aware that my own estimates suffered from this
bias (see Section III). Actually, only a double deflation procedure for
inputs and output would provide a correct alternative. By double
deflation is meant independent deflation, with their own price indices,
of final production and intermediate inputs, so real value added is
obtained as a residual. Cf. Cassing (1996). 5. In order to reduce the downward bias for manufacturing, CEN (1945,
1965) overweighted electricity output. 5. In order to reduce the downward bias for manufacturing, CEN (1945,
1965) overweighted electricity output. 6. Notes 1. Attempts to provide historical GDP at benchmark years have been
carried out by economic historians. Bairoch (1976) and Crafts (1983,
1984) included Spain in their estimates for the nineteenth century
computed along Beckerman and Bacon (1966) indirect approach. Following Deane (1957), Prados de la Escosura (1982) reconstructed
Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and
derived a set of benchmark estimates for Spanish national income for
1832–1894. In addition, GDP estimates for seven benchmarks over the
period 1800–1930 from the industry of origin approach are provided in
Prados de la Escosura (1988). 1. Attempts to provide historical GDP at benchmark years have been
carried out by economic historians. Bairoch (1976) and Crafts (1983,
1984) included Spain in their estimates for the nineteenth century
computed along Beckerman and Bacon (1966) indirect approach. Following Deane (1957), Prados de la Escosura (1982) reconstructed
Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and
derived a set of benchmark estimates for Spanish national income for
1832–1894. In addition, GDP estimates for seven benchmarks over the
period 1800–1930 from the industry of origin approach are provided in
Prados de la Escosura (1988). L. Prados de la Escosura L. Prados de la Escosura Mining was allocated 22.68% of total industrial output; utilities (rep-
resented by electric energy), 20.96%; and manufacturing only 56.36%. If the size of the industrial sample (2077 million pesetas) is compared to
Banco Urquijo ‘s estimate of industrial output circa 1924, its coverage
represents 25% of total industrial value added. 6. Mining was allocated 22.68% of total industrial output; utilities (rep-
resented by electric energy), 20.96%; and manufacturing only 56.36%. If the size of the industrial sample (2077 million pesetas) is compared to
Banco Urquijo ‘s estimate of industrial output circa 1924, its coverage
represents 25% of total industrial value added. 7. CEN (1945) used an arithmetic average of Banco Urquijo (1924) and
Vandellòs (1925) estimates assuming that were independent from each
other. Assessments of CEN (1945) income figures are provided by
Guerreiro (1946), Hemberg (1955) and Fuentes Quintana (1958), all
reprinted in Schwartz (1977). Hemberg (1955) pioneering computation
of income using a production approach showed that there were enough
statistical data to carry out a direct estimate of GDP from the supply side. 8. The purpose of CPD estimates was to provide statistical background for
the econometric model used in simulations during the third ‘plan de
desarrollo’, an instrument of planification indicatif in the early 1970s. 9. Fixed value-added weights from 1954 National Accounts were accepte 10. National accounts are named after the benchmark year used for its
construction. Thus, CNE58 is Contabilidad Nacional de España with
1958 as the base year. 163 8
New GDP Series and Earlier Estimates … 8
New GDP Series and Earlier Estimates … 11. The weights tried to reflect the relative importance of private con-
sumption (70%) and the rest of the demand components of GDP
(30%). 11. The weights tried to reflect the relative importance of private con-
sumption (70%) and the rest of the demand components of GDP
(30%). 12. Alcaide carried out another revision of the historical accounts for the
period 1901–1985 that did not challenge, however, his earlier findings
for real product in the pre-national accounts period (Banco de Bilbao
1986). Nevertheless, nominal levels were revised upwards as the his-
torical series were linked to more recent figures from Banco de Bilbao’s
own GDP estimates. Alcaide (2000) revised his estimates for the early
twentieth century, starting in 1898, and spliced them with Fundación
BBV’s GDP estimates for 1955–1998 (also Alcaide’s own work). Unfortunately, Alcaide neither discusses his methods nor substantiates
his arguments with empirical evidence, while no sources are provided. 13. Weights were 0.4 for agriculture, 0.25 for industry and 0.35 for services. Since historical active population figures are only available at census
years, either Alcaide interpolated census data or applied participation
rates, derived at census intervals, to available yearly figures for total
population. Alcaide claimed to having adjusted employment in services
‘to accute changes in total production’ (Alcaide 1976: 1129). As stressed
by Tortella (1987), using employment as a proxy for output implies the
assumption of stagnant labour productivity in services. 14. Alcaide’s revision of CEN figures for 1940–1954 is also far from clear. He relies on a revision of CEN’s real output carried out by Tamames
without providing the reference. Moreover, while in the case of GDP
only the wholesale price index seems to have been used, it appears that
Alcaide reflated real national income with the cost of living and
wholesale price indices weighted by the shares of consumption and
investment in 1954 national accounts, respectively. 15. Naredo (1991) illustrated his argument by referring to the 26% increase
in agricultural output in a single year (1951), following the abolishment
of food rationing, which partially liberalized the domestic market. 16. The first independent attempt to derive national income estimates on an
yearly basis was carried out by José Castañeda (1945) who provided an
estimate of national expenditure from a sample of indirect taxes and
government’s monopoly revenues, deflated by a wholesale price index,
for the period 1901–1934. p
17. 8
New GDP Series and Earlier Estimates … Each of the 26 groups of goods and services, defined according to the
1958
input–output
table’s
(TIOE58)
classification
of
economic 17. Each of the 26 groups of goods and services, defined according to the
1958
input–output
table’s
(TIOE58)
classification
of
economic 17. Each of the 26 groups of goods and services, defined according to the
1958
input–output
table’s
(TIOE58)
classification
of
economic 164 L. Prados de la Escosura activities, was constructed as a Laspeyres volume index with 1958
weighting. In ICE estimates, the coverage of output was far superior to
CEN’s, with 227 and 45 basic series for industry and services. For
agricultural output (excluding livestock, forestry and fishing, for which
21 basic new series were used), CEN revised index was adopted. Weights applied to agriculture, industry and services to derive the
“general index of total production” were 0.2693, 0.3200 and 0.4107,
respectively. 18. An indicator is, according to Balke and Gordon (1989), a time-series
variable that is correlated with real product in the time period when real
GDP is known, i.e. the post-1954 years. 19. The only precedent of Carreras‘ demand approach is CPD (1972), but it
did not represent an independent estimate. 20. Some objections can be raised to the use of a 1958 benchmark as it
comes from an autarchic period in which prices were intervened by
government regulation and protection. This is a similar case to those of
Italy’s 1938 (Bardini et al. 1995:123) and Germany’s 1937 (Broadberry,
1997) benchmarks. It can be argued, however, that the 1958 input–
output table is not only the first one available but also the most detailed
Spanish one (207 sectors) to date. 21. Food and clothing represent 70% of total consumption in the bench-
mark year 1958 (CNE58). However, the sample of consumption goods
used in the construction of the annual index only reaches a coverage of
20% up to 1928, and 41% thereafter, as measured for the 1958
benchmark (Carreras 1985: 38–39, 45). Naredo (1991: 144) claimed
that Carreras reliance on García Barbancho’s (1960) food consumption
data led him to use out-dated, downward biased agricultural output
statistics. 22. Income elasticity of demand for housing, durables, personal care,
transport, recreation, etc. was significantly higher than for food and
clothing in 1958 Spain (Lluch, 1969: 68, 78). 22. Income elasticity of demand for housing, durables, personal care,
transport, recreation, etc. 8
New GDP Series and Earlier Estimates … 165 official values for exports and imports that exaggerate commodity trade
deficit for most of the period up to 1913 (see Sect. 7.3). official values for exports and imports that exaggerate commodity trade
deficit for most of the period up to 1913 (see Sect. 7.3). official values for exports and imports that exaggerate commodity trade
deficit for most of the period up to 1913 (see Sect. 7.3). p
p
24. Actually, my yearly estimates indicate a sharper decline between 1935
and 1938, at −11% per year, followed by a recovery up to 1944. 8
New GDP Series and Earlier Estimates … was significantly higher than for food and
clothing in 1958 Spain (Lluch, 1969: 68, 78). 22. Income elasticity of demand for housing, durables, personal care,
transport, recreation, etc. was significantly higher than for food and
clothing in 1958 Spain (Lluch, 1969: 68, 78). 23. Two other objections could also be raised to Carreras’ pathbreaking
contribution. Government consumption was deflated by a wholesale
price index, and not by a consumer price index, a better suited deflator,
as wages and salaries constituted its main component, since no com-
prehensive CPI was available at the time the paper was written. In
addition, the trade balance only covers commodities. Carreras used 8
New GDP Series and Earlier Estimates … Castañeda, J. 1945. El consumo de tabaco en España y sus factores. Revista de
Economía Política, I, 1: 195–292. Partially reprinted in P. Schwartz, ed. References Alcaide Inchausti, J. 1976. Una revisión urgente de la serie de renta nacional en
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años 1898 a 1998. In 1900–2000 Historia de un esfuerzo colectivo, ed. J. Velarde Fuertes, 2 vols., 375–449. Madrid: Planeta. Bairoch, P. 1976. Europe’s Gross National Product: 1800–1975. Journal of
European Economic History V 2: 273–340. Balke, N.S., and R.J. Gordon. 1989. The Estimation of Prewar Gross National
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Broadberry, S.N. 1997. Anglo-German Productivity Differences 1870–1990: A
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berry, S.N. 1997. Anglo-German Productivity Differences 1870–1990: A Sectoral Analysis. European Review of Economic History 1 (2): 247–26 Carreras, A. 1985. Gasto nacional bruto y formación de capital en España,
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Samarán y Compañía. 168 L. Prados de la Escosura Open Access This chapter is licensed under the terms of the Creative Commons
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https://openalex.org/W2283987154 | https://figshare.com/ndownloader/files/2636230 | English | null | AKT1E17K Is Oncogenic in Mouse Lung and Cooperates with Chemical Carcinogens in Inducing Lung Cancer | PloS one | 2,016 | cc-by | 162 | The ARRIVE Guidelines Checklist
Animal Research: Reporting In Vivo Experiments
Carol Kilkenny1, William J Browne2, Innes C Cuthill3, Michael Emerson4 and Douglas G Altman5
1The National Centre for the Replacement, Refinement and Reduction of Animals in Research, London, UK,
2School of Veterinary
Science, University of Bristol, Bristol, UK,
3School of Biological Sciences, University of Bristol, Bristol, UK,
4National Heart and Lung
Institute, Imperial College London, UK,
5Centre for Statistics in Medicine, University of Oxford, Oxford, UK. ITEM
RECOMMENDATION
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paragraph
1,5,6
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paragraph 1, 2
The ARRIVE guidelines. Originally published in PLoS Biology, June 2010
1 The ARRIVE guidelines. Originally published in PLoS Biology, June 2010
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https://openalex.org/W2083611954 | https://europepmc.org/articles/pmc3459871?pdf=render | English | null | Age-Related Patterns in Human Myeloid Dendritic Cell Populations in People Exposed to Schistosoma haematobium Infection | PLoS neglected tropical diseases | 2,012 | cc-by | 10,884 | Age-Related Patterns in Human Myeloid Dendritic Cell
Populations in People Exposed to Schistosoma
haematobium Infection Norman Nausch1*, Delphine Louis2,3, Olivier Lantz2,3,4, Isabelle Peguillet2,3, Franc¸ois Trottein5,
Isobel Y. D. Chen1, Laura J. Appleby1, Claire D. Bourke1¤a, Nicholas Midzi6¤b, Takafira Mduluza7,
Francisca Mutapi1 Norman Nausch1*, Delphine Louis2,3, Olivier Lantz2,3,4, Isabelle Peguillet2,3, Franc¸ois Trottein5,
Isobel Y. D. Chen1, Laura J. Appleby1, Claire D. Bourke1¤a, Nicholas Midzi6¤b, Takafira Mduluza7,
Francisca Mutapi1 1 Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, Ashworth Laboratories, University of
Edinburgh, Edinburgh, United Kingdom, 2 Institut Curie, De´partement de Biologie des Tumeurs, Paris, France, 3 Centre d’Investigation Clinique IGR-Curie, CIC-BT-507
Paris, France, 4 Unite´ Inserm 932, Institut Curie, Paris, France, 5 Center for Infection and Immunity of Lille, Inserm U 1019, CNRS UMR 8204, Universite´ Lille Nord de France
Institut Pasteur de Lille, Lille, France, 6 National Institute of Health Research, Causeway, Harare, Zimbabwe, 7 Department of Biochemistry, University of Zimbabwe, Mount
Pleasant, Harare, Zimbabwe Abstract This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the World Health Organisation (grant no. RPC264), the Wellcome Trust (grant no. WT082028MA; www.wellcome.co.uk)
and by Thrasher Research Funds (www.thrasherresearch.org). The funders had no role in study design, data collection and analysis, decision to publish, or
preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exis * E-mail: nnausch@staffmail.ed.ac.uk ¤a Current address: Biology Department, University of York, York, United Kingdom
¤b Current address: Research Council of Zimbabwe, Harare, Zimbabwe ¤a Current address: Biology Department, University of York, York, United Kingdom
¤b Current address: Research Council of Zimbabwe, Harare, Zimbabwe infection levels increasing to peak in early to late childhood,
typically around 9–15 years and then declining in adulthood [2–
4]. This profile is believed to be largely reflective of the gradual
development of protective acquired immunity reducing re-
infection levels [2,5,6]. The consequence of this age profile is that
individuals with comparable infection levels who have resided in a
schistosome endemic area since birth (e.g. egg negative children Abstract Background: Urogenital schistosomiasis is caused by the helminth parasite Schistosoma haematobium. In high transmission
areas, children acquire schistosome infection early in life with infection levels peaking in early childhood and subsequently
declining in late childhood. This age-related infection profile is thought to result from the gradual development of
protective acquired immunity. Age-related differences in schistosome-specific humoral and cellular responses have been
reported from several field studies. However there has not yet been a systematic study of the age-related changes in human
dendritic cells, the drivers of T cell polarisation. Methods: Peripheral blood mononuclear cells were obtained from a cohort of 61 Zimbabwean aged 5–45 years with a S. haematobium prevalence of 47.5%. Two subsets of dendritic cells, myeloid and plasmacytoid dentritic cells (mDCs and
pDCs), were analyzed by flow cytometry. Findings: In this population, schistosome infection levels peaked in the youngest age group (5–9 years), and declined in late
childhood and adulthood (10+ years). The proportions of both mDCs and pDCs varied with age. However, for mDCs the age
profile depended on host infection status. In the youngest age group infected people had enhanced proportions of mDCs
as well as lower levels of HLA-DR on mDCs than un-infected people. In the older age groups (10–13 and 14–45 years)
infected people had lower proportions of mDCs compared to un-infected individuals, but no infection status-related
differences were observed in their levels of HLA-DR. Moreover mDC proportions correlated with levels of schistosome-
specific IgG, which can be associated with protective immunity. In contrast proportions of pDCs varied with host age, but
not with infection status. Conclusions: Our results show that dendritic cell proportions and activation in a human population living in schistosome-
endemic areas vary with host age reflecting differences in cumulative history of exposure to schistosome infection. Citation: Nausch N, Louis D, Lantz O, Peguillet I, Trottein F, et al. (2012) Age-Related Patterns in Human Myeloid Dendritic Cell Popula
Schistosoma haematobium Infection. PLoS Negl Trop Dis 6(9): e1824. doi:10.1371/journal.pntd.0001824 s D, Lantz O, Peguillet I, Trottein F, et al. (2012) Age-Related Patterns in Human Myeloid Dendritic Cell Populations in People Exposed to
m Infection. PLoS Negl Trop Dis 6(9): e1824. doi:10.1371/journal.pntd.0001824 Editor: Rodrigo Correa-Oliveira, Rene´ Rachou Research Center, Brazil Received October 13, 2011; Accepted August 6, 2012; Published September 27, 2012 Received October 13, 2011; Accepted August 6, 2012; Published September 27, 2012 Copyright: 2012 Nausch et al. Author Summary Since in most
schistosome endemic areas people are exposed to infection from as
young as 6 months old [41], and may already be carrying heavy
infections within the first decade of life [8], these early infection
events may have a profound effect on the proportions of the DCs
present in the host. Characterising the role of these cells during
natural immune responses to helminth infection in the different
age groups is vital for vaccine development, since people targeted
by anti-schistosome vaccines in endemic areas will have been
previously exposed to infection and their cellular immune
responses will already be primed by repeated exposure to parasite
antigens. In this context variations in antigen presenting cell
populations, including DCs, might directly affect the efficacy of
vaccination in different age groups. Lessons from the discontinued
human hookworm vaccine trials, illustrate the importance of
characterising existing natural immune responses in endemic
populations and designing vaccine to avoid undesirable patholog-
ical outcomes of vaccination [42]. Therefore, the aim of this study
was to characterise the relationship between age and DCs during
natural schistosome infections and determine if these patterns are
affected by host infection status across different age groups
reflecting different dynamics in the acquisition and loss of
schistosome infection. versus egg negative adults) can differ significantly in their immune
response against the parasite and thus their levels or resistance to
re-infection. Several
studies
characterizing
human
immune
responses to schistosome infections have shown age related
differences in antibody levels [7–9], plasma cytokines [10],
parasite-specific cytokines [11] and regulatory T cell proportions
[12]. This concept is supported by theoretical modelling of the
development of acquired immunity, which predicts that correla-
tions between immunological responses and infection is positive in
younger age groups and subsequently decreasing and potentially
turning in a negative correlation [13]. Moreover this pattern is not
restricted to schistosome infections, but is a characteristic of
immune responses associated with protection from a variety of
helminth species in endemically-exposed populations [14,15]. As investigations of the nature and development of protective
acquired immunity progress, there has been a move to decipher
the mechanisms and pathways behind these observed age-related
patterns. Human field studies show that the immune response
against schistosomes is characterized by a very complex interaction
of TH1, TH2 and regulatory responses [10–12,16–18] with
differences between natural human infections and experimental
mouse models [19,20]. Author Summary A characteristic feature of most helminth infections is the
convex age infection profile, where infection levels rise to
peak in early childhood and decline in adulthood, a
pattern thought to result from the development of
protective acquired immunity. Thus, several investigations
characterizing protective responses to inform vaccine
research have focused on responses present in older
people, who despite continued exposure to infection carry
little or no infection. To date, such studies have identified
key responses which are correlates of resistance. However,
there is a paucity of information on cell types that are
mediators rather than effectors of the immune responses. One such group where there are limited studies in human
schistosome infections is dendritic cells which are impor-
tant for the polarizations of CD4+ T cell responses. Therefore, we characterized the age profile of dendritic
cells in Zimbabweans exposed to Schistosoma haemato-
bium infection. We found an age-related pattern in the
proportions
of
myeloid dendritic
cells (a
subset of
dendritic cells) in this population. Furthermore, in the case
myeloid dendritic cells, the age profile differed between
schistosome infected and un-infected people. Thus our
study suggests that activation and migration of myeloid
dendritic cells also develop in an age-related pattern
consistent with the cumulative history of exposure to
schistosome parasites. In particular, studies analysing DCs directly from humans
exposed to schistosomes are limited. The first study addressing this
question, published by Everts and colleagues in 2010, elegantly
showed changes in DCs during chronic schistosomiasis (S. haematobium) [32] suggesting that chronic schistosomiasis can
suppress DCs, which might play a role in immune modulation
by schistosomes. y
Peripheral blood DCs can be divided in two major subsets
[33,34], myeloid dendritic cells (mDC; or conventional DC) and
plasmacytoid (pDC). Myeloid DCs express CD11c, but low levels
of CD123 and have a more pronounced role in antigen processing
and initiation of T cell response [35]. Plasmacytoid DCs express
CD303 (BDCA-2), ILT7, high levels of CD123 (IL-3Ra), but are
negative for the classical marker CD11c [33,36–38]. These pDCs
play a critical role in anti-viral immunity as well as in immune
tolerance [39,40]. Everts et al’s [32] study focusing on people aged
17–39 years showed that the frequencies of mDCs and pDCs are
reduced in infected people compared to un-infected and that
mDCs are functionally impaired in response to toll-like receptor
ligands and in driving T cell responses ex vivo. Introduction Schistosoma haematobium helminth parasites cause urogenital
schistosomiasis which affects about 112 million people mainly in
rural areas of subtropical countries [1]. Infections with S. haematobium are most common in school-age children. Populations
in endemic areas show a characteristic age-infection profile with September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org PLOS Neglected Tropical Diseases | www.plosntds.org 1 Myeloid Dendritic Cells and S.haemtobium Infection and early TH2-promoing activities can be diminished by TLR-3
[30]. Overall studies are rare addressing the role of the innate
immune cells in the immune response against schistosomes [31]. Author Summary Nevertheless, the induction of a TH2
response is important in the immune response against schistosomes
[21] and in particular for the development of protection [22]. As a
major antigen-presenting cell population dendritic cells (DCs) are
responsible for acquiring, processing and presenting parasite
antigens to T cells and the latter interaction leads to activation
and polarisation of the acquired immune response. The impor-
tance of DCs in the induction of the TH2 immune responses in the
context of schistosome infections has been recently highlighted in
an experimental mouse model [23]. This study indicates that DCs
are required for the induction and development of TH2 responses
during schistosome infections supporting other studies showing the
importance of DCs in the context of TH2 induction [24–27]. PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 Study population and parasitology This study was performed in Chipinda village which is located
in the Mashonaland East Province in Zimbabwe (31u949E;
17u679S). The village was selected because health surveys regularly
conducted in the region showed little or no infection with soil-
transmitted helminths (STH) and a low S. mansoni prevalence
(,2%), which elicit immune responses that cross-react with those
against S. haematobium [43,44,45]. The low STH and S. mansoni
prevalence is consistent with earlier surveys in this area of
Zimbabwe [46–48]. Villagers are subsistence farmers who have
frequent contact with water sources posing a risk of infection (as
assessed by questionnaires) due to insufficient safe water provision
and low coverage of sanitation facilities as is typical in rural
Zimbabwe. Drinking water is collected from open wells while
bathing and washing is conducted in perennial rivers surrounding
the village. This area has not been included in any Schistosome It has been shown that schistosome derived compounds can
activate dendritic cells by toll-like receptors (TLR)-2 and 3 [28,29] PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 2 Myeloid Dendritic Cells and S.haemtobium Infection Myeloid Dendritic Cells and S.haemtobium Infection Control Programmes and therefore participants had not received
any
anti-helminthic
treatment
for
schistosomiasis
or
other
helminth infections prior to this study. Thus their natural immune
responses could be assessed in the absence of drug-altered
schistosome-specific responses [49,50]. Urine and stool samples
were collected on three consecutive days and examined micro-
scopically for S. haematobium (urine filtration, Mott method [51]) or
S. mansoni and intestinal helminths (Kato-Katz method [52])
respectively using standard procedures. Participants were screened
for malaria by microscopic examination of Giemsa stained blood
smears and HIV status was determined by immunochromato-
graphy (DoubleCheckGoldTM HIV 1&2, Orgenics) with HIV
positive samples subsequently re-tested by a second rapid assay
(Determine HIV 1/2 Ag/Ab Combo, InvernessMedical) to
confirm HIV status [53]. Study participants had to meet the
following criteria: (1) be life-long residents in this area (assessed by
questionnaires) so that age would be a proxy for duration of
exposure to S. haematobium infection, (2) should not have received
anti-helminthic treatment prior to this study, (3) should have
provided at least two urine and two stool samples on consecutive
days for parasitological diagnosis, (4) should have tested negative
for intestinal helminths including S. Blood collection and isolation of PBMC Depending on age of the participants up to 25 ml of venous
blood was collected in heparinized tubes of which approximately
5 ml was used for serological assays as well as microscopic
detection of malaria parasites. The remaining blood was used for
the isolation of peripheral blood mononuclear cells (PBMC)
through density gradient centrifugation using Lymphoprep (Axis-
Shield, Cambridgeshire, UK). These PBMC were subsequently
enumerated, cryo-preserved in 10% DMSO, 90% fetal calf serum
and stored in liquid nitrogen in Zimbabwe prior to shipping to
Edinburgh in dry shippers for assaying. Ethical statement Permission to conduct the study in the region was obtained from
the Provincial Medical Director and institutional and ethical
approval was received from the University of Zimbabwe’s Institute
Review Board and the Medical Research Council of Zimbabwe
respectively. Only compliant participants were recruited and they
were free to drop out at any point during the study. At the
beginning of the study, participants and their parents/guardians
(in case of children) had the aims and procedures of the project
explained fully in the local language, Shona, and written consent
was obtained from participants and parents/guardian before
parasitology and blood samples were obtained. After collection of
all samples, all participants were offered anti-helminthic treatment
with the recommended dose of praziquantel (40 mg/kg of body
weight). DC phenotyping Thawing of cryo-preserved PBMC was performed by rotating
cryovials in a 37uC water bath until a small crystal was remaining
in the cell suspension. Cells were then slowly re-suspended in
RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine
and 100 U Penicillin/Streptomycin (all Lonza, Verviers, Belgium). Cells were washed twice with media, counted and viability assessed
using trypan blue (Sigma-Aldrich, Dorsert, UK). The median
viability of the PBMCs was 71.4% which is within the range of
published values [54]. In addition it was confirmed that including
a viability marker did not change analysis of subsets. Afterwards,
cells were washed with Dulbecco’s-PBS (Lonza) and surface
stained with the following antibodies: Qdot-605-conjugated anti-
CD14 (clone TUK4, Invitrogen), FITC-conjugated anti-CD11c
(clone
Bu15, Invitrogen),
APC-H7-conjugated
anti-HLA-DR
(clone L243, BD Biosciences), PE-Cy5. anti-CD123 (clone 9F5,
BD Biosciences) and V450 BD Horizon-conjugated anti-CD86
(clone 2331, BD Biosciences), PE-conjugated anti-BDCA-2 (clone
AC144, Miltenyi Biotec) and APC-conjugated anti-BDCA-4
(clone AD5-17F6, Miltenyi Biotec). Stained cells were acquired
on a FACSCantoII (BD Biosciences) and analyzed using FlowJo
software software (TreeStar, USA). Study population and parasitology mansoni to focus on single
infections with S. haematobium, (5) should be negative for HIV and
malaria (Prevalence of both HIV and malaria were too small for
inclusion in the statistical analysis (HIV prevalence in Chipinda
village was 8% and no-one was positive for malaria infection at the
time of sampling) and (6) have provided a sufficient volume of
blood to isolate peripheral blood mononuclear cells (PBMC). The
selected cohort comprised 61 individuals and details to the cohort
are provided in Table 1. Epidemiology of study population p
gy
y p p
This study was designed to focus on the immune modulation in
a population exposed to S. haematobium. The northeast part of
Zimbabwe is endemic for S. haematobium with many regions having
a moderate to high prevalence of S. haematobium, but low
prevalence of S. mansoni and soil-transmitted helminths [47,48]. The overall prevalence in Chipinda was (39%). This is defined by
the World Health Organisation (WHO) as a moderate transmis-
sion area [58]. The overall prevalence of S. haematobium in the
selected study population (N = 61) was 47.5% which is higher but
not significantly different from (x2 = 1.688, df = 1, p = 0.097) the
village prevalence of 39% and still within the WHO definition of
moderate transmission. The difference in infection prevalence
between the youngest age group (35.3%) compared to more than
50% in the older age groups was not significant (x2 = 0.806, df = 1,
p = 0.185; details in Table 1). However, youngest individuals (5–9
years) who were infected carried high infection levels (Figure 1 and
Table 1). Individuals aged 10–13 years still showed high infection
levels, but with a higher prevalence than the first age group. In
contrast, in the oldest age group (14–45 years), the prevalence
remained high, but most individuals show lower infection
intensities (Figure 1). The consequence of the infection profile is
that individuals who are life long residents in the area and have
never received treatment with anti-helminthic drugs (see selection
criteria in Methods) differ in their cumulative histories of exposure
despite
carrying
comparable
infection
intensities. This
was
supported by an analysis of the serum levels of adult worm
specific (whole worm homogenate – WWH) antibody levels. As
shown in Figure 2A and B levels of WWH-specific IgE and IgG,
which are associated with history of infection and resistance to
infection [59–61], increase significantly with age. In contrast IgM
against WWH as marker of current infection starts to decrease in
the oldest age group (Figure 2C). Statistical analysis y
The proportions of DC cell subsets were square root arcsine
transformed whereas expression levels of HLA-DR and CD86
were square root transformed to allow the use of parametric tests
in subsequent analyses [56]. To analyse which factors influence the
proportion of DC subsets, a univariate analysis of variance using
sex (male/female), host age groups (group 1: 5–9 years; group 2:
10–13 years; group 3: 14+ years) and infection status (un-
infected = 0 mean egg count per 10 ml and infected .0 mean
egg count per 10 ml; all variables categorical) as independent
variables was performed. The three different age groups were
selected to reflect epidemiological groupings (i.e. where infections
are acquired, peak and decline) by age and infection intensity and
to obtain comparable sample sizes between the groups. Post hoc
tests between infected and un-infected individuals were conducted
in each age group. In addition post hoc analysis was performed to
determine differences in pDCs between the three age groups. To
determine if the mDC populations showed an age profile
consistent with those for protective immune responses as predicted
by quantitative studies [13], correlation analyses between infection
intensity (log10 (mean egg count+1) transformed) and proportions
of mDCs was conducted after allowing for the effect of sex. The
correlation coefficients were then tested for homogeneity using the
Fisher’s r-to-z transformation [57]. Correlation analyses between
WWH-specific IgG and DC cell subsets were performed after
allowing for the effects of sex, age and infection intensity. All
statistical tests were conducted using the software package SPSS
v14 and p values were taken to be significant at p,0.05. Figure 1. Age – infection profile of the study population. The
study population was divided into three age groups: 5–9 years (N = 17),
10–13 years (N = 23) and 14+ years (N = 21). Mean infection intensities
from at least two urine samples for each individual are given. The mean
for each group is indicated. doi:10.1371/journal.pntd.0001824.g001 Characterization of mDCs and pDCs in total study
population To analyze mDCs and pDCs, PBMC were gated on CD14negHLA-
DR+ cells (Figure 3A, B). Gated cells were stained with CD123 and
CD11c to distinguish mDCs (CD11c+CD123neg/low) from pDCs
(CD123hiCD11cneg; Figure 3C). To further verify specificity of pDC
gated CD123hiCD11cneg were analysed for the expression of BDAC-
2/CD303 and BDCA-4/CD304 [62] and granularity of gated cells
was analysed in an FSC/SSC plot (Figure 3D). Therefore other cell
types such as basophiles or B cell potentially able to express CD123 are
excluded from the analysis. mDC did not express either BDCA-2 or
BDCA-4 (Figure 3E). Subsets were expressed as percentages of PBMC
or as percentage of CD14negHLA-DR+ cells. Both subsets were
subsequently analysed for the expression of CD86 (Figure 3D, E) and
levels of HLA-DR within the two different DC populations as
indicators of DC activation status and their ability to present antigen
and co-stimulatory signals to T cells. When the study population was portioned by infection status (un-
infected versus infected), neither mDCs (Figure 4A) nor pDCs
(Figure 4B) showed a significant difference between both popula-
tions. Comparable results were obtained if DC subsets were
expressed as percentage of CD14negHLA-DR+ (data not shown). Myeloid DCs showed a significant association with sex (Table 2), in
which female had slightly higher proportions than males. This was
then statistically accounted for in all subsequent analyses. Antibody ELISAs y
Serum antibody levels were measured by enzyme-linked
immunosorbent assays (ELISA) following established protocols
[8,55]. Whole worm homogenate (WWH) was obtained from the
Theodor Bilharz Research Institute (Giza, Egypt). In short,
microtiter plates were coated overnight at 4uC at 10 mg/ml. Serum samples were diluted at 1:20 for WWH-IgE and 1:100 for
WWH-IgG and IgM and incubated for 2 hours at 37uC. Horse-
radish peroxide conjugated antibodies were diluted 1:1000 for
IgG, IgE and IgM and incubated for 1 hour at 37uC. ELISAs were
developed using ABTS (Southern Biotech) and stopped after
15 minutes for IgG and IgM, and 30 minutes for IgE. Absorbance
was read at 405 nm. Serum was available from 45 out of 61
individuals. Table 1. Study population. Table 1. Study population. S. haematobium
Age group
N
mean age in years (range)
Male/female
Prevalence in % (95% CI)
Mean egg count ± SEM (range)
Total
61
14.1 (5–45)
27/34
47.5 (35.6–59.9)
51.6619.3 (0–859)
Group 1
17
7.6 (5–9)
8/9
35.3 (15.9–54.8)
78.1651.4 (0–859)
Group 2
23
11.1 (10–13)
8/15
52.2 (36.0–68.5)
47.7625.9 (0–571)
Group 3
21
22.6 (14–45)
11/10
52.4 (35.0–69.9)
34.5626.0 (0–550)
SEM – Standard error of mean, CI – Confidence interval. doi:10.1371/journal.pntd.0001824.t001
PLOS Neglected Tropical Diseases | www.plosntds.org
3
September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org Myeloid Dendritic Cells and S.haemtobium Infection Figure 1. Age – infection profile of the study population. The
study population was divided into three age groups: 5–9 years (N = 17),
10–13 years (N = 23) and 14+ years (N = 21). Mean infection intensities
from at least two urine samples for each individual are given. The mean
for each group is indicated. doi:10.1371/journal.pntd.0001824.g001 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org Expression of CD86 and HLA-DR on mDCs and pDCs Expression of CD86 and HLA-DR on mDCs and pDCs
Up-regulation of CD86 is hallmark of maturation and activation
of DCs and their ability to provide co-stimulatory signals to T cells. HLA-DR expression can be used as an indicator both of DC
activation status and their potential to activate antigen-specific T
cells. Neither infection status nor the interaction between infection
status and age group influenced expression of CD86 on mDC as Age dependent pattern of mDCs and pDCs Age dependent pattern of mDCs and pDCs The age in the total population ranged from 5–45 years. Age
group significantly affected the proportions of pDCs (Table 2), September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 4 Myeloid Dendritic Cells and S.haemtobium Infection Figure 2. Schistosome-specific antibody profiles. Serum levels of WWH-specific IgE (A), IgG (B) and IgM (C) were analysed by ELISA. Obtained
data are presented after diving into the three indicated age groups. Correlation coefficient b and significant values are indicated. The effect of sex has
been statistically allowed for. doi:10.1371/journal.pntd.0001824.g002 Figure 2. Schistosome-specific antibody profiles. Serum levels of WWH-specific IgE (A), IgG (B) and IgM (C) were analysed by ELISA. Obtained
data are presented after diving into the three indicated age groups. Correlation coefficient b and significant values are indicated. The effect of sex has
been statistically allowed for. doi:10.1371/journal.pntd.0001824.g002 with a significant increase between 5–9 year olds (age group 1) and
14+ year olds (age group 3; p = 0.033). In contrast for mDCs the
relationship with age varied depending on infection status
(significant interaction between age group and infection status;
Table 2). Based on these results post hoc analysis of mDC
proportions by infection status was performed after partitioning
the study population into the three different age groups (details in
Table 1). In the youngest age group (Figure 5A) infected people
had significantly higher mDC percentages than un-infected
people. Results were comparable if expressed as percentage of
CD14negHLA-DR+ (Figure S1A). This pattern differed in the
second age group, where infected individuals showed fewer mDCs
than un-infected individuals (Figure 5B) a difference which was
even more pronounced in the oldest age groups (Figure 5C). A
comparable analysis could be made by correlating infection
intensity (rather than infection status) to percentages of mDCs in
the three different age groups. In the youngest age group both
parameters were positively correlated (b = 0.707, p = 0.001),
whereas in the second age group the correlation was instead
negative (b = 20.441, p = 0.018). This negative correlation was
more pronounced in the third group (b = 20.540, p = 0.007;
Figure 6). Age dependent pattern of mDCs and pDCs A test for the homogeneity of the correlations
coefficients showed a significant difference between age group
one and two (z = 3.89, p = 0.0001) and between the first and the
third age group (z = 4.17, p,0.0001). Interaction between mDCs and WWH-IgE Interaction between mDCs and WWH IgE
Adult worm specific IgG can be used as a marker development
of resistance against infection [59–61]. WWH-specific IgG
increases with age and in our population especially between the
first and second age group (Figure 2B) and to the same time
changes in mDC proportions between un-infected and infected
individuals occurred. Therefore the interaction between mDC and
WWH-specific IgG was analysed. As indicated in Table S1,
WWH-specific IgG is influenced by sex, age and infection
intensity, but addition also by proportions of mDC. mDC are
directly correlated to WWH-specific IgG after allowing for the
effects of sex, age and infection (Figure 9A). Although showing the
same tendency pDCs and WWH-specific IgG were not signifi-
cantly correlated (Figure 9B). This correlation was most obvious in
the oldest age group (Table S2) and overall more significant in un-
infected (protected) individuals. Correlation between mDC pro-
portions and WWH-specific IgE and IgM were not significant. In contrast, to the clear picture in the case of mDCs, there was
no significant difference in the proportion of pDCs (expressed
either relative to live PBMC or CD14negHLA-DR+) between un-
infected and infected people in any of the three age groups as
shown in Figure 7, Figure S1B and Table 2. Age dependent pattern of mDCs and pDCs A test for the homogeneity of the correlations
coefficients showed a significant difference between age group
one and two (z = 3.89, p = 0.0001) and between the first and the
third age group (z = 4.17, p,0.0001). determined by ANOVA (Table 2), which was confirmed by post
hoc tests comparing CD86 expression between un-infected and
infected people after partitioning into age group (Figure 8A). However HLA-DR expression was significantly influenced by an
interaction of age group and infection status (Table 2). Post hoc
test showed that HLA-DR expression differed between un-infected
and infected individuals, in the youngest age group. In this age
group HLA-DR was significantly lower on mDCs from infected
people compared to un-infected (Figure 8B). In contrast no
difference was observed in HLA-DR expression in people 10–13
years of age or in the oldest age group. Neither CD86 nor HLA-
DR expression on pDCs were dependent on age group, infection
status or the interaction of these variables (Table 2). with a significant increase between 5–9 year olds (age group 1) and
14+ year olds (age group 3; p = 0.033). In contrast for mDCs the
relationship with age varied depending on infection status
(significant interaction between age group and infection status;
Table 2). Based on these results post hoc analysis of mDC
proportions by infection status was performed after partitioning
the study population into the three different age groups (details in
Table 1). In the youngest age group (Figure 5A) infected people
had significantly higher mDC percentages than un-infected
people. Results were comparable if expressed as percentage of
CD14negHLA-DR+ (Figure S1A). This pattern differed in the
second age group, where infected individuals showed fewer mDCs
than un-infected individuals (Figure 5B) a difference which was
even more pronounced in the oldest age groups (Figure 5C). A
comparable analysis could be made by correlating infection
intensity (rather than infection status) to percentages of mDCs in
the three different age groups. In the youngest age group both
parameters were positively correlated (b = 0.707, p = 0.001),
whereas in the second age group the correlation was instead
negative (b = 20.441, p = 0.018). This negative correlation was
more pronounced in the third group (b = 20.540, p = 0.007;
Figure 6). PLOS Neglected Tropical Diseases | www.plosntds.org Discussion Urogenital schistosomiasis caused by S. haematobium shows a
characteristic age-infection profile with increasing infections
intensities during early childhood, peaking usually between the
age of 9–15 years and than slowly declining towards adulthood [2– September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 5 Myeloid Dendritic Cells and S.haemtobium Infection Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c
and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA-
4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10.1371/journal.pntd.0001824.g003 Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c
and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA-
4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10.1371/journal.pntd.0001824.g003 Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c
and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA-
4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10 1371/journal pntd 0001824 g003 4]. This study investigated whether the age-related changes in
schistosome infection pattern impacted on the proportions and
phenotype of DCs. 4]. This study investigated whether the age-related changes in
schistosome infection pattern impacted on the proportions and
phenotype of DCs. specific IgG are correlated with proportions of mDCs. This effect
was more significant in the oldest age group, in which protective
immunity becomes effective. We provide evidence that indeed there is an age-related pattern
in the proportions of mDCs, if infected and un-infected people
were compared. The proportion of mDCs were found to be
present in significantly higher proportions in infected individuals
compared to un-infected individuals in the youngest age group
carrying heaviest infection levels. This subsequently changes in
older age groups, were older infected individuals had lower
relative numbers of mDCs compared to un-infected people. September 2012 | Volume 6 | Issue 9 | e1824 Discussion PBMC (N = 61) were analysed for proportions of (A) CD123neg/lowCD11c+ mDCs or (B)
CD123hiCD11cneg pDCs (expressed as % of PBMC). Data of the total population were divided in un-infected (N = 32, white box) and infected
individuals (N = 29, gray box). Data are presented as Whiskers boxplot (10–90 percentiles). Differences were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g004 Plasmodium or HIV, that in Gabon had co-infections with
microfilaria
observed
in
48%
of
the
schistosome
infected
individuals which could affect the pDCs proportions. clearly shown for schistosome-specific IgG, IgE and IgM. The
importance of DC in TH2 induction has been recently shown [23]. By altering cytokine responses DC could finally be involved in
isotype switching and development of protective immunity. This is
supported by our finding of the correlation between schisotosome-
specific IgG and mDCs. Both our study and that of Everts et al [32] clearly indicate the
difference in mDC populations between infected and un-infected
adults. However, since infections in moderate to high transmission
areas occur at relatively young age, we were interested in the
dynamics of the DCs over time, which was not possible in Evert’s
study. We wanted to determine when if at all the difference
between infected and un-infected people was established. There-
fore, we analysed DC cell populations in younger age groups. Our
study demonstrates that a lower frequency of mDCs in infected
people can be already observed in 10–13 year olds. This is
accordance with changes in other immunological parameters as Changes with age have been also observed for serum cytokines
in other study populations with moderate/high schistosome
transmission [10,11,64]. For instance, high levels of parasite-
specific or serum levels of IL-10 have been reported already at this
age in different populations [11,65] and might contribute to such
changes. For example, DCs treated with the regulatory cytokine
IL-10 inhibit T cell activation [66–69]. Earlier studies showed that
T cell hypo-responsiveness can be already observed at early ages Table 2. Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on
both subsets. e group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on Table 2. Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA
both subsets. Table 2. Discussion The
gradual change between the three age groups became more
apparent when the correlation between infection intensity (rather
than infection status) and mDCs proportions were considered. In
this case both parameters were positively correlated in the
youngest age group and became a negative correlation with
increasing age. This pattern is consistent with that predicted by
quantitative studies for protective immune responses and has
already been demonstrated for antibody responses associated with
protection
to
re/infection
in
human
hookworm
[63]
and
schistosome infections [64]. Importantly levels of adult worm Our data confirm some of the major findings of a previous study
of DC populations in human schistosomiasis conducted by Everts
et al [32]. Proportions of mDCs were lower in an age group 14–45
years (mean 22.6 years) which is comparable to the population
studied by Everts et al (17–39 years). Since cellular immune
responses might depend on many different parameters such as
transmission dynamics or genetic background of the investigated
study population the consistency in DC proportions in schisto-
some-exposed human between our study and that by Everts et al,
by itself is an important finding. A major difference between the
two studies is that we did not observe differences in pDC
percentages in regards to infection status, although we had high
variation in pDC levels in the oldest age group. In deed a slight
tendency of lower pDC proportions (expressed as percentage of
PBMC) was observed in this age group. Differences in co-
infections may also account for the differences between our
observations and those of Everts et al [32] in Gabon. While the
population in Zimbabwe had no co-infection with other helminths, September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 6 Myeloid Dendritic Cells and S.haemtobium Infection Figure 4. Proportions of DCs in the study population. PBMC (N = 61) were analysed for proportions of (A) CD123neg/lowCD11c+ mDCs or (B)
CD123hiCD11cneg pDCs (expressed as % of PBMC). Data of the total population were divided in un-infected (N = 32, white box) and infected
individuals (N = 29, gray box). Data are presented as Whiskers boxplot (10–90 percentiles). Differences were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g004 Figure 4. Proportions of DCs in the study population. Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in
bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression.
doi:10 1371/journal pntd 0001824 t002 PLOS Neglected Tropical Diseases | www.plosntds.org
7
September 2012 | Volume 6 | Issue 9 | e1824 Discussion Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on
both subsets. Dependent variable
Proportions of DCs
HLA-DR expression
CD86 expression
DC population
Explanatory variable
df
F – value
p – value
df
F – value
p – value
df
F – value
p – value
mDC
sex
1, 60
4.659
0.35
1, 60
2.049
0.158
1, 60
0.297
0.588
age group
2, 60
0.646
0.528
2, 60
0.068
0.934
2, 60
0.064
0.938
infection status
1, 60
3.392
0.071
1, 60
0.372
0.544
1, 60
0.424
0.518
Age group * infection status
2, 60
11.963
,0.001
2, 60
3.865
0.027
2, 60
0.763
0.471
pDC
sex
1, 60
2.509
0.119
1, 60
2.240
0.140
1, 60
0.015
0.902
age group
2, 60
3.544
0.036
2, 60
0.075
0.928
2, 60
0.092
0.912
infection status
1, 60
1.237
0.271
1, 60
0.842
0.363
1, 60
1.184
0.281
Age group * infection status
2, 60
0.074
0.929
2, 60
1.246
0.296
2, 60
1.267
0.290
Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in
bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression. doi:10.1371/journal.pntd.0001824.t002 Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in
bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression. doi:10.1371/journal.pntd.0001824.t002 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 7 Myeloid Dendritic Cells and S.haemtobium Infection Figure 5. Proportions of mDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B)
and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as %
percentage of PBMC. Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g005 Figure 5. Proportions of mDCs in different age groups. Discussion The study population was divided into three age groups: 5–9 years (A), 10–13 years (B)
and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as %
percentage of PBMC. Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g005 [70,71]. The role of mDCs in induction of this impairment
remains to be further investigated. cytokines as well as IL-10 in older individuals (17–39 years). The
mechanisms involved are still unclear since despite this impair-
ment of DC function, older individuals carrying schistosome
infection can show enhanced immunopathology [74,75] indicating
an effective immune response. Other reasons for reduced relative numbers of mDCs in
infected individuals in older age groups remain to be determined,
e.g. enhanced apoptosis, reduced bone marrow output or
increased migration to inflamed tissues or lymphoid organs were
proposed by Everts et al [32]. Indeed enhanced migration in the
context of TH2 priming DCs has been reported [25,72]. This was
induced by eosinophil-derived neurotoxin; a molecule elevated in
serum of S. haematobium infected people [73]. Everts et al reported a
more general impairment of DCs affecting both TH1 and TH2 In contrast, our data show that in the younger individuals (5–9
years) mDCs proportions were higher in peripheral blood of
infected individuals in comparison to un-infected. Potential
reasons for this include enhanced bone marrow output or reduced
migration of DCs in the context of blood-born antigens [76]. Infection levels were highest in the youngest age group of our Figure 6. Correlation between infection intensity and mDCs. The study population was divided into three age groups: 5–9 years (left panel),
10–13 years (middle panel) and 14+ years (right panel). Proportions of mDCs expressed as % of PBMC are plotted against infection intensity (log10
(mean egg count+1) transformed). Correlation coefficient b and significant values of a correlation analysis after allowing for the effect of sex are
indicated. doi:10.1371/journal.pntd.0001824.g006 Figure 6. Correlation between infection intensity and mDCs. The study population was divided into three age groups: 5–9 years (left panel),
10–13 years (middle panel) and 14+ years (right panel). Proportions of mDCs expressed as % of PBMC are plotted against infection intensity (log10
(mean egg count+1) transformed). Correlation coefficient b and significant values of a correlation analysis after allowing for the effect of sex are
indicated. Discussion doi:10.1371/journal.pntd.0001824.g006 September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 8 Myeloid Dendritic Cells and S.haemtobium Infection Figure 7. Proportions of pDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B)
and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as
percentage of PBMC (B). Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g007 Figure 7. Proportions of pDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B)
and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as
percentage of PBMC (B). Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after
accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g007 study population and young people might have more blood
migrating schistosome stages affecting proportions of circulating
mDCs. In
contrast
enhanced
immune
response
including
enhanced migration of mDCs might lead to increased killing of
infiltrating schistosomula in older age groups. we observed no changes in expression of CD86 in infected
people. However HLA-DR levels differed. In the youngest age
group (5–9 years), where we found higher percentages of
mDCs, expression levels of HLA-DR were lower in infected
people. Reduced HLA-DR expression might be an indication
of less matured and possibly fewer migrating cells, which
subsequently could result in a less pronounced induction of T
cell response in an early phase of exposure to schistosomes we observed no changes in expression of CD86 in infected
people. However HLA-DR levels differed. In the youngest age
group (5–9 years), where we found higher percentages of
mDCs, expression levels of HLA-DR were lower in infected
people. Reduced HLA-DR expression might be an indication
of less matured and possibly fewer migrating cells, which
subsequently could result in a less pronounced induction of T
cell response in an early phase of exposure to schistosomes Dendritic cell activation/maturation is characterised by up-
regulation of cell-surface markers such as CD86 and MHC
class II molecules. As previously reported by Everts et al [32], Figure 8. PLOS Neglected Tropical Diseases | www.plosntds.org Discussion Expression levels of CD86 and HLA-DR on mDCs. PBMC were gated on mDCs as indicated in Figure 2 and analysed for the
expression of CD86 (A) and HLA-DR (B). Data partitioned into three age groups as indicated and compared between un-infected (white columns) and
infected individuals (gray columns). doi:10.1371/journal.pntd.0001824.g008 Supporting Information accompanied by a more regulatory environment due to Tregs
and parasite-specific IL-10 [11,12,65]. Analysis of Tregs from
another study cohort from the same population revealed a
comparable pattern as recently published by our group [12]. In
addition a direct comparison of mDCs and Tregs would need a
larger sample size, since statistical power is lost by comparing
the two parameters in the presence of other potentially
confounding variables such as host age. Figure S1
Proportions of mDCs and pDCs expressed as
percentage of CD14neg-HLA-DR+ cells. The study popula-
tion was divided into three age groups: 5–9 years (A), 10–13 years
(B) and 14+ years (C). Proportions of mDCs (A) or pDC (B) were
compared between un-infected (white box) and infected (gray box)
individuals and expressed as % percentage of CD14neg-HLA-
DR+. Differences between un-infected and infected groups in the
different age groups were analysed by univariate analysis after
accounting for the effect of sex. (TIF) In contrast to the study by Everts et al, we did not observe a
significant difference of HLA-DR levels in the older age groups. Again more significant changes of HLA-DR in these age groups
might be due to cumulative effect of co-infections, not present in
our study population. Acknowledgments In summary this study clearly shows there is an age-related
pattern in the proportions mDCs in people exposed to S. haematobium infection as is typical for many already investigated
humoral and cellular responses. Furthermore, in the case of
mDCs, this pattern differs between schistosome infected and un-
infected people and also follows the age profile with infection of
protective responses, which is supported by the correlation
between schistosome-specific IgG and proportions of mDCs. We would like to thank the residents and children of Chipinda village as
well as the teachers from Chipinda primary and secondary school for
their participation and generous and kind support of this study. We are
also very grateful for the co-operation of the Ministry of Health and
Child Welfare in Zimbabwe. We like to thank the Provincial Medical
Director of Mashonaland East, the Environmental Health Workers,
nursing staff at Chitate Clinics and Murehwa Hospital. We are grateful
to the members of the National Institutes of Health in Harare and the
Biochemistry Department at University of Zimbabwe for technical and
logistical support. The mechanism and consequences (such as alterations in the
potential to induce different T cell phenotypes) behind the
association between mDCs and infection remain to be determined. Understanding the nature and dynamics of immunological
parameters in natural helminth infections and, in particular,
changes of DCs involved in polarising the immune responses has
an important impact on the development of vaccines against
schistosomes. Table S1
Interaction between WWH-IgE and mDC or
pDC. Inhibition of up-regulation of activation markers such as CD86 has
been suggested to be involved in induction of tolerogenic DCs [66]. However we did not see changes in the activation marker CD86. There is need to analyse other markers, such as B7-H1, B7-H2, lg-like
transcripts 3 and 4 which might play a role in the function of
tolerogenic DCs [77–81], particularly in younger age groups. Figure 8. Expression levels of CD86 and HLA-DR on mDCs. PBMC were gated on mDCs as indicated in Figure 2 and analysed for the
expression of CD86 (A) and HLA-DR (B). Data partitioned into three age groups as indicated and compared between un-infected (white columns) and
infected individuals (gray columns). doi:10.1371/journal.pntd.0001824.g008 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 9 Myeloid Dendritic Cells and S.haemtobium Infection Figure 9. Correlation between WWH-IgG and proportions of mDCs and pDCs. Serum levels of WWH-specific IgG were measured by ELISA. The effects of sex, age and infection intensity was statistically allowed for and residuals of this analysis were plotted against proportions of mDCs (A)
or pDCs (B) in percentage of PBMC. b-coefficient and p- values of a linear correlation are indicated. doi:10.1371/journal.pntd.0001824.g009 Figure 9. Correlation between WWH-IgG and proportions of mDCs and pDCs. Serum levels of WWH-specific IgG were measured by ELISA. The effects of sex, age and infection intensity was statistically allowed for and residuals of this analysis were plotted against proportions of mDCs (A)
or pDCs (B) in percentage of PBMC. b-coefficient and p- values of a linear correlation are indicated. doi:10.1371/journal.pntd.0001824.g009 Table S2
Correlation between WWH-IgE and mDC or
pDC. p
(TIF) Functional studies, will be very informative and will clarify some
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levels of Schistosoma mansoni infection but very different durations of residence. Trans R Soc Trop Med Hyg 98: 125–136. 62. Dzionek A, Inagaki Y, Okawa K, Nagafune J, Rock J, et al. (2002) Plasmacytoid
dendritic cells: from specific surface markers to specific cellular functions. Hum
Immunol 63: 1133–1148. 75. Myeloid Dendritic Cells and S.haemtobium Infection Mohamed-Ali Q, Elwali NE, Abdelhameed AA, Mergani A, Rahoud S, et al. (1999) Susceptibility to periportal (Symmers) fibrosis in human schistosoma mansoni
infections: evidence that intensity and duration of infection, gender, and
inherited factors are critical in disease progression. J Infect Dis 180: 1298–1306. 63. Quinnell RJ, Bethony J, Pritchard DI (2004) The immunoepidemiology of
human hookworm infection. Parasite Immunol 26: 443–454. 64. Mutapi F, Mduluza T, Gomez-Escobar N, Gregory WF, Fernandez C, et al. (2006) Immuno-epidemiology of human Schistosoma haematobium infection:
preferential IgG3 antibody responsiveness to a recombinant antigen dependent
on age and parasite burden. BMC Infect Dis 6: 96. p
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concomitant Schistosoma haematobium infection on the serum cytokine levels
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ICOS in directing T cell responses: ICOS-dependent induction of T cell anergy
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tolerance by IL-10-treated dendritic cells. J Immunol 159: 4772–4780. 67. Steinbrink K, Graulich E, Kubsch S, Knop J, Enk AH (2002) CD4(+) and
CD8(+) anergic T cells induced by interleukin-10-treated human dendritic cells
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myelomonocytic cells express an inhibitory receptor for classical and nonclassical
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80. Selenko-Gebauer N, Majdic O, Szekeres A, Hofler G, Guthann E, et al. (2003)
B7-H1 (programmed death-1 ligand) on dendritic cells is involved in the
induction and maintenance of T cell anergy. J Immunol 170: 3637–3644. References (2012) Schistosoma
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anti-schistosome and anti-mite antibodies. Parasite Immunol. 27. Faveeuw C, Angeli V, Fontaine J, Maliszewski C, Capron A, et al. (2002)
Antigen presentation by CD1d contributes to the amplification of Th2 responses
to Schistosoma mansoni glycoconjugates in mice. J Immunol 169: 906–912. September 2012 | Volume 6 | Issue 9 | e1824 11 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 Myeloid Dendritic Cells and S.haemtobium Infection PLOS Neglected Tropical Diseases | www.plosntds.org Myeloid Dendritic Cells and S.haemtobium Infection 69. Torres-Aguilar H, Aguilar-Ruiz SR, Gonzalez-Perez G, Munguia R, Bajana S,
et al. (2010) Tolerogenic dendritic cells generated with different immunosup- 81. Sumpter TL, Thomson AW (2011) The STATus of PD-L1 (B7-H1) on
tolerogenic APCs. Eur J Immunol 41: 286–290. September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 12 |
https://openalex.org/W4298076168 | https://zenodo.org/records/7129551/files/SciRoc_WP2%20-%20ERL-SR%20Rulebook%20Update%20(a)%20-%20Deliverable%202.1%20-%20V1.0.pdf | English | null | SciRoc_WP2 - ERL-SR Rulebook Update (a) - Deliverable 2.1 - V1.0 | Zenodo (CERN European Organization for Nuclear Research) | 2,018 | cc-by | 36,625 | Deliverable 2.1
ERL-SR* Rulebook Update (a)
*Note: currently named ERL Consumer Service Robots
Project acronym:
SCIROC
Project number:
780086
Project title
European Robotics League plus Smart Cities Robot
Competitions
WP number and title:
WP2 – ERL Service Robots
WP leader:
IST-ID
Organisation responsible for
deliverable:
Associação do Instituto Superior Técnico para a
Investigação e Desenvolvimento (IST-ID)
Deliverable author(s):
Pedro Lima (IST-ID)
Meysam Basiri (IST-ID)
Deliverable version number:
1.0
Actual delivery date:
28/09/2018
Dissemination Type
Report
Dissemination level:
Public
Change log
Version
Date
Author
Reason for change
0.1
11/09/2018
Pedro Lima, Meysam Basiri N/A
1.0
28/09/2018
Pedro Lima, Meysam Basiri
Reviewed by Matthew Studley
Release approval
Version
Date
Name and organisation
Role
1.0
28/09/2018
Matthew Studley
Coordinator
This project has received funding from the European Union’s European Union’s Horizon 2020
research and innovation programme under grant agreement n° 780086. This project has received funding from the European Union’s European Union’s Horizon 2020
research and innovation programme under grant agreement n° 780086. European Robotics League plus
Smart Cities Robot Competitions
Horizon 2020
ERL Consumer
European Robotic League for Consumer Service Robots
Latest Update:
Editors:
Contributors:
September 10, 2018
Meysam Basiri, Pedro Lima
Aamir Ahmad, Francesco Amigoni, Iman Awaad,
Jakob Berghofer, Rainer Bischo, Andrea Bonarini,
Rhama Dwiputra, Giulio Fontana, Frederik Hegger,
Nico Hochgeschwender, Luca Iocchi, Gerhard Kraetzschmar,
Pedro U. Lima, Matteo Matteucci, Daniele Nardi, Pedro Miraldo,
Viola Schiaonati, Sven Schneider, Meysam Basiri,
Emanuele Bastianelli, Pedro Resende, João Mendes European Robotics League plus
Smart Cities Robot Competitions
Horizon 2020 European Robotics League plus
Smart Cities Robot Competitions
Horizon 2020 Introduction The European Robotic League (ERL) is an innovative concept for robot competitions. The ERL is composed of multiple across-the-year Local Tournaments, held in dierent
certied test beds located across Europe, and Major Tournaments, where the competition
takes place as part of a major conference or event such as RoboCup. From 2019 on, Smart
City tournaments will also take place every other year in European cities. Smart City
tournaments are a single annual event. During each across-the-year ERL Season, teams
participate in a minimum of two tournaments (Local and/or Major) and get scores based
on their performances on Task Benchmarks (TBM) and Functionality Benchmarks (FBM). A nal Season score is computed for each team, using the team best two participations
in the Season Tournaments, and teams are ranked based on their nal score. Prizes for
the top teams are awarded during the next year's European Robotics Forum (ERF). For
more information, please visit: Note: This version of the ERL Consumer rule book is valid until 28.02.2019. Contents Contents
v
I: ERL Consumer in a Nutshell
ix
1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2
The ERL Consumer User Story . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
3
ERL Consumer Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
3.1
ERL Consumer Environment . . . . . . . . . . . . . . . . . . . . . . . . . 1
3.2
ERL Consumer Benchmarks . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3.2.1
Task Benchmarks
. . . . . . . . . . . . . . . . . . . . . . . . . . 2
3.2.2
Functionality Benchmarks . . . . . . . . . . . . . . . . . . . . . . 3
3.3
ERL Consumer Robots
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
II: ERL Consumer Rulebook
i
1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2
How to Read and Outline of the Document
. . . . . . . . . . . . . . . . . . . . . 1
3
Task Benchmarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
3.1
Task Getting to know my home . . Contents . . . . . . . . . . . . . . . . . . . . . . 1
3.1.1
Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3.1.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3.1.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 2
3.1.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 5
3.1.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 5
3.1.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.2
Task Welcoming visitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2.1
Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 7
3.2.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 8
3.2.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 9
3.2.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.3
Task Catering for Granny Annie's Comfort
. www.robotics-league.eu The ERL Consumer Service Robots Challenge (ERL Consumer for short) stems
from its predecessors, the RoCKIn@Home Challenge, and the ERL Service Robots
Challenge, and covers the domain of consumer service robotics, with current focus on
domestic applications. This document describes the rules of the ERL Consumer Challenge
for the season 2018/2019. Note: The top performing teams from all Challenges (ERL Consumer, ERL Professional
and ERL Emergency) of the ERL 2018/19 Season will qualify to participate in the Smart
City tournament that will take place in Milton Keynes, United Kingdom in the Fall of
2019. c⃝2018 by ERL Consumer Revision 1.1 iv Contents . . . . . . . . . . . . . . . . 11
3.3.1
Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.3.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.3.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 12
3.3.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 12
3.3.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 13
3.3.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.4
Task Visit my home
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4.1
Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 14 v Contents Contents 3.4.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 15
3.4.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 16
3.4.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 16
4
Functionality Benchmarks . . . . . Contents . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.1
Object Perception Functionality
. . . . . . . . . . . . . . . . . . . . . . . 17
4.1.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 17
4.1.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.1.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 17
4.1.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 18
4.1.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 18
4.1.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2
Navigation Functionality . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 19
4.2.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 19
4.2.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 20
4.2.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 20
4.2.6
Scoring and Ranking . . . . . . . . . . . . . Contents . . . . . . . . . . . . 20
4.3
Speech Understanding Functionality . . . . . . . . . . . . . . . . . . . . . 22
4.3.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 22
4.3.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.3.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 25
4.3.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 26
4.3.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 26
4.3.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.4
People Perception Functionality . . . . . . . . . . . . . . . . . . . . . . . . 27
4.4.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 27
4.4.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.4.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 28
4.4.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 28
4.4.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 28
4.4.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.5
Person Following Functionality . . Contents . . . . . . . . . . . . . . . . . . . . . . 29
4.5.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 29
4.5.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.5.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 29
4.5.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 29
4.5.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 30
4.5.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.6
Object Grasping and Manipulation Functionality . . . . . . . . . . . . . . 30
4.6.1
Functionality Description . . . . . . . . . . . . . . . . . . . . . . 30
4.6.2
Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.6.3
Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 31
4.6.4
Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 31
4.6.5
Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 31
4.6.6
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 32
A
ERL Consumer Award Categories . . . . . . . . . . . . . . . . . . . . . . . . . Contents . . 33
B
The ERL Consumer Test bed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
B.1
Environment Structure and Properties . . . . . . . . . . . . . . . . . . . . 34
B.2
Task-Relevant Objects in the Environment . . . . . . . . . . . . . . . . . . 39
B.2.1
Navigation-Relevant Objects . . . . . . . . . . . . . . . . . . . . 39 c⃝2018 by ERL Consumer vi Contents Contents B.2.2
Manipulation-Relevant Objects . . . . . . . . . . . . . . . . . . . 40
B.2.3
Perception-Relevant Objects
. . . . . . . . . . . . . . . . . . . . 42
B.3
Non-Task-Relevant Objects in the Environment . . . . . . . . . . . . . . . 43
B.4
Referee, Scoring and Benchmarking Box . . . . . . . . . . . . . . . . . . . 44
B.4.1
Communication between Benchmarking Equipment and Robots . 46
B.5
Networked Devices in the Environment . . . . . . . . . . . . . . . . . . . . 46
B.6
Benchmarking Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
C
Robots and Teams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
C.1
General Specications and Constraints on Robots and Teams . . . . . . . 49
C.2
Safety Check and Robot Inspection . . . . . . . . . . . . . . . . . . . . . . 50
C.3
Benchmarking Equipment and Data Logging on the Robot . . . . . . . . . 51
C.3.1
Setup for the Motion Capture System . . . . Contents . . . . . . . . . . . 51
C.3.2
Internal Data Logging . . . . . . . . . . . . . . . . . . . . . . . . 51
C.4
YAML Data File Specication . . . . . . . . . . . . . . . . . . . . . . . . . 53
C.4.1
File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
C.4.2
YAML-to-ROSbag Conversion Tool
. . . . . . . . . . . . . . . . 54
D
General Procedure and Scoring for Task Benchmarks . . . . . . . . . . . . . . . . 55
D.1
Safety check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
D.2
General Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
D.2.1
Start Procedure
. . . . . . . . . . . . . . . . . . . . . . . . . . . 55
D.2.2
Restart Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . 56
D.2.3
Exit Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
D.3
Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
E
The ISRoboNet@Home Test Bed at IST . . . . . . . . . . . . . . . . . . . . . . . 58
E.1
Environment Structure and Properties . . . . . . . . . c⃝2018 by ERL Consumer Contents . . . . . . . . . . . 58
E.2
Objects in the Environment . . . . . . . . . . . . . . . . . . . . . . . . . . 59
E.3
Network Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 c⃝2018 by ERL Consumer Revision 1.1 vii Contents Contents c⃝2018 by ERL Consumer Revision 1.1 viii 2
The ERL Consumer User Story Granny Annie is an elderly person, who lives in an in ordinary apartment. Granny Annie is
suering from typical problems of ageing people: She has some mobility constraints. She tires
fast. She needs to have some physical exercise, though. She needs to take her medicine regularly. She must drink enough. She must obey her diet. She needs to observe her blood pressure and
blood sugar regularly. She needs to take care of her pets. She wants to have a vivid social life and
welcome friends in her apartment occasionally, but regularly. Sometimes she has days not feeling
so well and needs to stay in bed. She still enjoys intellectual challenges and reads books, solves
puzzles, and socializes a lot with friends. For all these activities, ERL Consumer is looking into ways to support Granny Annie in
mastering her life. The context for performing such activities by technical systems is set in the
subsequent scenario description. 3
ERL Consumer Scenario The ERL Consumer scenario description is structured into three sections: environment, tasks
and their functionalities, and robots: • The environment section species the environment in which the tasks have to be performed. This information is also relevant for building test beds and simulators. • The environment section species the environment in which the tasks have to be performed. This information is also relevant for building test beds and simulators. • The tasks and functionalities section provides some more detail on the tasks the partic-
ipating teams are expected to solve through the use of one or more robots and possibly
additional equipment. Since task benchmarks are seen in ERL Consumer as a composition
of functionality benchmarks, several functionalities are also introduced. This information
tells teams what to prepare for. • The robot section species some constraints and requirements for participating robots,
which mainly arise for practical reasons (size and weight limitations, for example) and/or
due to the need to observe safety regulations. • The robot section species some constraints and requirements for participating robots,
which mainly arise for practical reasons (size and weight limitations, for example) and/or
due to the need to observe safety regulations. I: ERL Consumer in a Nutshell 1. Introduction 1. Introduction Contents 1
Introduction ERL Consumer is a competition that aims at bringing together the benets of scientic bench-
marking with the attraction of scientic competitions in the realm of consumer service robotics. The objectives are to bolster research in consumer service robotics for home applications and
to raise public awareness of the current and future capabilities of such robot systems to meet
societal challenges like healthy ageing and longer independent living. Currently, ERL Consumer
raises challenges in domestic environments that resemble similar challenges to be posed in smart
city environments (e.g., shopping malls), such as recognising and picking objects from shelves,
moving outside the home to populated areas, and/or taking elevators between oors, so as to
prepare teams for the Smart City Tournaments. Revision 1.1 3.2
ERL Consumer Benchmarks Two types of Benchmarks are dened and used in across-the-year ERL Consumer Local/Major
Tournaments: Task Benchmarks and Functionality Benchmarks. 3.1
ERL Consumer Environment The current setup of the ERL Consumer environment reects an ordinary European apartment
with all its environmental aspects, like walls, windows, doors or blinds as well as common house-
hold items, furniture, decoration and so on. The apartment depicted in Figure 1.1 serves as a
guideline. More detailed specications are given in the rule book. The following embedded devices may be installed and are accessible within the apartment's
WLAN: Revision 1.1 c⃝2018 by ERL Consumer 1 1 3. ERL Consumer Scenario Contents Figure 1.1: Granny Annie's apartment. Figure 1.1: Granny Annie's apartment. • A networkable, camera-based intercom at the front door. It allows to see who is in front
of the door. • A networkable, camera-based intercom at the front door. It allows to see who is in front
of the door. • The lamps in the bedroom (e.g. on the bed stand) are accessible and controllable via
network. • The lamps in the bedroom (e.g. on the bed stand) are accessible and controllable via
network. • The shutters on the bedroom or living room window are accessible and controllable via
network. • The shutters on the bedroom or living room window are accessible and controllable via
network. Currently, ERL Consumer is not using these networked devices except for possible demos
during Local Tournaments in the test beds equipped with them. 3.2.1
Task Benchmarks The following Task Benchmarks will be available in all test beds and Local/Major Tourn 1. Getting to know my home: The robot must detect new changes in the environment,
and update the semantic map of the apartment, within a limited time frame. The task shall
be performed by the robot autonomously, though it may include moments of symbiotic
interaction with a user in the apartment, e.g., to learn more about an object or a location. At the end of the knowledge acquisition phase, the robot must show the understanding of
the new environment, namely by handling one of the changed objects. 2. Welcoming visitors: The robot needs to handle a set of known and unknown visitors,
who will arrive individually at the home entrance in random sequence. The robot must 2. Welcoming visitors: The robot needs to handle a set of known and unknown visitors,
who will arrive individually at the home entrance in random sequence. The robot must c⃝2018 by ERL Consumer 2 Revision 1.1 2 Contents 3. ERL Consumer Scenario correctly recognize the known visitors and interact with the unknown visitors to identify
them and understand their purpose of visit. The robot must then perform a set of visitor-
specic behaviors that could range from manipulating and delivering of objects to guiding
and following the visitors. correctly recognize the known visitors and interact with the unknown visitors to identify
them and understand their purpose of visit. The robot must then perform a set of visitor-
specic behaviors that could range from manipulating and delivering of objects to guiding
and following the visitors. 3. Catering for Granny Annie's comfort: This task aims at providing general purpose
requests of Granny Annie inside the apartment. It focuses on the integration of dierent
robot abilities such as human-robot interaction, navigation and robot-object interaction. After waking up in the morning, Granny Annie calls the attention of the robot by touching
a button on a tablet computer. When the robot arrives, she gives a single speech command
composing of three actions from the following three categories: (a) Finding an item or a person in the apartment (b) Manipulating and delivering an object (c) Accompanying a person inside or outside the apartment These three actions are randomly generated into a single command using a command
generator in no predened order. The robot is required to understand the actions and
execute them accordingly. 3.2.1
Task Benchmarks 4. Visiting my home: This TBM focuses on safe navigation in dynamic environments,
obstacle avoidance, tracking and recognizing a person and human following and guiding
navigation modes. In this task, the robot should visit a set of predened waypoints while
avoiding and/or interacting with dierent obstacles based on the nature of the obstacle. Furthermore, the robot must interact and follow a previously unknown person outside the
arena through a small crowd and then guide that person back to the arena. 3.2.2
Functionality Benchmarks The Functionality Benchmarks may be available in Local/Major Tournaments (number and type
of Functionalities may vary across test beds). The Functionality Benchmarks may be available in Local/Major Tournaments (number and type
of Functionalities may vary across test beds). 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide
range of objects. A set of objects, selected from the list of ERL Consumer items, will be
positioned, one at the time, on a table located directly in front of the robot. For each object
presented, the robot has to perform the following activities: i) Object detection: perception
of the presence of an object on the table and association between the perceived object and
one of the object classes. ii) Object recognition: association between the perceived object
and one of the object instances belonging to the selected class. iii) Object localization:
estimation of the 3D pose of the perceived object with respect to the surface of the table. 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide
range of objects. A set of objects, selected from the list of ERL Consumer items, will be
positioned, one at the time, on a table located directly in front of the robot. For each object
presented, the robot has to perform the following activities: i) Object detection: perception
of the presence of an object on the table and association between the perceived object and
one of the object classes. ii) Object recognition: association between the perceived object
and one of the object instances belonging to the selected class. iii) Object localization:
estimation of the 3D pose of the perceived object with respect to the surface of the table. 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide
range of objects. A set of objects, selected from the list of ERL Consumer items, will be
positioned, one at the time, on a table located directly in front of the robot. For each object
presented, the robot has to perform the following activities: i) Object detection: perception
of the presence of an object on the table and association between the perceived object and
one of the object classes. ii) Object recognition: association between the perceived object
and one of the object instances belonging to the selected class. 3.2.2
Functionality Benchmarks In particular, it assesses the object picking and placing capabilities
of robots suitable for many consumer applications such as setting up a dining table in
domestic environments. 6. Grasping and Manipulation: Evaluates the ability of a robot to correctly grasp and
manipulate objects. In particular, it assesses the object picking and placing capabilities
of robots suitable for many consumer applications such as setting up a dining table in
domestic environments. 3.2.2
Functionality Benchmarks iii) Object localization:
estimation of the 3D pose of the perceived object with respect to the surface of the table. 2. Navigation: Evaluates the ability of a robot to correctly, safely, and autonomously nav-
igate in a ordinary apartment, including: the navigation in a apartment-like environment
with furniture, walls, and doors, i.e. in a previously mapped area; avoiding collisions with
dierent type of unknown obstacles, in unknown positions (not previously mapped); and
navigating in the presence of people in the arena. 3. Speech Understanding: Evaluates the ability of a robot to understand speech com-
mands that a user gives to a robot in a consumer environment, including all the related
issues, such as background noise caused by other ongoing activities and by the robot mo-
tion. A set of spoken sentences, recorded in dierent environments, will be broadcast
through a speaker. The robot needs to interpret the commands and produce an output
according to a dened representation. c⃝2018 by ERL Consumer Revision 1.1 3 3. ERL Consumer Scenario Contents 4. People Perception: Evaluates the ability of a robot to locate and recognize humans. Similarly to object perception, the robot must recognize a person who is standing inside a
target area and to estimate the location of this person. 4. People Perception: Evaluates the ability of a robot to locate and recognize humans. Similarly to object perception, the robot must recognize a person who is standing inside a
target area and to estimate the location of this person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target
around and through obstacles and crowd of walking people. The benchmark requires that
the robot accompanies a human target and always maintain a desired distance with this
person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target
around and through obstacles and crowd of walking people. The benchmark requires that
the robot accompanies a human target and always maintain a desired distance with this
person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target
around and through obstacles and crowd of walking people. The benchmark requires that
the robot accompanies a human target and always maintain a desired distance with this
person. 6. Grasping and Manipulation: Evaluates the ability of a robot to correctly grasp and
manipulate objects. 3.3
ERL Consumer Robots Participating teams can use one or two robots to solve the tasks. The robots must t through a
door of 80cm width and weigh no more than 250kg. They must be fully autonomous, i.e. neither
power supply via cable nor any kind of tele-operation is permitted. Each robot must be safe to operate in the environment. Robots polluting or damaging the
environment or presenting a threat to humans in the environment are not allowed to participate. A mechanism to stop the robots in case of emergencies must exist. Robots must be properly equipped to be able to solve the tasks at least in principle. For
example, it is not permitted to substitute for lack of speech understanding by entering commands
on the keyboard. Teams are not allowed to modify the environment, or to install their own embedded devices
in the environment, e.g. additional sensors or actuators. c⃝2018 by ERL Consumer Revision 1.1 4 2
How to Read and Outline of the Document This remainder of this part is structured as follows: Section 3 describes in detail the ERL Con-
sumer Task Benchmarks, their goals, specic procedures, scoring methods and details. Section
4 does the same for ERL Consumer Functionality Benchmarks. This is the most relevant part of the rulebook, that an experienced ERL Con-
sumer participant should read carefully. Sections of former versions of this rulebook providing general information on awards, test
beds, robots and teams, as well as the general procedures, scoring and benchmarking methods
for Task Benchmarks, were now turned into appendices. Appendix A surveys the number and kind of awards that will be awarded and when, as
well as how the ranking of the award categories is determined based on individual benchmark
results. The certication requirements for a test bed to be used in ERL Consumer Tournaments
are described in some detail in Appendix B). Subsections of this appendix are devoted to the
specication of the structure of the environment and its properties (B.1), to the objects in the
environment relevant to the tasks on hand (B.2), to other objects not directly related to tasks
but possible aecting the robot's behavior in other ways (e.g. need to avoid them in navigation,
distractions and perceptual noise caused by them in robot vision) (B.3), to the networked devices
embedded in the environment and accessible to the robot (B.5), and to the benchmarking equip-
ment which may impose additional constraints to the robot's behavior (equipment presenting
obstacles to avoid) or add further perceptual noise (visible equipment) (B.6). In Appendix C),
we provide some specications and constraints applying to the robots and teams permitted
to participate in ERL Consumer, including the requirements for data logging. The general
procedure to run Task Benchmarks, as well as the scoring methods used to rank the teams,
are introduced in Appendix D. Appendix E depicts one instance of a ERL Consumer certied
testbed. Any ERL Consumer participant should read these appendices at least once. Ex-
perienced ERL Consumer participants should use them primarily for consultation
of details. 1
Introduction This part of the document describes in detail the actual competition rules for ERL Consumer
Benchmarks and it assumes that the reader has already read Part I of the document, with the
ERL Consumer nutshell information. The audience for the current part are teams who want to
participate in the competition, the organizers of ERL Consumer Tournaments, and the developers
of simulation software, who want to provide their customers and users with ready-to-use models
of the environment. They all need to know more details on the competition than the nutshell
document provides. 3
Task Benchmarks This chapter describes in detail each of the Task and Functionality Benchmarks that will be
available during the current ERL Consumer Season. II: ERL Consumer Rulebook II: ERL Consumer Rulebook 1. Introduction Contents Revision 1.1 3.1.1
Task Description Before each task run, some random changes in the environment are made with respect to the
nominal conguration given to the teams during the set-up days. These changes involve: • Closing a door connecting two rooms • Closing a door connecting two rooms • Moving two pieces of furniture from one room to another • Moving two known objects from one furniture to another • Placing an unknown object (trash) on the oor The robot has to detect all the changes, either automatically or with some limited help from
an untrained user (a person from the technical/organizing committee), and provide an explicit
representation of them referred to the map of the environment (that can be either acquired
on-line during the task run, o-line before the run, or merge o-line and on-line acquisition). 3.1
Task Getting to know my home This task is focused on acquiring knowledge about the environment and on its explicit representa-
tion. The robot is required to identify some changes in the environment either fully autonomously
or through some limited interactions with a human user. Revision 1.1 c⃝2018 by ERL Consumer 1 1 3. Task Benchmarks Contents 3.1.2
Input Provided The teams must create a semantic map of the apartment, during the set-up days, and label it
with pieces of furniture and objects. The names of rooms, furniture and objects, along with
their default locations, will be distributed to the teams before the competition. The objects and
furniture will also be available to the teams during the setup days for training purposes. The following information about the object locations is provided in advance to facilitate the
robot's searching process: • A list of four candidate locations (four pieces of furniture) where the changed objects
could be located will be given in advance. These four furniture are not among the moved
furniture and are always at their default locations. • One object is placed on every candidate location. Hence, two locations will contain the
changed objects to be found while the other two locations will contain one of the default
objects for that location. • An unknown manipulable object, such as an empty water bottle or an empty drink can,
acting as the trash, will be placed on the oor of one of the rooms in a noticeable location
(away from walls and furniture); • An unknown manipulable object, such as an empty water bottle or an empty drink can,
acting as the trash, will be placed on the oor of one of the rooms in a noticeable location
(away from walls and furniture); Phase 1: knowledge acquisition. The robot is expected to detect the changes and represent them in an explicit format (see
Expected Output below) either fully autonomously or semi-autonomously (with limited help
from a user). In case of a semi-autonomous approach the robot must be dominant in the task
and interact with an untrained user for assistance. More precisely: • The robot can only interrogate the user about the location and nature of the changed
doors and furniture. (Example: what furniture is changed? where to?) • The robot can only interrogate the user about the location and nature of the changed
doors and furniture. (Example: what furniture is changed? where to?) • The robot can request the user to guide the robot (through human-following) to the loca-
tion of any furniture and/or to point to a furniture. • The robot cannot interrogate or use information spontaneously provided by the user about
the nature or location of the changed objects, including the unknown item (trash). c⃝2018 by ERL Consumer 2 Revision 1.1 2 3. Task Benchmarks Contents • The robot cannot ask or follow direct motion commands (i.e. Speech commands: Go to,
Turn right, Move forward, Navigate to, etc are no longer allowed) At any time the teams can decide to move to Phase 2, even if not all changes have been
detected. However, the task in Phase 2 can refer only to objects acquired during Phase 1. (a) Predicates about doors and their status (a) Predicates about doors and their status • Denition:
type (door_ID ,
door ) . connect (door_ID , room_name , room_name ) . isOpen (door_ID ,
true | f a l s e
) . • Example:
type ( door36 , door )
connects ( door36 ,
kitchen ,
o f f i c e ) . isOpen ( door36 ,
true ) . (b) Predicates about location of pieces of furniture (b) Predicates about location of pieces of furniture Phase 2: knowledge use. The robot has to show the use of the new acquired knowledge. This will be accomplished
by moving one of the changed objects recognized in Phase 1 back to its default location. The
default location of the trash is considered as the trash bin. Expected output. The output provided by the teams is a set of les that must be saved in a
USB stick given to the teams before the test. The USB stick will be formatted with FAT32 le
system and all the les should be saved in a folder with the name of the team. The following les are expected: • semantic map le • pictures of changed objects and furniture • metric map les • metric map les 1. Semantic map le: this must be a text le named semantic_map.txt containing a set
of Prolog-like statements (or facts) in the following form: 1. Semantic map le: this must be a text le named semantic_map.txt containing a set
of Prolog-like statements (or facts) in the following form: predicate ( arg_1 ,
. . . ,
arg_n ) . predicate ( arg_1 ,
. . . ,
arg_n ) . The following predicates will be considered for evaluation: Revision 1.1 • Denition: • Denition:
type ( furniture_ID ,
furniture_name )
in ( furniture_ID , room_name)
picture ( furniture_ID ,
image_filename ) . • Example:
type ( ch1 ,
kitchen_chair ) . in ( ch1 ,
living_room ) . picture ( ch1 ,
image_ch1 . jpg ) . • Example:
type ( ch1 ,
kitchen_chair ) . in ( ch1 ,
living_room ) . picture ( ch1 ,
image_ch1 . jpg ) . Note: Only one piece of furniture for each type will be involved in the test and
described in the semantic map le. Note: Only one piece of furniture for each type will be involved in the test and
described in the semantic map le. c⃝2018 by ERL Consumer Revision 1.1 3 Contents 3. Task Benchmarks (c) Predicates about position, location and properties of objects) • Denition:
type ( object_ID ,
object_category ) . in ( object_ID , room_name ) . on ( object_ID ,
furniture_name ) . picture ( object_ID ,
image_filename ) . • Example:
type ( obj33 , apple ) . in ( obj33 , kitchen ) . on ( obj33 , kitchen_table ) . picture ( obj33 , image_obj33 . jpg ) . • Example:
type ( obj33 , apple ) . in ( obj33 , kitchen ) . on ( obj33 , kitchen_table ) . picture ( obj33 , image_obj33 . jpg ) . • Example: Note: Only the information about the door/furniture/objects that are involved in
the change during the test will be evaluated. Additional information about other
doors/furniture/objects can be included in the le as well, but they will not be used
for determining the score. 2. Pictures of objects: actual images in standard image format (JPEG, PNG, BMP, PPM)
named in the picture predicate of the semantic map. These images will be evaluated by
a referee through visual inspection. The object named in the semantic map le must be
visible in the foreground. 2. Pictures of objects: actual images in standard image format (JPEG, PNG, BMP, PPM)
named in the picture predicate of the semantic map. These images will be evaluated by
a referee through visual inspection. The object named in the semantic map le must be
visible in the foreground. 3. Metric map les: metric map (possibly acquired before the test) should be included,
preferably in ROS format (i.e. bitmap (PNG/PPM) + YAML le), using the global
reference system provided during the setup days. Note: this map will not be evaluated,
but it is useful for benchmarking and statistics. Complete Example:
A complete example is illustrated below, where the following
changes where executed: • the door connecting the kitchen and the hallway is closed, • a kitchen chair is moved to the living room, • a plant is moved to the hallway, • a can of coke is placed on the kitchen table in the kitchen, • a box of biscuits is placed on the coee table in the living room, and • an empty water bottle is placed on the oor of the dining room. The generated semantic map le which refers to the changes in the environment is given
below: The generated semantic map le which refers to the changes in the environment is given
below: type ( door_1 ,
door ) . connects ( door_1 ,
kitchen ,
hallway ) . isOpen ( door_1 ,
f a l s e ) . type ( door_1 ,
door ) . connects ( door_1 ,
kitchen ,
hallway isOpen ( door_1 ,
f a l s e ) . type ( kitchen_chair_1 ,
chair ) . in ( kitchen_chair_1 ,
living_room ) . picture ( kitchen_chair_1 ,
kitchen_chair_1 . jpg ) . type ( kitchen_chair_1 ,
chair ) . in ( kitchen_chair_1 ,
living_room ) . • Example: type ( kitchen_chair_1 ,
chair ) . type ( kitchen_chair_1 ,
chair ) . in ( kitchen_chair_1 ,
living_room ) . picture ( kitchen_chair_1 ,
kitchen_chair_1 . jpg ) . picture ( kitchen_chair_1 ,
kitchen_chair_1 . jpg ) . type ( plant_1 ,
plant ) . Revision 1.1 4 c⃝2018 by ERL Consumer 3. Task Benchmarks Contents in ( plant_1 ,
hallway ) . picture ( plant_1 ,
plant_1 . jpg ) . type ( object_1 ,
coke ) . in ( object_1 ,
kitchen ) . on ( object_1 ,
kitchen_table ) . picture ( object_1 ,
object_1 . jpg ) . picture ( object_1 ,
object_1 . jpg ) . type ( object_2 ,
b i s c u i t s ) . in ( object_2 ,
living_room ) . on ( object_2 ,
coffee_table ) . picture ( object_2 ,
object_2 . jpg ) . type ( object_3 ,
trash ) . in ( object_3 ,
dining_room ) . on ( object_3 ,
f l o o r ) . picture ( object_3 ,
object_3 . jpg ) . picture ( object_3 ,
object_3 . jpg ) . 3.1.5
Acquisition of Benchmarking Data During this Task Benchmarks, beside the information related to the semantic map of the envi-
ronment to be evaluated, the Internal Data described in Section C.3.2 will be collected. 3.1.4
Procedures and Rules Before the robot enters the apartment, any of the doors in the environment will be closed and
two randomly-selected pieces of furniture will be moved from their original position. In addition,
four randomly-selected objects will be placed in the four candidate locations (above some piece
of furniture) where only two of the objects are not in their default locations and need to be
identied as the changed objects. Note that the closed door could be also the entrance door. In
this case, this door will be closed immediately after the robot has entered the apartment. Phase 1 The robot can move around in the environment for up to the maximum time limit of
this task, possibly accompanied by a user (a person from the technical/organizing commit-
tee) and interacting with him/her: The robot has to detect the changes specied above,
and then represent them in an explicit format as described in sub-subsection 3.1.3. Phase 2 (Assuming that the robot has either nished the task requested in the previous steps,
or is incapable to do so) the robot can automatically, or via a speech command, proceed
to move one of the objects recognized in Phase 1 back to its default location. The knowledge acquired during Phase 1 must be reported in an explicit way by producing les
in the given output format and by automatically saving them on a USB stick given to the team
by the Technical Committee before the start of the run, as described in the Expected Output
section. No manual intervention on the robot is allowed to save les on the USB stick. c⃝2018 by ERL Consumer 3.2.3
Expected Robot Behavior or Output For each visiting person, the following two phases are expected. 3.1.6
Scoring and Ranking The set A of eight possible achievements for this task are: The set A of eight possible achievements for this task are: • The robot detects the door with changed state. (1) • The robot detects each piece of the moved furniture. (2) c⃝2018 by ERL Consumer 5 Revision 1.1 3. Task Benchmarks Contents • The robot detects each of the changed objects. (2) • The robot detects each of the changed objects. (2) • The robot locates the trash. (1) • The robot locates the trash. (1) • The robot grasps an object in Phase 2. (1) • The robot delivers the object to the default location. (1) • The robot delivers the object to the default location. (1)
The set PB of penalized behaviors for this task are: he set PB of penalized behaviors for this task are: • The robot requires repetitions of human gesture/speech. • The robot requires repetitions of human gesture/speech. • If following is used, the robot loses the user and it requires that explicit actions are per-
formed by the operator. • The robot bumps into the furniture. • The robot stops working. • The robot drops the object when delivering. • The robot drops the object when delivering. • Pictures are not taken or do not contain the target, for each piece of object/furniture (5)
Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: • The robot hits Annie or another person in the environment. • The robot hits Annie or another person in the environment. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 6 3. Task Benchmarks Contents 3.2
Task Welcoming visitors This task assesses the robot's capability to interact eectively with humans and to demonstrate
dierent behaviors when dealing with known and unknown people. 3.2.2
Input Provided The following information about the people acting as visitors is provided below. • Dr. Kimble is a known person from the Organizing or Technical Committee running all
the runs. Pictures of Dr. Kimble will be provided before the competition. • Dr. Kimble is a known person from the Organizing or Technical Committee running all
the runs. Pictures of Dr. Kimble will be provided before the competition. • The Postman is a known person from the Organizing or Technical Committee running all
the runs. He/she will also wear a known uniform. Images of the uniform and the Postman
will be given before the competition. • The Deli Man will be unknown beforehand (the actual person will change in every run). He/she will be carrying a shopping bag with the breakfast inside. • The Deli Man will be unknown beforehand (the actual person will change in every run). He/she will be carrying a shopping bag with the breakfast inside. • The Plumber will be unknown beforehand (the actual person will change in every run). He will carry a toolbox in his hand. Some privileges are given to the four dierent kinds of people, as reported in the following table,
and the robot has to act accordingly. Some privileges are given to the four dierent kinds of people, as reported in the following table,
and the robot has to act accordingly. Privileges
Dr. Kimble
Postman
Deli Man
Plumber
Allow to enter the house
Yes
No
Yes
Yes
Allow to deliver objects
No
Yes
Yes
Yes
Allow access to bathroom
Yes
No
No
Yes
Allow access to kitchen
Yes
No
Yes
Yes
Allow access to bedroom
Yes
No
No
No Pictures of the parcel used by the postman will be provided before the competition. The
dimensions of the parcel are 9.5 inches / 24.13 cm (width) x 6.5 inches / 16.51 cm (length) x
1.75 inches / 4.45 cm (height) and weights about 30 grams. 3.2.1
Task Description The task involves handling several known and unknown visitors arriving at the home entrance
in a random sequence, but separately from each other. The robot must recognize the known
visitors and interact with the unknown visitors to identify them. The robot must then perform
a set of visitor-specic behaviors. If a visitor has been admitted, the robot should guide him/her
out after the visit is over. Phase 2: executing the visitor-specic behavior. The following behaviors are expected depending on the visitor: Dr. Kimble: The robot guides the Doctor to Annie's bedroom; then it waits until the Doctor
exits the bedroom, follows him/her to the entrance door, and allows the Doctor to exit. The
human-following behavior must be observed. PostMan: The robot receives the postal mail using its manipulator(s), allows the Postman to
exit and delivers the mail to Granny Annie in the bedroom. A natural robot-human object
handover is preferred, however, the robot could also advise the postman on how to hold or hand
over the object. Deli Man: The robot guides the Deli Man to the kitchen, asking him/her to deliver the breakfast
box on the table; then it guides the Deli Man back to the entrance door, and allows him/her to
exit. The human-guiding behavior must be observed. Plumber: The robot asks the Plumber where he/she would like to visit, guides the Plumber
to the desired location, it waits for the plumber to nish his job; then it follows him/her back
to the entrance door. The robot must always keep a close eye on the plumber by maintaining a
close distance with him/her. The human guiding and following behaviors must be observed. After the execution of the visitor-specic behavior, the robot must return to the initial position
and wait for the next visitor. Phase 1: detection and recognition of the visitor. Doorbell: Whenever a person rings the door bell, the robot can use its own on-board audio
system to detect the bell ring(s) or the signal from the RSBB. Opening the door: Naturally, the front door will be closed. The robot can either use its own
manipulators to open the door or request the visitor to open it (e.g. using speech). An extra
achievement is assigned for the former case. Fig. 2.2 shows an example of the type of handle Revision 1.1 c⃝2018 by ERL Consumer 7 3. Task Benchmarks Contents that will be mounted on the entrance door. that will be mounted on the entrance door. Identifying the visitor: Once the door is open, the robot must then use its on-board sensing
to correctly identify the person rst as known or unknown visitor. If the visitor is known, the
robot should be able to recognize him/her. If the visitor is unknown the robot must interrogate
the person to learn who is visiting and what is the purpose of the visit. Greeting the visitor: For each detected visitor, the robot must greet the visitor with a spoken
sentence, demonstrating that it has recognized the visitor. For example, "Hi postman, I am
coming to get the post mail" or "Hello Plumber, where do you want to visit in the house?". Figure 2.2: Door handle at the main entrance Figure 2.2: Door handle at the main entrance 3.2.4
Procedures and Rules The test starts with the robot being in one of the available rooms. The exact room will be
announced at the beginning of the competition and will be same for all the teams. The visitors
will be from all the four categories mentioned previously. The following steps will be repeated
for each visitor (in a random order). c⃝2018 by ERL Consumer Revision 1.1 8 3. Task Benchmarks Contents Step 1 The door-bell will be rung by the visitor. At this point in time, the robot must recognize
the sound or use the RSBB, to see if someone rung the door bell. Step 1 The door-bell will be rung by the visitor. At this point in time, the robot must recognize
the sound or use the RSBB, to see if someone rung the door bell. Step 2 The robot must navigate to the entrance and open the entrance door either using its
manipulator(s) or by asking the visitor to open the door. Step 3 The robot must correctly identify the visiting person, greet him/her, and proceed to do
the behavior-specic actions as instructed in Section 3.2.3. Step 4 Once the visit is over, the robot will return to the initial position. 3.2.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected together with the additional information described in the following table Topic
Type
Frame Id
Notes
/ERLSCR/command1
std_msgs/String
/ERLSCR/visitor2
std_msgs/String
/ERLSCR/audio3
audio_common_msgs/AudioData
/ERLSCR/notication4
std_msgs/String
NOTE: the images and pointclouds in the Internal Data should contain the sensorial data
used to recognize the visitor. 1The event or command causing the activation of the robot. The result of any attempt by the robot to detect and classify a visi
3The audio signals of the conversation with the visitors. 3.3
Task Catering for Granny Annie's Comfort This benchmark aims at assessing the robot's performance for executing general purpose requests
of users in the apartment. It focuses on the integration of dierent robot abilities such as
human-robot interaction, navigation and robot-object interaction. The task does not have a
predened story or a predened set of actions requiring more than the traditional state machine-
like behaviors. Note: This task is an updated and merged version of the former ERL-SR Catering
for Granny Annie's Comfort and General Purpose Service Robots tasks. 3.2.6
Scoring and Ranking The set A of achievements for this task are: • The robot correctly recognizes Dr. Kimble. • The robot correctly recognizes the Postman. • The robot correctly identies the Deli Man. • The robot correctly identies the plumber. • The robot exhibits the expected behavior for interacting with Dr. Kimble. • The robot exhibits the expected behavior for interacting with the Deli Man. • The robot exhibits the expected behavior for interacting with the Postman. • The robot opens the entrance door using its manipulator at least one time during the task. The set PB of penalized behaviors for this task are: The set PB of penalized behaviors for this task are: • The robot stops working. • The robot fails in making the visitor respect the proper rights. • The robot fails in maintaining the original state of the environment. 1The event or command causing the activation of the robot. 2 2The result of any attempt by the robot to detect and classify a visitor
3The audio signals of the conversation with the visitors. g
4Any notications from the robot (e.g., alarm if a visitor shows anomalous behavior) c⃝2018 by ERL Consumer Revision 1.1 9 3. Task Benchmarks Contents • The robot requires extra repetitions of speech. • The robot requires extra repetitions of speech. he robot requires extra repetitions of speech. • The robot bumps into the furniture. Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: • The robot hits Annie or one of the visitors. • The robot hits Annie or one of the visitors. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 10 3. Task Benchmarks Contents 3.3.1
Task Description The robot is going to help a user with his/her daily tasks. After waking up in the morning, the
user calls the attention of the service robot by touching a button on a tablet computer. When
the robot arrives, the user gives a single speech command composing of three actions from the
following three categories: 1. Searching for an item or a person 1. Searching for an item or a person 2. Manipulating and delivering an object 3. Accompanying a person inside or outside the house These actions are randomly generated into a single sentence in no predened order. The robot
is required to understand the actions and execute them accordingly. Revision 1.1 Accompanying
guide, take, lead, accompany, follow, escort Searching
nd, locate, look for, search for, pinpoint, spot put, place, leave, set, get, grasp, take, retrieve, pick up, bring, deliver, give, hand 3.3.3
Expected Robot Behavior or Output After the robot is called, the robot is expected to reach the room where the user is located,
approaching in such a way that spoken communication is possible. The robot should then state
its readiness to receive the command. When the command is given, the robot should show that
it has understood all the actions in an appropriate way (e.g., by repeating it back to the user
and asking if it was correctly understood). The robot is then expected to successfully execute all of the actions in the order that was
given in the command. If the robot is unable to perform any of the actions it should announce
it and proceed with the other actions. The following are some examples selected from a large set of possible commands: The following are some examples selected from a large set of possible commands: The following are some examples selected from a large set of possible commands: • Locate Tracy, lead her to the bedroom, and bring me an apple from the kitchen cabinet • Locate Tracy, lead her to the bedroom, and bring me an apple from the kitchen cabinet. Find the bottle, place it in the trash bin, and take John from the bedroom to the exit. • Find the bottle, place it in the trash bin, and take John from the bedroom to the exit. Guide me to the bedroom, nd my glasses, and bring me a pear from the kitchen table. • Guide me to the bedroom, nd my glasses, and bring me a pear from the kitchen table. • Give me the cup on the coee table, nd John, and follow him. Give me the cup on the coee table, nd John, and follow him. Calling the Robot for Attention:
The initial location of the user will be announced in
advance. The user has a tablet computer which runs an application provided by the consortium. It allows the user to call the robot's attention. The communication with the tablet is realized
through the RSBB. Further details are specied in the ERL Wiki [1]. Alternatively, if the tablet
is unavailable in a testbed, the start signal of the task, sent from the RSBB, will be considered
as the calling signal. 3.3.2
Input Provided Objects and names
The list of objects and people's names used in the task will be provided
before the competition by the local organizers. For every object/person to be found by the robot
a set of possible locations with an associated likelihood will be provided: Object/Person
Location
Likelihood %
Object i
Furniture 1
60
Furniture 2
30
Furniture 3
10
Person i
Room 1
60
Room 2
30
Room 3
10 All of the objects will be made available to the teams for calibration during the setup days. Note: In the case of nding a person, only one person will be present at one of the target
locations. Commands:
A command will be generated randomly before the task run and is composed of
three actions as described in Section 3.3.1. The lexicon used in the commands will consist of the
names of people/objects/locations (provided to the teams before the competition), along with
the following verbs divided based on the action categories: Manipulating c⃝2018 by ERL Consumer Revision 1.1 11 3. Task Benchmarks Contents 3.3.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in SectionC.3.2 will be collected
together with the additional information described in the following table NOTE: the images and pointclouds in the Internal Data should contain the object to be
operated. 3.3.4
Procedures and Rules A successful execution of this task would be the robot going to the user (played by a member
of the OC/TC) and executing all or some of the actions in the command. The task involves the
following activities: 1. User initiates the task by calling the robot's attention. 2. The robot approaches the user in such a way that spoken communication is possible,
stating its readiness to receive commands. 3. The user provides the sentence from the predened list of possible commands. 4. The robot conrms that it understood the command and executes the corresponding ac-
tions in the command. 5. After completing the task, the robot returns to the user. Teams are allowed to give instructions as to how the user should speak to the robot. If the
robot fails to understand the original command after three times a team member can replace the
user to repeat the same command. Alternatively, if the robot is incapable of processing and understanding the original command
in full, a team member can decompose or interpret the command into a desired format that
is understandable by the robot. However, the achievements for "correctly understanding the
original command" and "executing the full command without any interruption" will not be
obtained. c⃝2018 by ERL Consumer 12 Revision 1.1 3. Task Benchmarks Contents Topic
Type
Frame Id
Notes
/erlc/command5
std_msgs/String
/erlc/audio6
audio_common_msgs/AudioData
Revision 1.1 5The command produced by the natural language analysis process. 3.3.6
Scoring and Ranking The set A of achievements for this task are: • The robot enters the room where the user is waiting. • The robot enters the room where the user is waiting. • The robot understands the user's original command without any interpretations. • The robot understands at least one of the actions to be executed. • The robot manages to nd the right object/person. • The robot correctly executes the accompanying action. • The robot grasps and picks up the object to be delivered. • The robot delivers the object to the desired location • The robot completes all three actions continuously without any interruptions. The set PB of penalized behaviors for this task are: • The robot requires multiple repetition of the command • The robot bumps into the furniture. • The robot drops an object. • The robot stops working. • The robot fails to return to user after task completion. • The robot fails to return to user after task completion. Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: • The robot hits the user or another person in the environment. • The robot damages or destroys the objects requested to manipulate. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. 5The command produced by the natural language analysis process. 3.4
Task Visit my home This task focuses on safe navigation in dynamic environments, obstacle avoidance, obstacle
interaction, and tracking and recognizing a previously unknown person. 3.4.2
Input Provided A Path consisting of four waypoints will be selected and announced to the teams during the
setup days. The rst waypoint will be reachable via at least two dierent paths, the second
waypoint will be blocked by an obstacle and the fourth waypoint will be outside the arena in an
unknown location. A human operator will be standing at the third waypoint who will guide the
robot to the fourth waypoint. The entrance door to the apartment will be initially closed while
all other doors are left open. The following information about the obstacles blocking the path of the robot is provided
below: (Objects will be available to the teams during the setup days) • Small object: A small Kraft paper shopping bag • Wheeled object: A rolling chair, cart, wheeled luggage or some other object with wheels. • Wheeled object: A rolling chair, cart, wheeled luggage or some other object with wheels. • Human obstacle: A person who is unknown beforehand. Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the
robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with
weight of less than 300 grams) Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the
robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with
weight of less than 300 grams) Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the
robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with
weight of less than 300 grams) 3.4.1
Task Description In this task, the robot should visit a set of predened waypoints while avoiding obstacles on
its path. The robot needs to interact with the obstacles based on the nature of the obstacle. Furthermore, the robot must interact and follow a person to an unknown location outside the
arena. Finally the robot needs to nd its way back to the arena. 5The command produced by the natural language analysis process. 6The audio of the conversation between user and the robot. Speech les from all teams and all bench-
marks (both Task benchmarks and Functionality benchmarks) will be collected and used to build a public
dataset. The audio les in the dataset will therefore include all the defects of real-world audio capture
using robot hardware (e.g., electrical and mechanical noise, limited bandwidth, harmonic distortion). Such les will be usable to test speech recognition software, or (possibly) to act as input during the
execution of speech recognition benchmarks. c⃝2018 by ERL Consumer Revision 1.1 13 3. Task Benchmarks Contents Phase 4: Human following After reaching Waypoint 2, the robot must navigate to Waypoint 3, in which a person is
standing. The robot must memorize this person and follow him/her outside the arena to Way-
point 4. This phase can include the following states: After reaching Waypoint 2, the robot must navigate to Waypoint 3, in which a person is
standing. The robot must memorize this person and follow him/her outside the arena to Way-
point 4. This phase can include the following states: • Training: The robot has to memorize the operator. The robot may instruct the operator
to follow a certain setup procedure and instruct the operator on what to do when the robot
needs to stop following. • Following: When the robot signals that it is ready to start following, the operator starts
walking in a natural way through a designated path outside the arena. The robot needs
to follow the operator until the operator asks the robot to stop. • Resuming: If the robot loses the operator, it can ask him/her to come back or give a signal
by waving to resume following, but will be penalized for doing so. • Stop following: Upon reaching Waypoint 4, the operator will command the robot to stop
following him as instructed in the training phase. • Stop following: Upon reaching Waypoint 4, the operator will command the robot to stop
following him as instructed in the training phase. Phase 5: Returning Home After reaching Waypoint 4 the robot must then go back to Waypoint 3. The robot has to
open the door of the apartment, closed by the referee after the robot left the arena, in order to
reach Waypoint 3. The robot is allowed to use its base to gently push the door open, but only
after it used a manipulator to initially open the door by the handle Phase 3: Obstacle interaction After reaching Waypoint 1, the robot must navigate to the second waypoint. The path to
this waypoint is blocked by one of the obstacles described in Section 3.4.2. The robot is expected
to identify, state the nature of the obstacle and interact with the obstacle accordingly. Possible
actions include: • Small object: Remove the small object from the path using the robot's manipulators, or
overcome the obstacle in case of bipedal robots. • Wheeled object: Gently push away the object to unblock the path using either the ma-
nipulators or the robot's body. • Human obstacle: Kindly ask the human to move away. If the robot is unable to remove the obstacle it can ask the referee to remove it to continue with
the task. Otherwise, the obstacle will clear or be cleared after roughly 45 seconds. Phase 2: Navigation and Path Planning After entering the arena, the robot must navigate to the rst waypoint that is reachable
via at least two paths. Whatever path the robot initially takes will be blocked as the robot
approaches and the robot should take the alternative path. Phase 1: Entering the arena The task starts with the robot waiting outside the arena and when the entrance door is
opened by the referee. The robot should detect the door-opening event and enter the arena c⃝2018 by ERL Consumer Revision 1.1 14 3. Task Benchmarks Contents autonomously. Alternatively, the team may start the robot using a start button without getting
the respective achievement. autonomously. Alternatively, the team may start the robot using a start button without getting
the respective achievement. Revision 1.1 3.4.4
Procedures and Rules The referee starts the test by opening the entrance door. The robot must navigate to the
waypoints in sequential order while respecting the expected behaviors described in Section 3.4.3. If a robot is unable to reach a waypoint, it must announce it and proceed to the next waypoint. Revision 1.1 c⃝2018 by ERL Consumer 15 3. Task Benchmarks Contents 3.4.5
Acquisition of Benchmarking Data During this Task Benchmark, the Internal Data described in Section C.3.2 will be collected. 4.1.1
Functionality Description Teams are provided with a list of individual objects (instances), subdivided into classes. The
benchmark requires that the robot, when presented with objects from such list, detects their
presence and estimates their class, instance, and location. For example, when presented with a
bottle of milk, the robot should detect a bottle (class) of milk (instance) and estimate its pose
w.r.t. a known reference frame. 4.1.2
Input Provided The set of individual objects, denoted as object instances, that will actually be presented to
the robot during the execution of the functionality benchmark will be provided to the teams
before the competition. All objects are commonplace items that can be found in domestic or
retail environments. Object instances are subdivided into classes of objects that have one or
more properties in common, here denoted as object classes. Objects of the same class share
one or more properties, not necessarily related to their geometry (for instance, a class may
include objects that share their application domain). Each object instance and each object class
is assigned a unique ID. More precisely, teams will be provided with the following information: • Descriptions of all the object instances; Subdivision of the object instances into object classes (for instance: boxes, mugs, cutlery • Reference systems associated to the table surface and to each object instance (to be used
to express object poses). • Reference systems associated to the table surface and to each object instance (to be used
to express object poses). 3.4.6
Scoring and Ranking The set A of achievements for this task are: • The robot enters the arena autonomously when the door is opened. • The robot enters the arena autonomously when the door is opened. • The robot reaches waypoint 1. • The robot reaches waypoint 2. • The robot reaches waypoint 3. • The robot reaches waypoint 4 following the operator. • The robot reaches waypoint 3 after visiting waypoint 4. • The robot recognizes properly the nature of the obstacle. • The robot interacts with obstacle accordingly to their nature. • The robot interacts with obstacle accordingly to their nature. The set PB of penalized behaviors for this task are: The set PB of penalized behaviors for this task are: • The robot bumps into a non-human obstacle. • If the robot loses the operator, it requires that explicit actions are performed by the
operator (e.g., waving) to retrieve them. • If the robot loses the operator, it requires that explicit actions are performed by the
operator (e.g., waving) to retrieve them. • The robot stops working. • Any behavior towards attendees and/or operator that is deemed as threatening by the
referees (e.g., rapidly moving towards a person, then stopping at moderate distance) • Any behavior towards attendees and/or operator that is deemed as threatening by the
referees (e.g., rapidly moving towards a person, then stopping at moderate distance) Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The
set DB of disqualifying behaviors for this task are: • The robot hits the operator or any other human. • The robot damages an object. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 16 4. Functionality Benchmarks Contents 4.1
Object Perception Functionality This functionality benchmark has the objective of assessing the capabilities of a robot in pro-
cessing sensor data in order to extract information about observed objects. Revision 1.1 4.1.3
Expected Robot Behavior or Output The objects that the robot is required to perceive are positioned, one at the time, on a table
(benchmark setup area) located directly in front of the robot. The actual pose of the objects
presented to the robot is unknown before they are set on the table. For each presented object,
the robot must perform all of the following: • Object detection (i.e., class recognition): perception of the presence of an object on the
table and association between the perceived object and one of the object classes (see
Information provided to the team). • Object recognition (i.e., instance recognition): association between the perceived object
and one of the object instances belonging to the selected class (see sub-subsection 4.1.2). • Object localization (i.e., pose estimation): estimation of the 3D pose of the perceived
object with respect to the benchmark setup reference frame. c⃝2018 by ERL Consumer Revision 1.1 17 4. Functionality Benchmarks Contents 4.1.4
Procedures and Rules Every run in all the stages of this functionality benchmark will be preceded by a safety-check
similar to that described for the task benchmark procedures. Each team is required to perform this functionality benchmark according to the steps men-
tioned below. The maximum time allowed for one functionality run is 10 minutes. Step 1 An object of unknown class and unknown instance will be placed on a table in front of
the robot. Step 2 The robot must determine the object's class, its instance within that class as well as the
2D pose of the object w.r.t. the reference system specied on the table (see Fig. 2.4). Figure 2.4: Reference frame on the FBM table. Figure 2.4: Reference frame on the FBM table. The preceding steps are repeated until the time runs out or the maximum number of objects
have been processed. 7The string with the notication of the perceived object should be in a tab separated string: CLASS
OBJECT_ID X Y THETA 4.2.2
Input Provided The following information will be provided in advance: • The starting position. • The number of waypoints that the robot must visit. • The maximum time allowed to the robot to go from each waypoint to the next waypoint,
without penalization. • The maximum time allowed to the robot to go from each waypoint to the next waypoint,
without penalization. Furthermore, the coordinates of the waypoints that the robot must visit will be communicated
sequentially to the robot during the run time. A waypoint encapsulates a X, Y and θ. The
coordinates are given in the test bed reference frame (which will be dened on site and provided
during the rst day to the teams). 4.2.1
Functionality Description This functionality benchmark aims at assessing the capabilities of a robot to correctly and au-
tonomously navigate in a typical apartment, containing furniture and objects spread through the
apartment's rooms. The benchmark will use the ERL Consumer test bed (see Sec. B). From a
predened starting position, the robot will receive a list of waypoints that it must visit to reach
a goal position. 4.1.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected together with the additional information described in the following table Topic
Type
Frame Id
Notes
/erlc/notication7
std_msgs/String
NOTE: the images and pointclouds in the Internal Data should contain the sensorial data
used to recognize each of the presented object, thus we expect to have 10 images (if recognition
uses a camera), 10 pointclouds (if recognition uses a depth sensor), and 10 notication strings. 7The string with the notication of the perceived object should be in a tab separated string: CLASS
OBJECT_ID X Y THETA c⃝2018 by ERL Consumer Revision 1.1 18 4. Functionality Benchmarks Contents Revision 1.1 4. Execution time (if less than the maximum allowed for the benchmark). The previous criteria are in order of importance: the rst criterion is applied rst and teams
will be scored according to the common accuracy metrics; the ties are broken by second criterion
which is the position error. Since the position error is aected by the precision of the ground
truth system we will use a set of accuracy classes in this as well and in case of ties we will resort
to the third criterion and nally the execution time. 4.1.6
Scoring and Ranking Evaluation of the performance of a robot according to this functionality benchmark is based on: 1. The number and percentage of correctly recognized objects. (i.e.,instance recognition) 1. The number and percentage of correctly recognized objects. (i.e.,instance recognition) 2. Pose error for all correctly identied objects. 3. The number and percentage of correctly classied objects. (i.e.,class recognition) 4. Execution time (if less than the maximum allowed for the benchmark). 4.2.4
Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned
below. The task must be performed exclusively in autonomous mode. No teleoperation is allowed. Teams will have up to ten minutes to complete the functionality benchmark. Step 1 The team is required to start their robot on a pre-dened starting position. This starting
position will be given to the teams before each run. Step 1 The team is required to start their robot on a pre-dened starting position. This starting
position will be given to the teams before each run. Step 2 When the procedure starts, the robot receives a sequence of waypoints, one by one, that
it must follow in the respective order, sending back a signal through the RSBB, each time
it reaches a waypoint. The robot must avoid hitting any obstacle it encounters in its path. Step 2 When the procedure starts, the robot receives a sequence of waypoints, one by one, that
it must follow in the respective order, sending back a signal through the RSBB, each time
it reaches a waypoint. The robot must avoid hitting any obstacle it encounters in its path. Step 3 The procedure stops when the robot noties it has reached the last waypoint, when the
time given to complete the test expires, or when the robot hard-hits an obstacle. Step 3 The procedure stops when the robot noties it has reached the last waypoint, when the
time given to complete the test expires, or when the robot hard-hits an obstacle. It is considered a hard hit when: It is considered a hard hit when: • A collision damages any of the obstacles; • The robot pushes or continually touches an obstacle for more than 3 seconds; • The robot forces its path through an obstacle; The obstacles can be of three types: • Static and previously mapped: Hardware already present in the house such as furni-
ture, doors, walls, dened in B.2.1. The teams should already have this obstacles mapped
from set-up days. These items will not change during this functionality benchmark. • Static and previously mapped: Hardware already present in the house such as furni-
ture, doors, walls, dened in B.2.1. The teams should already have this obstacles mapped
from set-up days. These items will not change during this functionality benchmark. 4.2.3
Expected Robot Behavior or Output Teams are required to set their robot on a specic starting position. Then, the robot receives,
through the RSBB, the start signal, as well as the rst waypoints that it must reach. The
robot must navigate to this waypoint and send back a signal to the RSBB, indicating that it
has reached the waypoint. At this time the RSBB will issue a new waypoint. This process is
repeated until the robot has reached the nal waypoint and a stop signal is issued by the RSBB. c⃝2018 by ERL Consumer Revision 1.1 19 4. Functionality Benchmarks Contents 4.2.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in SectionC.3.2 will be collected
together with the additional information described in the following table Topic
Type
Frame Id
Notes
/erlc/robot_pose_waypoint8
geometry_msgs/PoseStamped
/map
when reached
/erlc/marker_pose_waypoint9
geometry_msgsPoseStamped
/map
when reached This functionality benchmark will be fully automated (no human operation will be allowed)
and, for that, the robot has to communicate with the RSBB. It will receive the list of target
waypoints from the RSBB and it must send back a signal, each time it reaches a waypoint. 4.2.4
Procedures and Rules • Static: Items Granny Annie left lying on the ground. The obstacles may be of dierent
shapes and sizes, are not previously known by the teams, and may be dierent in between
runs. • Static: Items Granny Annie left lying on the ground. The obstacles may be of dierent
shapes and sizes, are not previously known by the teams, and may be dierent in between
runs. • Dynamic: Granny Annie's visitors. People moving inside the house. 8The 2D robot pose, once each waypoint is reached, at the oor level, i.e., z = 0 and only yaw rotation.
9The 3D pose of the marker in 6 degrees of freedom once each waypoint is reached. Revision 1.1 4.2.6
Scoring and Ranking At each run and for each team, three metrics will be used to score the performance: Accuracy,
number of obstacle hits, execution time. 8The 2D robot pose, once each waypoint is reached, at the oor level, i.e., z = 0 and only yaw rotation. 9The 3D pose of the marker in 6 degrees of freedom once each waypoint is reached. c⃝2018 by ERL Consumer Revision 1.1 20 4. Functionality Benchmarks Contents Topic
Type
Notes
/roah_rsbb/goal
geometry_msgs/Pose2D
List of waypoints, sent by the
RSBB to the robot, when start-
ing the task. /roah_rsbb/reached_waypoint
roah_rsbb_comm_ros/UInt8
Message sent by the robot to the
RSBB, when reaching a point. It must include the number of
the respective waypoint in the se-
quence (starting from zero). Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the
navigation functionality benchmark. Topic
Type
Notes
/roah_rsbb/goal
geometry_msgs/Pose2D
List of waypoints, sent by the
RSBB to the robot, when start-
ing the task. /roah_rsbb/reached_waypoint
roah_rsbb_comm_ros/UInt8
Message sent by the robot to the
RSBB, when reaching a point. It must include the number of
the respective waypoint in the se-
quence (starting from zero). Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the
navigation functionality benchmark. Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the
navigation functionality benchmark. • Accuracy scoring will be based on the the mathematical means of the distance from the
waypoints and and the corresponding orientation error. The distance mean from the robot
to the target waypoint follows the equation • Accuracy scoring will be based on the the mathematical means of the distance from the
waypoints and and the corresponding orientation error. The distance mean from the robot
to the target waypoint follows the equation A = 1
N
N
X
i
d (pi, ri) ,
(2.1) (2.1) where d (pi, ri) is the Euclidean distance from the robot's position ri to the target waypoint
pi (as shown in Figure 2.5) and N the total number of points. where d (pi, ri) is the Euclidean distance from the robot's position ri to the target waypoint
pi (as shown in Figure 2.5) and N the total number of points. 4.3.1
Functionality Description This functionality benchmark aims at evaluating the ability of a robot to understand speech
commands from users. A set of spoken sentences, recorded in dierent consumer environments,
will be broadcast through a speaker. All robots should be able to capture audio from an on-board
microphone, to record the captured audio in a le and to interpret the corresponding commands. The system should produce an output according to a nal representation dened in the following
sections. Such a representation will have to respect a command/arguments structure, where each
argument is instantiated according to the arguments of the command evoking verb. It is referred
to as Command Frame Representation (CFR) (e.g., go to the living room will correspond to
MOTION(goal:living room )). 4.2.6
Scoring and Ranking Considering the orientation, the mean is B = 1
N
N
X
i
δ (αi, βi) ,
(2.2) (2.2) where δ (α, β) is the absolute value of the dierence between the desired waypoint orien-
tation α and the robot's orientation β, such that δ (α, β) = |α −β| where δ (α, β) is the absolute value of the dierence between the desired waypoint orien-
tation α and the robot's orientation β, such that δ (α, β) = |α −β| After the computation of these accuracy scorings, they will be discretized and tted in one
of the following groups: 1: A < 10cm AND B < 20◦;
2: A < 30cm AND B < 45◦;
3: A < 50cm AND B < 90◦;
4: A < 80cm AND B > 90◦; 21
c⃝2018 by ERL Consumer c⃝2018 by ERL Consumer Revision 1.1 21 4. Functionality Benchmarks Contents A lower group number corresponds to the better performance. Therefore, teams will be
ranked starting from group 1. Note that for a team to be placed in any of the groups,
it must respect the limits for A and B. If a team has a score that does not t any of
groups dened above (e.g. mean of the error above 80cm), it will not receive scoring in
the respective Functionality Benchmark run; • If more than one team is found inside each of the previously dened group, the number of
obstacle hits will be used as a tie breaker, where the team with less hits will be ranked rst
and so on. Note that hits will only be considered as a tie breaker, i.e., a team in group 2
will never be ranked rst than any team in 1, despite of the number of hits (note that a
class of hard hits was dened which, if they happen, the procedure stops); • If teams are still tied, time will be the decisive tie breaker. • If teams are still tied, time will be the decisive tie breaker. Note that throughout the competition and according to the teams performance, the thresh-
olds for the classes of A and B can be changed. 4.3.2
Input Provided Some information about the lexicon (verbs and nouns of objects) used in the benchmark and a
sample audio le can be found in the ERL Wiki [1]. In order to evaluate the correct understanding of a command expressed in natural language
(e.g. through a sentence), a semantic representation formalism based on semantic frame has been
selected. Each frame corresponds to an action, namely a robot command. A set of arguments is
associated to each frame, specifying part of the command playing a particular role with respect
to the action expressed by the frame. For example, in the command go to the dining room the
Motion frame is expressed by the verb go, while the part of the sentence to the dining room
corresponds to the Goal argument, indicating the destination of the Motion action. The set of
frames dened and selected for this Benchmark is reported in the following list, together with
the set of associated arguments (current arguments are reported in bold italic inside the example
commands): • Motion: the action performed by the robot itself of moving from one position to another,
occasionally specifying a specic path followed during the motion. The starting point is
always taken as the current position of the robot. • Motion: the action performed by the robot itself of moving from one position to another,
occasionally specifying a specic path followed during the motion. The starting point is
always taken as the current position of the robot. Goal: the nal position in the space to be occupied at the end of the motion action,
e.g. Go to the kitchen; Go to the right of the sofa. Path: the trajectory followed while performing the motion towards the Goal, e.g. Move along the wall. c⃝2018 by ERL Consumer Revision 1.1 22 4. Functionality Benchmarks Contents • Searching: the action of inspecting an environment or a general location, with the aim of
nding a specic entity. Theme: the entity (most of the time an object) to be searched during the searching
action, e.g. Search for the glass. Ground: the environment or the general location in the space where to search for
the Theme, e.g. Find the glass in the living room. • Taking: the action of removing an entity from one place, so that the entity is in robot
possession. 4.3.2
Input Provided Theme: the entity (typically an object) taken through the action, e.g. Take the
cereal box. Source: the location occupied by the Theme before the action is performed and
from which the Theme is removed, e.g. Grab the mayo on the table; Remove
the sheets from the bed. • Placing: the action of placing an entity that the robot already posses in a place or position
in the space. Theme: the entity (typically an object) placed through the action, e.g. Drop the
jar. Goal: the location that should be occupied by the Theme after the action is per-
formed, e.g. Put the can on the counter. • Bringing: the action of changing the position of an entity in the space from a location to
another. Theme: the entity (typically an object), being carried during the bringing action,
e.g. Bring the garbage to the kitchen. Goal: the endpoint of the path along which the carrier (e.g. the robot - and thus
the Theme) travels, e.g. Bring the garbage to the kitchen. Source: the beginning of the path along which the carrier (e.g. the robot - and thus
the Theme) travels, e.g. Bring the garbage from the dining room to the kitchen. Beneficiary: the person to whom the Theme must be brought, e.g. Bring me
the mobile phone. Composition of actions is also possible in the CFR, corresponding to more complex action as
the Pick_and_place action, represented by a sequence of Taking frame followed by a Bringing
frame (e.g. for the command take the box and bring it to the kitchen). Composition of actions is also possible in the CFR, corresponding to more complex action as
the Pick_and_place action, represented by a sequence of Taking frame followed by a Bringing
frame (e.g. for the command take the box and bring it to the kitchen). The grammar specifying the correct syntax for a CFR will be also provided, and is reported
in the following. In order to represent the semantic frames extracted from the commands in a
compact way, a specic syntax has been dened, called Command Frame Representation (CFR). Such a representation will have to respect a command/arguments structure, resembling the
common syntax for a programming language method: the frame represents the method name,
while the arguments represent the method arguments. MOTION(goal:to the kitchen)#TAKING(theme:the tea cup). Frames can have more than one single arguments, as for the command take a towel from the
bathroom, corresponding to the following tagging and CFR: [take]Taking [a towel]Theme [from the bathroom]Source [take]Taking [a towel]Theme [from the bathroom]Source go to the kitchen and [take]Taking [the tea cup]Theme. go to the kitchen and [take]Taking [the tea cup]Theme. go to the kitchen and [take]Taking [the tea cup]Theme. The frame are associated to the verbs as they evoke the action expressed by the frames. This
double tagging of the semantic information will correspond to the conjunction of the CFR of the
two frames, that is: [go]Motion [to the kitchen]Goal and take the tea cup [go]Motion [to the kitchen]Goal and take the tea cup Action →MOTION | TAKING | BRINGING | SEARCHING | PLACING Action →MOTION | TAKING | BRINGING | SEARCHING | PLACING Arguments →Argument | Argument, Arguments Argument →Argument_name:Role_filler Argument_name →theme | goal | source | path | ground | beneficiary Role_filler →Defined_lexicon where Defined_lexicon is the lexicon that will be released to the team before the competition,
including names of rooms (e.g. hallway, living room, etc.) and objects (e.g. cereal box, jar, etc.). where Defined_lexicon is the lexicon that will be released to the team before the competition,
including names of rooms (e.g. hallway, living room, etc.) and objects (e.g. cereal box, jar, etc.). Composition of actions is also possible in the CFR, corresponding to more complex action
as the Pick_and_place action, represented by a sequence of Taking frame followed by a Placing
frame (e.g. for the command take the box and put it on the table). The corresponding CFR
will be: TAKING(theme:the box)#PLACING(theme:it,goal:on the table) A parser is available in the ERL Wiki [1] in order to check the format compliance of the
produced output in terms of interpretation. Here we provide some annotation examples. Considering the command go to the kitchen and
take the coee mug, where two frames are evoked (e.g. Motion, the two associated annotation
will be: 4.3.2
Input Provided For example, for the go to the dining
room command, where a Motion frame is expressed and the Goal argument is instantiated
with to the dining room, the corresponding CFR will be: MOTION(goal:to the dining room). It is worth underlying that more than one argument can be expressed in a command. c⃝2018 by ERL Consumer Revision 1.1 23 4. Functionality Benchmarks Contents Results of the Speech Understanding Functionality must be presented according to the CFR
formalism. The grammar specifying the correct syntax for a CFR will be also provided, and is
reported in the following. Command →Single_command | Composed_command Command →Single_command | Composed_command Composed_command →Single_command#Command Single_command →Action(Arguments) Single_command →Action(Arguments) Revision 1.1 SEARCHING(theme:my jacket). More detailed information about the available audio datasets, the parser and the lexicon can
be found in the ERL Wiki [1]. SEARCHING(ground:the bedroom,theme:for my wristwatch). Finally, some commands have been enriched with colloquial forms, as the use of modal verbs,
e.g. could you please nd my jacket?. These particles are not considered in the tagging, as they
represent only inections that, in this case, don't aect the general meaning of the command: could you please [find]Searching [my jacket]Theme ? Revision 1.1 TAKING(theme:a towel,source:from the bathroom). In a sentence, it will be possible to nd some arguments that have not been tagged. These
will be only arguments not dened for this task (and thus not reported in the list in Section
4.3.2) as, for example, the Manner argument, representing the manner in which the action c⃝2018 by ERL Consumer 24 Revision 1.1 4. Functionality Benchmarks Contents take place. For example, in the command Search carefully the bedroom for my wristwatch, the
adverb carefully, representing the Manner, is not tagged: [search]Searching carefully [the bedroom]Ground [for my wristwatch]Theme 4.3.3
Expected Robot Behavior or Output The robot should be able to understand a command starting from the speech input. The robot
should correctly transcribe the command and recognize the action to perform, resulting in the
correct command frame (e.g. MOTION for a motion command) and the arguments involved (e.g. the
goal of a motion command). The output of the robot should provide the CFR format for each
command, as reported in Section 4.3.1 and dened in Section 4.1.2. For each command, the system should generate the corresponding transcription and the
interpretation in the CFR format. This information have to be saved in an output text le called
results.txt. In this le, a line has to be added for each command, following the format 4.3.4
Procedures and Rules The robots will be disposed in circle around a 360◦speaker that will broadcast a set of spoken
sentences. These sentences are pre-recorded commands in dierent consumer environments and
are played continuously while containing a small pause between the commands. For every com-
mand the command number is also announced in advance. An example can be downloaded from:
https://sites.google.com/site/erlsrlisbon/resources/test.mp3 NOTE: An autonomous detection of the command number is highly preferred, however, teams
can also indicate the start of a new command by pressing a single button (either a button in a
GUI or a key on the keyboard). The benchmarking procedure is performed for all the teams in parallel. Each team receives a
USB stick before the benchmark begins to connect to their robots. Once the benchmark is over,
only one button can be pressed to store the output le and all teams must then deliver their
USB sticks. 4.3.5
Acquisition of Benchmarking Data During the execution of the benchmark, the following data will be collected: During the execution of the benchmark, the following data will be collected: • Sensor data (in the form of audio les) used by the robot to perform speech recognition10 • Sensor data (in the form of audio les) used by the robot to perform speech recognitio • The set of all possible transcription for each user utterance; • The nal command produced during the natural language analysis process; • Intermediate information produced or used by the natural language understanding system
during the analysis as, for example, syntactic information. 10Speech les from all teams and all benchmarks (both Task benchmarks and Functionality bench-
marks) will be collected and used to build a public dataset. The audio les in the dataset will therefore
include all the defects of real-world audio capture using robot hardware (e.g., electrical and mechani-
cal noise, limited bandwidth, harmonic distortion). Such les will be usable to test speech recognition
software, or (possibly) to act as input during the execution of speech recognition benchmarks. command_numberi|command_transcriptioni|CFRi where Command_number, command_transcription and CFR represent respectively the number,
the transcription and the interpretation of the i-th audio le, separated by a pipe (|). The
results.txt le must be encoded using standard UTF-8 character encoding: les with a dierent
encoding will be automatically rejected. where Command_number, command_transcription and CFR represent respectively the number,
the transcription and the interpretation of the i-th audio le, separated by a pipe (|). The
results.txt le must be encoded using standard UTF-8 character encoding: les with a dierent
encoding will be automatically rejected. NOTE: the correspondence between the data in the results le and the audio command
numbers must be consistent. If the Automatic Speech Recognition fails in transcribing a sentence, the label BAD_RECOGNITION
must be used. Similarly, if the semantic frame extraction does not produce any correct result,
the NO_INTERPRETATION label must be reported. An example of results.txt le is reported in
the following: command_1|move to the living room|MOTION(goal:living room )
command_2|BAD_RECOGNITION|NO_INTERPRETATION command_1|move to the living room|MOTION(goal:living room )
command_2|BAD_RECOGNITION|NO_INTERPRETATION NOTE: every line not respecting the format required and described above will be skipped
during the evaluation phase. In addition to saving the output on the text le, which will be used for scoring, the organizing
committee might ask the teams to also send the output to the RSBB, after every command, in
order to visualize the results in real-time for the audience. Revision 1.1 c⃝2018 by ERL Consumer 25 4. Functionality Benchmarks Contents 3. Time utilized (if less than the maximum allowed for the benchmark). 3. Time utilized (if less than the maximum allowed for the benchmark). The nal score will be evaluated considering both the AcC and the AgC. Only the F-Measure
will be considered for both measures, each one contributing for 50% of the score. The AgC
F-Measure will be evaluated for each argument, and the nal F-Measure for the AgC will be the
sum of the single F-Measure of the single arguments divided by the number of arguments. This
nal score has to be considered as an equivalence class. If this score will be the same for two or
more teams, the WER will be used as penalty to evaluate the nal ranking. This means that a
team belonging to an equivalence class can not be ranked lower than one belonging to a lower
one, even though the nal score, considering the WER of the rst is lower than the score of the
second. 4.4
People Perception Functionality This functionality benchmark aims at assessing the capabilities of a robot to correctly detect,
locate and recognize humans. Human perception is one of the most important capabilities re-
quired for human-robot interactions and essential for a successful deployment of robots in many
consumer environments. 4.4.1
Functionality Description The benchmark requires that the robots correctly detects the presence of a human inside a
predened target area, recognizes the person and accurately estimates his/her position. Revision 1.1 4.3.6
Scoring and Ranking During the functionality benchmark, dierent aspects of the speech understanding process will
be assessed: During the functionality benchmark, dierent aspects of the speech understanding process will
be assessed: 1. The Word Error Rate on the transcription of the user utterances, in order to evaluate the
performance of the speech recognition process. 2. For the generated CFR, the performance of the system will be evaluated against the
provided gold standard version of the CFR, that is conveniently paired with the analyzed
audio le and transcription. Two dierent performances will be evaluated at this step. One measuring the ability of the system in recognizing the main action, called Action
Classication (AcC), and one related to the classication of the action arguments, called
Argument Classication (AgC). In both cases the evaluations will be carried out in term
of Precision, Recall and F-Measure. This process is inspired to the Semantic Role Labeling
evaluation scheme proposed in [2]. For the AcC this measures will be dened as follow: • Precision: the percentage of correctly tagged frames among all the frames tagged by
the system; • Precision: the percentage of correctly tagged frames among all the frames tagged by
the system; • Recall: the percentage of correctly tagged frames with respect to all the gold standard
frames; • Recall: the percentage of correctly tagged frames with respect to all the gold standard
frames; c⃝2018 by ERL Consumer Revision 1.1 26 4. Functionality Benchmarks Contents • F-Measure: the harmonic mean between Precision and Recall. • F-Measure: the harmonic mean between Precision and Recall. • F-Measure: the harmonic mean between Precision and Recall. Similarly, for the AgC, Precision, Recall and F-Measure will be evaluated, given an action
f, as: • Precision: the percentage of correctly tagged arguments of f with respect to all the
arguments tagged by the system for f. • Precision: the percentage of correctly tagged arguments of f with respect to all the
arguments tagged by the system for f. • Recall: the percentage of correctly tagged arguments of f with respect to all the gold
standard arguments for f. • Recall: the percentage of correctly tagged arguments of f with respect to all the gold
standard arguments for f. • F-Measure: the harmonic mean between Precision and Recall. 4.4.3
Expected Robot Behavior or Output The participating team is required to position their robot on any desired initial position, that
could be anywhere outside the specied target area, from which it can best perceive this area. The human targets that the robot is required to perceive will move into the target area one
at the time. The identity and location of the person presented to the robot is unknown before
he/she moves and stands inside the area. For each presented person, the robot must perform
the following: • Person localization: Locate the 2D position of the person with respect to the benchmark
setup reference frame. • Person localization: Locate the 2D position of the person with respect to the benchmark
setup reference frame. • Person recognition: Recognize the person inside the target area. For each person, the robot must communicate the results to the RSBB, or announce that
it is incapable of perceiving the person. In addition, for the interest of the audience, the robot
must announce the name of the recognized person after recognition. 4.4.2
Input Provided A bounded rectangular target area, of approximately 3m×3m, will be dened on the oor that
will accommodate humans during the benchmark. The coordinates of the target area along with
the reference frame will be communicated to the teams during the setup days. This area will
only accommodate one person at a time. The test area will be surrounded by motion tracking cameras, such as an Optitrack system,
to locate the precise position of the person and automatically evaluate the performance of the
robots in locating people. Up to 10 persons will be chosen from the technical and organizing committee as well as from
the team members of the competing teams during the setup days. Each team will be given
the opportunity to meet the people and to collect training data before the beginning of the
benchmark. c⃝2018 by ERL Consumer Revision 1.1 27 4. Functionality Benchmarks Contents 4.4.4
Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned
below: Step 1 The participating team is required to set their robot on any desired initial position
outside the target area. Step 1 The participating team is required to set their robot on any desired initial position
outside the target area. Step 2 Once the start signal is sent out from the RSBB, the robot is required to detect and
localize the person standing inside the target area. 3 The robot sends the results to the RSBB and announces its readiness for the next person Step 3 The robot sends the results to the RSBB and announces its readiness for the next person. Step 4 The RSBB requests the person to move out of the area and the randomly selects the
next person to move into the area. Step 4 The RSBB requests the person to move out of the area and the randomly selects the
next person to move into the area. This process is repeated until all people are presented to the robot. Teams will have up to ten
minutes to complete the functionality benchmark. This process is repeated until all people are presented to the robot. Teams will have up to ten
minutes to complete the functionality benchmark. 4.4.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected. 4.5.3
Expected Robot Behavior or Output Initially, a human will stand in front of the robot that is placed at a previously dened location
in the arena. Once the benchmark starts, the person will start to walk and visit dierent regions
of the arena. The robot is expected to follow and maintain its original distance with this person
at all times while avoiding obstacles and other people that will interrupt the motion of the robot. If the robot loses or cant keep up with the target, it can request the person to come back,
walk slower, wait or stand in front of the robot to resume the walking behavior. However, such
interruptions will have a direct impact on the performance score that is computed automatically
by the system. 4.4.6
Scoring and Ranking Evaluation of the performance of a robot according to this functionality benchmark is based on: Evaluation of the performance of a robot according to this functionality benchmark is based on:
1
The number and percentage of correctl
recogni ed persons 1. The number and percentage of correctly recognized persons. 1. The number and percentage of correctly recognized persons. 2. Location error for all detected persons. 3. Execution time (if less than the maximum allowed for the benchmark). The previous criteria are in order of importance: the rst criterion is applied rst and teams
will be scored according to the common accuracy metrics; the ties are broken by second criterion
which is the position error. Since the position error is slightly aected by the precision of the
ground truth system we will use a set of accuracy classes, and in case of ties we will resort to
the third criterion. c⃝2018 by ERL Consumer Revision 1.1 28 4. Functionality Benchmarks Contents 4.5
Person Following Functionality Human accompanying is an important capability required by many service robots for human-
robot interactions. This functionality benchmark aims at assessing the capabilities of mobile
robots in eectively following humans. The human following capability is expected to be one of
the essential capabilities required for the robots planning to take part in the upcoming Smart
City Major Competitions. 4.5.1
Functionality Description The benchmark requires that the robot accompanies a human and always maintain a desired
distance with this person. In this benchmark, a person will initially stand in front of the robot
and then will start to walk around the arena. The robot must always follow this person while
avoiding obstacles or other humans who are passing by. 4.5.2
Input Provided The test is executed inside an apartment-like arena that will include stationary and dynamic
obstacles such as furniture or people. The initial pose of the robot and the person will be
communicated to the teams before the competition. Since the main aim of this benchmark is to evaluate the following capabilities of robots,
and the human-perception is not the main focus of the test, teams are open to exploit any
preferred perceptual technique for their robots to display an ecient following behavior. This can
range from anything such as laser range scanners, ultrasound sensors to vision-based perception
systems. Furthermore, teams are allowed to instruct the person to wear tags, markers, colored
shirt or anything that will minimize the perceptual errors. 4.5.6
Scoring and Ranking The evaluation of the performance of a robot is performed autonomously with the aid of a motion
capture system that precisely measures the true pose of the robot and the person at all times. The performance score is computed based on: 1. The accuracy in keeping the desired relative distance to the target. 1. The accuracy in keeping the desired relative distance to the target. 2. The total distance covered by the robot when it is following the target. The robot is
automatically considered to be following when it is within a tolerance distance from the
desired relative distance. 2. The total distance covered by the robot when it is following the target. The robot is
automatically considered to be following when it is within a tolerance distance from the
desired relative distance. The previous criteria are considered to be of equal importance, encouraging both accurate
and fast solutions with minimum interruptions. 4.5.4
Procedures and Rules All teams are required to perform this functionality benchmark according to the steps described
below. The task must be done exclusively in autonomous mode and no teleoperation is permitted. Step 1 The robot is placed on the starting position facing a standing human. Step 2 The benchmark starts after the start signal is communicated by the RSBB. Step 2 The benchmark starts after the start signal is communicated by the RSBB. Step 3 The person starts to walks in normal walking speed and visits dierent areas of the
apartment, occasionally stopping and then resuming the walking. The robot must exhibit
the following behaviour as described in Section 4.5.3 . Step 4 The benchmark will stop automatically after the timeout. An End signal will be issued
by the RSBB at timeout. Step 4 The benchmark will stop automatically after the timeout. An End signal will be issued
by the RSBB at timeout. This benchmark will last 5 minutes. This benchmark will last 5 minutes. c⃝2018 by ERL Consumer Revision 1.1 29 4. Functionality Benchmarks Contents 4.5.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected. 4.6
Object Grasping and Manipulation Functionality This functionality benchmark evaluates the capabilities of a robot to correctly grasp and ma-
nipulate objects. In particular, it assesses the object picking and placing capabilities of service
robots that is an essential requirement for many consumer applications, for example to set up a
dining table. 4.6.3
Expected Robot Behavior or Output The participating team is required to set their robot in front of the working table. After an
object is placed on the table and the benchmark starts, the robot must grasp and pick up the
object from the table surface and then deliver and place it on the target position specied by
the RSBB. If required, the robot can further manipulate the object to improve the pose of the
object. Once the robot has completed the task, or it is incapable of completing it, it must send
the end command to the RSBB for the next object to be placed on the table. 4.6.1
Functionality Description In this benchmark the robots are required to correctly grasp, lift and move a set of objects over
a tabletop. Objects will be placed one by one on top of a table located in front of the robot. The
initial pose of the object is not known beforehand. The robot must grasp the object and deliver
it to a target position over the table that is specied and communicated by the RSBB. Figure
2.6 describes an illustration of the benchmarking procedure. Figure 2.6: Illustration of the Grasping and manipulation functionality benchmark where
the robot is required to grasp, pick up and place the object on a dened target position. Motion capture markers are attached on the object and are used for measuring the object
pose and automatic evaluation Figure 2.6: Illustration of the Grasping and manipulation functionality benchmark where
the robot is required to grasp, pick up and place the object on a dened target position. Motion capture markers are attached on the object and are used for measuring the object
pose and automatic evaluation c⃝2018 by ERL Consumer Revision 1.1 30 4. Functionality Benchmarks Contents 4.6.4
Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned
below: Step 1 The participating team is required to set their robot on any desired initial position in
front of the working table. Step 2 The start signal will be communicated to the robot by the RSBB to indicate the start
of the benchmark. Step 2 The start signal will be communicated to the robot by the RSBB to indicate the start
of the benchmark. Step 3 Once the robot announces its readiness to the RSBB by sending the Prepared signal, an
object is randomly selected by the RSBB, from the list of possible objects, and is manually
placed over the table by the referee. Step 3 Once the robot announces its readiness to the RSBB by sending the Prepared signal, an
object is randomly selected by the RSBB, from the list of possible objects, and is manually
placed over the table by the referee. Step 4 The execution command along with the target position of the object will be issued from
the RSBB. Step 4 The execution command along with the target position of the object will be issued from
the RSBB. Step 4 The execution command along with the target position of the object will be issued from
the RSBB. Step 5 The robot must grasp, pick up and place the object on the specied target location. Step 5 The robot must grasp, pick up and place the object on the specied target location. Step 6 The robot sends the end signal to the RSBB and announces its readiness for the next
object. Step 6 The robot sends the end signal to the RSBB and announces its readiness for the next
object. This process is repeated until all objects are presented to the robot. Teams will have up to ten
minutes to complete the functionality benchmark. This process is repeated until all objects are presented to the robot. Teams will have up to ten
minutes to complete the functionality benchmark. 4.6.2
Input Provided A set of 3D-printed objects of dierent shapes will be used for this benchmark. The 3D models of
all objects, in digital format, will be available to the teams before the competition allowing them
to train their robots in simulation or in real-world by 3D-printing the objects. Furthermore,
objects are also provided to the teams during the setup days. As the focus of this benchmark is on evaluation of the grasping and manipulation capabilities
of robots and object, object perception is simplied by using 3D printed single-color objects over
a white table. Furthermore, the nature of objects will be communicated to the robot through
the RSBB to further assist the robot with the perception. The reference frame will be marked on the table as in the object perception functionality,
see Figure 2.4, and the test area will be surrounded by motion tracking cameras, such as an
Optitrack system, to precisely locate the objects and evaluate the performance of robots. 12Internal robot data referring to end eector 3D position 11Any notication from the robot 4.6.5
Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected together with the additional information described in the following table During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be
collected together with the additional information described in the following table c⃝2018 by ERL Consumer 31 Revision 1.1 Contents 4. Functionality Benchmarks Topic
Type
Frame Id
Notes
/erlc/notication11
std_msgs/String
/erlc/gripper_pose12
geometry_msgs/Pose
Individual tournament awards: Awards will be given to the best teams for each of the Task Benchmarks (TBMs) and Function-
ality Benchmarks (FBMs) per tournament by the local organizers. In every Local/Major Tournament, each team is requested to perform several trials of the
available TBMs and FBMs. The team score for a given TBM/FBM in a Local/Major Tournament
is computed as follows: 1. Select the best ve trials of the TBM/FBM by the team (all the trials if less than ve trial
attempts are oered by the local organizers) 1. Select the best ve trials of the TBM/FBM by the team (all the trials if less than ve trial
attempts are oered by the local organizers) 2. The team score is the median of the scores of the trials selected in 1. The team with the highest score in each of the task benchmarks will be awarded the title (ERL
Consumer Best-in-class Task Benchmark <task benchmark title>). The teams with the highest
score ranking for each of the functionality benchmarks will be awarded the title (ERL Consumer
Best-in-Class Functionality Benchmark <functionality benchmark title> and 'ERL Consumer
Second-Best-in-Class Functionality Benchmark <functionality benchmark title>). The team with the highest score in each of the task benchmarks will be awarded the title (ERL
Consumer Best-in-class Task Benchmark <task benchmark title>). The teams with the highest
score ranking for each of the functionality benchmarks will be awarded the title (ERL Consumer
Best-in-Class Functionality Benchmark <functionality benchmark title> and 'ERL Consumer
Second-Best-in-Class Functionality Benchmark <functionality benchmark title>). Notes: • The number of TBM/FBM trial attempts oered in a tournament is recommended to be
a minimum of 3 and a maximum of 7 trials. • The number of TBM/FBM trial attempts oered in a tournament is recommended to be
a minimum of 3 and a maximum of 7 trials. • When a single team participates in a given benchmark, the corresponding benchmark
award will only be given to that team if the Executive and Technical Committees consider
the team performance of exceptional level. • When a single team participates in a given benchmark, the corresponding benchmark
award will only be given to that team if the Executive and Technical Committees consider
the team performance of exceptional level. 4.6.6
Scoring and Ranking Evaluation of the performance of a robot for this functionality benchmark is performed au-
tonomously and is based on: 1. The number and percentage of correctly grasped objects. An object is considered to be
grasped by the RSBB system once it is lifted completely from the table. 1. The number and percentage of correctly grasped objects. An object is considered to be
grasped by the RSBB system once it is lifted completely from the table. 2. Final pose error of the object with respect to the specied target location. 3. Execution time (if less than the maximum allowed for the benchmark). The rst criterion is applied rst and teams will be scored according to the common accuracy
metrics; the ties are broken by second criterion which is the position error. Since the position
error can be slightly aected by the precision of the ground truth system, a set of accuracy classes
is dened and used, in case of ties we will resort to the the execution time. c⃝2018 by ERL Consumer Revision 1.1 32 A. ERL Consumer Award Categories Contents Individual tournament awards: • When less than three teams participate in a given functionality benchmark, only the ERL
Consumer Best-in-class Functionality Benchmark <functionality benchmark title> award
will be given to a team, and only if the Executive and Technical Committees consider that
team's performance as excellent A
ERL Consumer Award Categories Individual tournament awards: Best ERL Consumer team award: Only one nal Best ERL Consumer team award will be awarded to the best performing team
at the end of the Season. The Season ranking is computed as follows: Only one nal Best ERL Consumer team award will be awarded to the best performing team
at the end of the Season. The Season ranking is computed as follows: • To be eligible for an award, a team must have executed valid (i.e., scored) trials of at least
one TBM in minimum two Local/Major Tournaments of the Season; • Only TBMs are considered for computing the nal score; • A score is computed for every TBM as the median of the pooled trials used for scoring
the best two performances of a team in the Local/Major Tournaments of the Season (see
above); • A score is computed for every TBM as the median of the pooled trials used for scoring
the best two performances of a team in the Local/Major Tournaments of the Season (see
above); • The team nal score is then calculated by summing up all the TBM scores; • A minimum score value will be required in order for the award to be given. c⃝2018 by ERL Consumer Revision 1.1 33 B. The ERL Consumer Test bed Contents B
The ERL Consumer Test bed The test bed for ERL Consumer consists of the environment in which the competition will
happen, including all the objects and artefacts in the environment, and the equipment brought
into the environment for benchmarking purposes. An environment tting quite well the user story is depicted by Figure 7. Figure 7: Granny Annie's apartment. Figure 7: Granny Annie's apartment. Note: There is considerable discussion in the community, as to how specic and precise the
description of the environment should be, especially in the light of benchmarking. In order to
require teams to develop robots which can be easily and exibly adapted to a wide range of dif-
ferent environments, can deal with a wide variety of objects, etc., and to avoid overengineering of
solutions, it would be highly advisable to keep the description as exible as possible. We reect
this in the specications below by providing comparatively generous boundary conditions, e.g. on
room sizes, and by complementing them by a recommendation, which should be understood as a
default size and the size we target to use at least for the rst iteration of the competition. Com-
petition organizers should plan with these recommended sizes and objects, while the developers
of simulation software should provide means to easily modify models, e.g. by resizing rooms or
by changing the properties of the environment or replacing objects, etc. The recommended environment for the ERL Consumer Challenge is illustrated in Figure 8. Participating teams should assume the competition environment to be as illustrated; deviations
should only occur if on-site constraints (space available, safety regulations) enforce them. An
example of a certied ERL Consumer test bed and its corresponding environment is provided in
Appendix E. Environment Specication B.4 (List of Rooms) The environment features the following ve spatial areas: hallway, living room, dining room,
kitchen, and bedroom. Environment Specication B.2 (Flat Environment) All spatial areas all located on the same level, except where specied otherwise. There are
no stairs in the environment. Environment Specication B.3 (Spatial Areas and Rooms) Spatial areas completely enclosed by walls are referred to as rooms. The apartment follows
an open plan architecture, i.e. several spatial areas are connected to each other by open space
(openly connected) and are only jointly surrounded by walls. In human-robot interaction,
such spatial areas may still referred to as rooms. B.1
Environment Structure and Properties The following set of scenario specications must be met by the ERL Consumer environment. Environment Specication B.1 (Structured Environment)
The environment consist of an ensemble of ve spatial areas. c⃝2018 by ERL Consumer Revision 1.1 34 B. The ERL Consumer Test bed Contents Hallway
Kitchen
Living Room
Bathroom
Bedroom
Dining Room
Patio
Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will
not be accessible to the robots in this edition). Bathroom Bedroom Kitchen
Living Room
Dining Room
Patio
Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will
not be accessible to the robots in this edition). Kitchen Living Room Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will
not be accessible to the robots in this edition). c⃝2018 by ERL Consumer Revision 1.1 35 B. The ERL Consumer Test bed Contents Two additional areas are foreseen for future extensions; they may be provided as part of a test
bed, but they are not foreseen and not accessible to the robots, yet. We do not further consider
them in the following specications. Robots are expected to cope with rooms and spatial areas of dierent sizes. Robots are expected to cope with rooms and spatial areas of dierent sizes. Robots are expected to cope with rooms and spatial areas of dierent sizes. The minimum sizes of the spatial areas are as follows: hallway 120cm × 200cm, bedroom
400cm × 300cm, kitchen 200cm × 240cm, dining room 300cm × 300cm, living room 400cm ×
400cm. The whole apartment should t into bounding rectangular box having a minimum are
f 50m2 and a maximum area of 200m2. The recommended sizes of the spatial areas are as follows: hallway 120cm × 200cm,
bedroom 400cm × 300cm, kitchen 300cm × 260cm, dining room 300cm × 300cm, living room
400cm × 580cm. Bedroom
Dining
Room
Living
Room
Inside
Hallway
Outside
Hallway
Kitchen
area accessible to the robot
door
area not accessible to the robot
open space
Figure 9: Graph showing the topological structure of environment. Figure 9: Graph showing the topological structure of environment. Environment Specication B.8 (Walls) The walls of the environment must meet the following criteria: Material features: The bedroom walls have to be made of some sti material, such as
wood, wood-based materials (chipboards), stone, concrete, or metal. For competition
arenas, walls will usually be made of chipboards in combination with wood or metallic
frames. The color of the walls will usually be some light color (such as white, ivory,
yellow, light green, to name a few examples). One or two walls per room may be
painted with some darker color (such dark red, aubergine, mocca, dark grey, dark
brown, to name a few examples) for decorative purposes. Patterned wallpaper may be
used for nishing the walls. The walls are not translucent. If some kind of translucent
material, such as glass, Plexiglass R
⃝, Perspec R
⃝, or Lucite R
⃝is used, then these wall areas
are dened as windows. Shape/form: The walls are upright. No slanted walls will be used. Osets up to 5cm are
allowed to ease construction of test beds. Shape/form: The walls are upright. No slanted walls will be used. Osets up to 5cm are
allowed to ease construction of test beds. Size: The minimum height of the walls is 80cm. The recommended wall height is 240cm. Exceptions may be made for up to two connecting walls of each room in order to allow
better visibility for the audience at competitions. The length of the walls is dened by
the connecting oor shapes. The width (thickness) of the walls must be large enough
to ensure sucient stability. The drawings assume a wall thickness of 20cm. If the
construction of an environment foresees inside walls with less thickness, then the space
of the connecting spatial areas will grow accordingly. Uniqueness: The walls may be unique or not, i.e. the wall colors and patterns may be the
same as in other spatial areas of the apartment or they may be dierent. Environment Specication B.7 (Floors) The oor of each spatial area must be such that safe operation of robots meeting the
specications laid down in Section C is possible. The following criteria must be met: Material features: The oor is either carpet or parquet oor. No constraints exist with
respect to the colors or patterns used. Slope: The oor should be well-leveled, but slopes of up to 2◦and unevenness of up to 5mm
are acceptable. Uniqueness: The oor may be unique or not, i.e. a oor in a room be the same as in other
room, or it may be dierent. Environment Specication B.6 (Connectivity of Spatial Areas) The environment is accessible from outside through a front door to the hall way. The
hallway is openly connected to the living room by a portal. The living room is connected
to the bedroom by a door. The living room is openly connected to the kitchen. The living c⃝2018 by ERL Consumer Revision 1.1 36 B. The ERL Consumer Test bed Contents room is openly connected to the dining room. The dining room is openly connected to the
kitchen. room is openly connected to the dining room. The dining room is openly connected to the
kitchen. room is openly connected to the dining room. The dining room is openly connected to the
kitchen. connectivity of the spatial areas is illustrated by the topological graph depicted in Figure he connectivity of the spatial areas is illustrated by the topological graph depicted in Figure 9. nvironment Specication B.7 (Floors) The connectivity of the spatial areas is illustrated by the topological graph depicted in Figure 9. Environment Specication B.7 (Floors) Environment Specication B.7 (Floors) Environment Specication B.9 (Ceilings) p
(
g )
The rooms may or may not be covered by a ceiling. If it is not covered by a ceiling, then
special constructions may be foreseen for xing lamps, sensors, or other objects. If it is
covered by a ceiling, the following specications apply:
Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Uniqueness: The ceiling is not unique. The rooms may or may not be covered by a ceiling. If it is not covered by a ceiling, then
special constructions may be foreseen for xing lamps, sensors, or other objects. If it is
covered by a ceiling, the following specications apply: Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Uniqueness: The ceiling is not unique. c⃝2018 by ERL Consumer 37 Revision 1.1 B. The ERL Consumer Test bed Contents Environment Specication B.12 (Dining Room) The dining room has a window and the furniture includes a dining table seating four, and
four chairs. The dining room has a window and the furniture includes a dining table seating four, and
four chairs. Environment Specication B.11 (Living Room) Environment Specication B.11 (Living Room)
The living room has a large window front side to the patio. These windows cannot be
opened. These windows have inside blinds that are operated electrically. The furniture
includes a large carpet, a coee table, a couch, two armchairs, a low-height sideboard, and a
bookshelf. A TV set is located on the sideboard. The lighting includes central ceiling lights,
a band of dimmable ceiling spots, and a large oor light. Environment Specication B.10 (Bedroom) The furniture includes a double bed, two bedside tables, a large wardrobe, a large mirror, a
dressing table, and a carpet. The lighting includes two bedside lamps. n example conguration of the bedroom is depicted in Figure 10. An example conguration of the bedroom is depicted in Figure 10. Figure 10: An example bedroom created with the IKEA bedroom planner. Figure 10: An example bedroom created with the IKEA bedroom planner. Environment Specication B.13 (Kitchen) The kitchen has no window and no door. The furniture includes several cupboards with
drawers and doors. The installation include a fridge/freezer combination, a sink, a dish-
washer, a stove, a baking oven, and an exhaust hood. Two rows of ceiling lights are available
for the lighting. (Details of the kitchen will be specied in more detail as needed.) Environment Specication B.14 (Hallway) The hallway has no windows. The furniture consists of a coat rack. The lighting consists of
lamps mounted on the walls. The hallway has no windows. The furniture consists of a coat rack. The lighting consists of
lamps mounted on the walls. c⃝2018 by ERL Consumer Revision 1.1 38 B. The ERL Consumer Test bed Contents Environment Specication B.15 (Navigation-Relevant Object Types) The navigation-relevant objects that may be present in the environment include the following
types of objects: • Rugs, which may be placed on top of oors, covering the oor usually only partially. • Rugs, which may be placed on top of oors, covering the oor usually only partially. F
i
hi h i
l
d i
h
i • Rugs, which may be placed on top of oors, covering the oor usually only partially. • Furniture, which is placed in the environment. • Furniture, which is placed in the environment. • Furniture, which is placed in the environment. • Doors, which connect rooms and may be in various dierent states. • Doors, which connect rooms and may be in various dierent states. • Any other kind of object, task-relevant or not, and including networked embedded
devices and benchmarking equipment, if placed in the environment such that the object
occupies space in the robot's workspace. • Any other kind of object, task-relevant or not, and including networked embedded
devices and benchmarking equipment, if placed in the environment such that the object
occupies space in the robot's workspace. B.2
Task-Relevant Objects in the Environment The test bed environment will contain numerous objects, some of which are explicitly relevant
for one or more of the task benchmarks or functionality benchmarks described in Section 3 and
4, respectively. We distinguish three major categories of task relevance: Navigation-Relevant Objects: This class of objects comprises of all objects which have extent
in physical space and do (or may) intersect (in 3D) with the robot's navigation space. All
such objects must be avoided during navigation, i.e. whenever the robot moves, it may not
bump into these objects or touch them, unless otherwise specied by a task. Navigation-
relevant objects may be known by name or not. If these objects have a unique name, then
the object may occur as a destination, e.g. for a navigation or manipulation operation. Manipulation-Relevant Objects: This class contains all objects that the robot may have
manipulative interactions with, which may include touching (a switch), grasping (a glass),
lifting (a book), holding (a cup), placing (a parcel), dropping (waste), carrying (a glass),
pushing (a drawer), pulling (a drawer), turning (a book), lling ( a glass), pouring (from
a cup), etc. For these objects, the most comprehensive information will be provided. Perception-Relevant Objects: These are objects that the robot must only be able to per-
ceive. By perceive we mean that the robot should be able to recognize if such an object
is in its view, that it should be able to identify the object if it is unique or to classify it
if not (e.g. an instance of a cup, if several non-unique instances exist), and that it should
be able to localize the object. Objects that are only perception-relevant usually occur in
tasks where the robot is supposed to nd and localize these objects, but is not required to
manipulate them. Perception-Relevant Objects: These are objects that the robot must only be able to per-
ceive. By perceive we mean that the robot should be able to recognize if such an object
is in its view, that it should be able to identify the object if it is unique or to classify it
if not (e.g. an instance of a cup, if several non-unique instances exist), and that it should
be able to localize the object. Objects that are only perception-relevant usually occur in
tasks where the robot is supposed to nd and localize these objects, but is not required to
manipulate them. B.2
Task-Relevant Objects in the Environment Subsequently, we describe a complete collection of all objects relevant for the task benchmarks
and functionality benchmarks. Object Specication B.1 (Rugs) The ERL Consumer Competition does not foresee any rugs in the environment, yet The ERL Consumer Competition does not foresee any rugs in the envir Object Specication B.2 (Furniture) Object Specication B.2 (Furniture)
The furniture placed in each room or spatial area is listed in the environment specications
B.10 to B.14. Further details on the furniture are provided in the ERL wiki. The furniture placed in each room or spatial area is listed in the environment specications
B.10 to B.14. Further details on the furniture are provided in the ERL wiki. The furniture placed in each room or spatial area is listed in the environment specications
B.10 to B.14. Further details on the furniture are provided in the ERL wiki. Environment Specication B.16 (Manipulation-Relevant Object Types) The manipulation-relevant objects that may be present in the environment include the
following types of objects: • Personal items, like keys connected by key rings, mobile phones, tablet computers, MP3
players, eyeglasses/spectacles and their cases, wallets/purses and billfolds, watches,
bracelets and rings. • Personal items, like keys connected by key rings, mobile phones, tablet computers, MP3
players, eyeglasses/spectacles and their cases, wallets/purses and billfolds, watches,
bracelets and rings. • Mail items, like letters and parcels, and print material, like newspapers, magazines,
journals, paperbacks and books. • Mail items, like letters and parcels, and print material, like newspapers, magazines,
journals, paperbacks and books. • Household items, such as glasses, cups, plates, knifeware, and such. • Groceries in containers of various forms, like cartons, cans, bottles, tubes, bags. • Switches for lighting and electronic appliances. • Handles of doors, including handles of wardrobe doors and drawers. • Any other kind of object provided that it meets all of the object constraints B.1 to
B.4. Object Specication B.3 (Doors) (
)
The doors used in the environment have a door handle on both sides. Doors are dynamic
objects that can be in dierent states at dierent times. At any time, a door may be in one of
Revision 1.1
39
c⃝2018 by ERL Consumer The doors used in the environment have a door handle on both sides. Doors are dynamic
objects that can be in dierent states at dierent times. At any time, a door may be in one of
Revision 1 1
39
c⃝2018 by ERL Consumer Revision 1.1 c⃝2018 by ERL Consumer 39 B. The ERL Consumer Test bed Contents the following four states: open, ajar, closed, locked. A door is considered open if its opening
angle is 80◦or more. A door is considered closed, if its opening angle is 0◦and the door is
latched but not locked. In case the door is locked as well, the door state obviously is locked. In all other cases, the door is considered to be ajar. the following four states: open, ajar, closed, locked. A door is considered open if its opening
angle is 80◦or more. A door is considered closed, if its opening angle is 0◦and the door is
latched but not locked. In case the door is locked as well, the door state obviously is locked. In all other cases, the door is considered to be ajar. The personal items to be used include: The personal items to be used include: • keys with a key ring and lanyard. • mobile phones. • tablet computers (e.g. iPad). • eyeglasses with cases, e.g. rimless, horn-rimmed or sunglasses. • purses with dierent colors. • wristwatches. Object Specication B.5 (Mail Items and Print Material)
The mail items to be used include:
• A parcel as specied in Section 3.2.2. Object Specication B.6 (Household Items)
The household items to be used include:
• coee mugs, in a dierent color or pattern
• coee cups with saucers, all identical. • dessert plates
• cake plates
• small and large glasses
• water jugs
c⃝2018 by ERL Consumer
40
Revision 1.1 The mail items to be used include: c⃝2018 by ERL Consumer Revision 1.1 40 B. The ERL Consumer Test bed Contents • coee machine • electric kettle • electric kettle c⃝2018 by ERL Consumer Object Specication B.8 (Switches) Switches are buttons and may be latching (e.g. power button of a washing machine) or
non-latching (e.g. power button of a PC). Digital switches are connected to either lamps or
shutters. Switches are used as follows: • Switches embedded into walls for operating the lighting. These may be simple on/o
switches, changeover switches, or intermediate switches. • Switches embedded into walls for operating the lighting. These may be simple on/o
switches, changeover switches, or intermediate switches. • Switches embedded into walls for operating blinds or shutters. These switches come
as a pair of pushbuttons, one for each direction of operation, and require to remain
pushed for the duration of the operation. • Switches embedded into walls for operating blinds or shutters. These switches come
as a pair of pushbuttons, one for each direction of operation, and require to remain
pushed for the duration of the operation. Object Specication B.7 (Groceries) The grocery items to be used include: • cartons of dierent size and coloring, containing food items such as cornakes, cereal,
pasta, salt, cornstarch, • cartons of dierent size and coloring, containing food items such as cornakes, cereal,
pasta, salt, cornstarch, • tin cans in at least three dierent sizes, containing tinned food such as tomato paste,
sauerkraut, tuna, and fruits such as pears, peaches, and pineapples • tin cans in at least three dierent sizes, containing tinned food such as tomato paste,
sauerkraut, tuna, and fruits such as pears, peaches, and pineapples • tin cans, all of the same size, but dierently colored, containing soft drinks. • glass jars in at least two dierent sizes, containing food such as pickled vegetables like
cucumber, onions, corn, and beetroot, or pasta sauces, mustard, mayonnaise, or jams
and jellies. • PET bottles, containing water, soft drinks, or juices. • No tubes or bags are foreseen yet. The next two object specications concern objects relevant for manipulation, which themselves
are embedded either directly into the environment or into objects placed into the environment,
like furniture. c⃝2018 by ERL Consumer Revision 1.1 41 B. The ERL Consumer Test bed Contents Object Constraint B.3 (Object Consistency, Rigidity, Stiness) Object Constraint B.3 (Object Consistency, Rigidity, Stiness)
Any objects foreseen for manipulation tasks must be suciently rigid such that grasping by
a robot is possible. There may be constraints on where objects can or may be grasped. Some
objects may be foreseen which can appear in dierent shapes, e.g. glasses or a bunch of keys. Object Constraint B.4 (Object Content)
Objects may not consist of or contain any kind of hazardous material. The content of objects
may be solid matter (e.g. paper, nutrition), uids (e.g. water or juices), or gases (e.g. air). If the object contains uids or solid matter in the form of loose material (e.g. cornakes or
chips), the object must have a lid or other kind of xture which ensures that the content is
properly contained in the object and not spilled. Object Constraint B.1 (Object Weight) The objects foreseen for manipulation can have a maximum weight of 1kg. The objects foreseen for manipulation can have a maximum weight of 1kg. The door handles to be used include: • Each of the doors in the environment has a door handle on each side of the door. • Furniture features some handles, but they will not be relevant for manipulation. • Furniture features some handles, but they will not be relevant for manipulatio Fig. 2.2 illustrates the look and feel of one door handle in the environment. Fig. 2.2 illustrates the look and feel of one door handle in the environment. Object Constraint B.2 (Object Size) The default minimum width/length/depth/diameter/thickness (henceforth: size) of an ob-
ject foreseen for manipulation is 2cm, and the default sum of the length, width, and height of
the smallest bounding box around the object (henceforth: box sum) is 6cm. An object may
have a lower size than 2cm, down to 5mm, in up to two dimensions, if the other dimensions
compensate for it, i.e. if the box sum is still at least 6cm. The default minimum width/length/depth/diameter/thickness (henceforth: size) of an ob-
ject foreseen for manipulation is 2cm, and the default sum of the length, width, and height of
the smallest bounding box around the object (henceforth: box sum) is 6cm. An object may
have a lower size than 2cm, down to 5mm, in up to two dimensions, if the other dimensions
compensate for it, i.e. if the box sum is still at least 6cm. Object Constraint B.3 (Object Consistency, Rigidity, Stiness) B.2.3
Perception-Relevant Objects This section provides some clarications with respect to perception. This section provides some clarications with respect to perception. Environment Specication B.17 (Perception-Relevant Object Types) Environment Specication B.17 (Perception-Relevant Object Types) Environment Specication B.17 (Perception-Relevant Object Types) The perception-relevant objects in the environment include the following types of objects: The perception-relevant objects in the environment include the following types of objects The perception-relevant objects in the environment include the following types o • The basic environment structure including oors, walls, and ceilings. • The basic environment structure including oors, walls, and ceilings. • All navigation-relevant objects, including rugs, furniture, and any other physical object
in the workspace. • All navigation-relevant objects, including rugs, furniture, and any other physical object
in the workspace. c⃝2018 by ERL Consumer Revision 1.1 42 B. The ERL Consumer Test bed Contents • All dynamic navigation-relevant objects, i.e. objects with changeable state, like doors,
windows, and some furniture. • All dynamic navigation-relevant objects, i.e. objects with changeable state, like doors,
windows, and some furniture. • All manipulation-relevant objects, some of which may be uniquely identiable while
others are not (identical copies present) • All manipulation-relevant objects, some of which may be uniquely identiable while
others are not (identical copies present) • Target locations for navigation and manipulation may require the capability to identify
objects (such as furniture items) that are not manipulation-relevant. Examples include
objects the robot is supposed to move nearby (e.g. the bedside table) or objects the
robot is supposed to grasp or place objects (e.g. the kitchen counter) • Non-task-relevant objects (see Section B.3) will not have to be perceived as part of task
benchmarks or functionality benchmarks, but due to their presence in the environment,
they will present perceptual noise. • Non-task-relevant objects (see Section B.3) will not have to be perceived as part of task
benchmarks or functionality benchmarks, but due to their presence in the environment,
they will present perceptual noise. The perception-relevant objects are already specied in various other sections. Further details
on the target locations (and respective objects) are provided in the ERL wiki. The perception-relevant objects are already specied in various other sections. Further details
on the target locations (and respective objects) are provided in the ERL wiki. Environment Specication B.18 (Non-Task-Relevant Object Types) Environment Specication B.18 (Non-Task-Relevant Object Types) The non-task-relevant objects that may be present in the environment include the following
types of objects: The non-task-relevant objects that may be present in the environment include the following
types of objects: • Textile objects, like curtains, tablecloth, placesets, napkins, and pillows, either axed
to walls/ceilings or sitting on top of furniture. • Textile objects, like curtains, tablecloth, placesets, napkins, and pillows, either axed
to walls/ceilings or sitting on top of furniture. • Mirrors, usually xed to walls or furniture. • Mirrors, usually xed to walls or furniture. • Lamps, on the oor or on top of furniture. • Floristic objects, like owers and plants, and associated objects like ower pots and
vases, which may be on the oor, on window sills, or on top of furniture. • Floristic objects, like owers and plants, and associated objects like ower pots and
vases, which may be on the oor, on window sills, or on top of furniture. • Pictorial objects, like posters, photographs, drawings, and paintings, either axed to
walls or sitting on furniture. • Pictorial objects, like posters, photographs, drawings, and paintings, either axed to
walls or sitting on furniture. • Other decorative objects, like plates and bowls, candles, and miniatures, usually sitting
on top of furniture items. • Other decorative objects, like plates and bowls, candles, and miniatures, usually sitting
on top of furniture items. B.3
Non-Task-Relevant Objects in the Environment The test bed environment for ERL Consumer is supposed to resemble a realistic apartment
inhabited by an elderly person.Aside of the already listed and specied objects, which make
up the environment itself, and objects relevant for navigation and manipulation, as well as
networked embedded devices (see Section B.5) and benchmarking equipment (see Section B.6),
the environment will contain numerous other objects, mostly for decoration and providing the
required realism. The decoration objects to be used include: • plates
• bowls
• triplets of candles. • miniatures or other decorative objects. The oristic objects to be used include: • small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. • small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. B.4
Referee, Scoring and Benchmarking Box The Referee, Scoring and Benchmarking Box (RSBB) software is available at the following repos-
itory: The pictorial objects to be used include: The pictorial objects to be used include: • small framed pieces of photographs or drawings, each sized less than A4. • medium-sized pieces of posters or prints, each sized about A3. • small framed pieces of photographs or drawings, each sized less than A4. • medium-sized pieces of posters or prints, each sized about A3. • large pieces of paintings or posters, each sized about A1. • large pieces of paintings or posters, each sized about A1. • large pieces of paintings or posters, each sized about A1. Object Specication B.11 (Mirrors)
The mirror objects to be used include: • a tall mirror, e.g. in the hallway. Object Specication B.12 (Lamps) The lamps to be used include: • small lamp(s), e.g. on top of the bedside tables. • oor lamp(s), e.g. in the living room. • oor uplighters, e.g. in the living room. Note that ceiling lamps are already specied with the environment. Note that ceiling lamps are already specied with the environment. The textile objects to be used include: B.4
Referee, Scoring and Benchmarking Box Object Specication B.11 (Mirrors)
The mirror objects to be used include:
• a tall mirror, e.g. in the hallway. • a large mirror, e.g. in the bedroom The textile objects to be used include: The textile objects to be used include: The textile objects to be used include:
• curtains for the bedroom windows. • tablecloths for the dining table. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile napkins, each set consisting of four items. • pillows for couch and chairs in the living room. • linens, pillows, and coverlets for the bed in the bedroom. • curtains for the bedroom windows. • tablecloths for the dining table. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile napkins, each set consisting of four items. • pillows for couch and chairs in the living room. • linens, pillows, and coverlets for the bed in the bedroom. c⃝2018 by ERL Consumer Revision 1.1 43 B. The ERL Consumer Test bed Contents Object Specication B.11 (Mirrors)
The mirror objects to be used include:
• a tall mirror, e.g. in the hallway. • a large mirror, e.g. in the bedroom
Object Specication B.12 (Lamps)
The lamps to be used include:
• small lamp(s), e.g. on top of the bedside tables. • oor lamp(s), e.g. in the living room. • oor uplighters, e.g. in the living room. Note that ceiling lamps are already specied with the environment. Object Specication B.13 (Floristic Objects)
The oristic objects to be used include:
• small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. Object Specication B.14 (Pictorial Objects)
The pictorial objects to be used include:
• small framed pieces of photographs or drawings, each sized less than
• medium-sized pieces of posters or prints, each sized about A3. • large pieces of paintings or posters, each sized about A1. Object Specication B.15 (Decoration Objects)
The decoration objects to be used include:
• plates
• bowls
• triplets of candles. • miniatures or other decorative objects. Revision 1.1 https://github.com/rockin-robot-challenge/rsbb During the benchmarks, a human referee enforces the rules. This referee must have a way
to transmit his decisions to the robot, and receive some progress information. To achieve this c⃝2018 by ERL Consumer 44 Revision 1.1 B. The ERL Consumer Test bed Contents in a practical way, an assistant referee is seated at a computer communicating verbally with the
main referee. The assistant referee uses the Referee, Scoring and Benchmarking Box (RSBB). Besides basic starting and stopping functionality, the RSBB is also designed to receive scoring
input and provide ne grained benchmark control for functionality benchmarks that require so. in a practical way, an assistant referee is seated at a computer communicating verbally with the
main referee. The assistant referee uses the Referee, Scoring and Benchmarking Box (RSBB). Besides basic starting and stopping functionality, the RSBB is also designed to receive scoring
input and provide ne grained benchmark control for functionality benchmarks that require so. g
y
The Referee, Scoring and Benchmarking Box was designed to support the following feature Benchmark starting and stopping: Benchmark can only start if robot clock skew is below
100 milliseconds. Stop can be issued manually by the referee, by the robot if it completed
the benchmark or automatically by the RSBB if the time for the benchmark is over or if
the robot does not declare that it is saving oine data. Benchmark starting and stopping: Benchmark can only start if robot clock skew is below
100 milliseconds. Stop can be issued manually by the referee, by the robot if it completed
the benchmark or automatically by the RSBB if the time for the benchmark is over or if
the robot does not declare that it is saving oine data. Devices communication: the ERL Consumer competition area includes automated home de-
vices such as lights and window blinds. The RSBB provides an interface to control these
devices, enabled only in certain benchmarks, so that the robot does not command the
devices directly. The assistant referee can control the devices from his graphical interface. Tablet communication: the ERL Consumer competition area includes a tablet device that
can be used to communicate with the robot. Tablet communication passes through the
RSBB and is enabled only for certain benchmarks. Schedule: the full schedule of the competition is stored in the RSBB, allowing for automated
progression with no setup time before each benchmark. B.4.1
Communication between Benchmarking Equipment and Robots For some types of internal benchmarking data (i.e. provided by the robot), logging is done on
board the robot, and data are collected after the benchmark (for instance, via USB stick). Other
types of internal benchmarking data, instead, are communicated by the robot to the test bed
during the benchmark. In such cases, communication is done by interfacing the robot with
standard wireless network devices (IEEE 802.11n) that are part of the test bed, and which
therefore become a part of the benchmarking equipment of the test bed. However, it must be
noted that network equipment is not strictly dedicated to benchmarking: for some benchmarks,
in fact, the WLAN may be also (or exclusively) used to perform interaction between the robot
and the test bed. Due to the need to communicate with the test bed via the WLAN, all robots participating
to the ERL Consumer Competition are required to: 1. possess a fully functional IEEE 802.11n network interface13; 1. possess a fully functional IEEE 802.11n network interface13; 2. be able to keep the wireless network interface permanently connected to the test bed
WLAN for the whole duration of the benchmarks 2. be able to keep the wireless network interface permanently connected to the test bed
WLAN for the whole duration of the benchmarks https://github.com/rockin-robot-challenge/rsbb Schedule: the full schedule of the competition is stored in the RSBB, allowing for automated
progression with no setup time before each benchmark. Online data: data produced by the robot during benchmarks falls in two categories: online and
oine. Oine data is saved in a USB stick for latter analysis. Online data is transmitted
to the RSBB. The RSBB displays and saves the data. Online data: data produced by the robot during benchmarks falls in two categories: online and
oine. Oine data is saved in a USB stick for latter analysis. Online data is transmitted
to the RSBB. The RSBB displays and saves the data. Logging: the RSBB saves a full log for each benchmark. Logging: the RSBB saves a full log for each benchmark. Referee interface: the RSBB includes a fully featured graphical interface to be used by the
assistant referee. Referee interface: the RSBB includes a fully featured graphical interface to be used by the
assistant referee. Single client communication interface: the RSBB includes all features in a single communi-
cation interface. This way, participating teams only have to implement one communication
mechanism. State information: the RSBB continuously displays what state the benchmark is in. Client libraries are available and should be integrated in the teams software https://github. com/rockin-robot-challenge/at_home_rsbb_comm_ros. This repository also includes the pro-
tocol to access the home automation devices and as well as the tablet application. Passwords:
a password will be given to each team at the beginning of the competition. These
can be used to set up the private communication channel with the RSBB and to get access to
the home automation devices. Security note:
the password security mechanism is only designed to prevent unintentional
honest mistakes from the teams, like accessing the camera over WLAN, while another team is
executing a benchmark. Any team caught trying to hack, circumvent or change the behaviour
of any component described here for any purpose will be punished. c⃝2018 by ERL Consumer Revision 1.1 45 B. The ERL Consumer Test bed Contents B.5
Networked Devices in the Environment Networked sensors and actuators may be provided as a part of the environment. These devices
are as enumerated and described below. (Note: Currently, ERL consumer is not using these networked devices except for possible
demos during Local Tournaments in the test beds equipped with them. Furthermore, the use of
the xed IP camera at the entrance is no longer permitted for any of the tasks) Home automation controller: This device will run as a server on the local area network
within the test bed. It will be accessible from all `permitted' devices (wi-enabled laptop-
s/single board computers, etc. on the robots) on the same network. Using this controller,
devices such as motorized window blinds/shutters, some of the room lights, motorized tilt-
able windows, etc. can be controlled. The controller will be able to receive messages (in a
specic format provided to the teams) from the `permitted' devices in order to control all
the aforementioned devices. An example of such a controller can be found here14. Ethernet Camera: There will be a standard IP camera mounted a the front door, e.g. to
retrieve images from the ringing visitors. The camera can have its parameters (frame rate,
resolution, color gains) changed over Ethernet and it is not motor-controlled (no pan-tilt). One way to access the camera is by receiving the MJPEG stream published by the cam-
era15. During the setup days, the camera can be congured directly by each team to t
the needs (with admin but not root access). The OC/TC will save the conguration of
each team and load them before each benchmark. Teams are free to use any protocol or
conguration which the camera supports. A ROS package that can be used to acquire images from the camera is available16 Ethernet Camera: There will be a standard IP camera mounted a the front door, e.g. to
retrieve images from the ringing visitors. The camera can have its parameters (frame rate,
resolution, color gains) changed over Ethernet and it is not motor-controlled (no pan-tilt). One way to access the camera is by receiving the MJPEG stream published by the cam-
era15. During the setup days, the camera can be congured directly by each team to t
the needs (with admin but not root access). The OC/TC will save the conguration of
each team and load them before each benchmark. B.5
Networked Devices in the Environment Teams are free to use any protocol or
conguration which the camera supports. A ROS package that can be used to acquire images from the camera is available16. A ROS package that can be used to acquire images from the camera is available16. A ROS package that can be used to acquire images from the camera is available16 The diagram in Fig. 11 illustrates the network infrastructure which will be used throughout
the competition. The network consists of the following devices: The diagram in Fig. 11 illustrates the network infrastructure which will be used throughout
the competition. The network consists of the following devices: • Server: computer used to manage the network. 13It must be stressed that full functionality also requires that the network interface must not be
hampered by electromagnetic obstacles, for instance by mounting it within a metal structure and/or by
employing inadequate antenna arrangements. Network spectrum in the Competition area is typically
very crowded, and network equipment with impaired radio capabilities may not be capable of accessing c⃝2018 by ERL Consumer Revision 1.1 46 B. The ERL Consumer Test bed Contents AP
SMARTIF
Server
Ethernet
Camera
Server
SMARTIF IO
Device1
Switch
Ethernet
Non-Ethernet
Device2
DeviceN
(...)
Figure 11: Network infrastructure of the ERL Consumer Competition AP Switch Ethernet
Camera Figure 11: Network infrastructure of the ERL Consumer Competition • Switch: Ethernet switch used to connect all the devices. • Switch: Ethernet switch used to connect all the devices. • AP: access point where the robot is supposed to connect to. This is the only connec
between the robot and the network. • AP: access point where the robot is supposed to connect to. This is the only connection
between the robot and the network. • Ethernet Camera: perspective camera outside at the main entrance door. • Devices: dierent devices may exist in the environment, such as a motor to control the
window blinds, controlled power plugs, light dimmers or a door bell button. • Devices: dierent devices may exist in the environment, such as a motor to control the
window blinds, controlled power plugs, light dimmers or a door bell button. • SMARTIF IO: module to control the dierent devices/sensors existing in the house. They can only be accessed via the SMARTIF server. Teams do not have to interact with
each device separately. the test bed WLAN, even if correctly working in less critical conditions.
14http://rollertrol.com/store/en/vera-home-automation-control/87-vera-v3.html
15For example by using http://team_name:PASSWORD@10.0.0.2/mjpg/video.mjpg
16https://github.com/rockin-robot-challenge/at_home_ipcam
17http://www.smartif.com B.5
Networked Devices in the Environment • SMARTIF Server: device which is responsible for the communication between the
SMARTIF IO and the network. It can only be accessed from the server. Teams do
not have to interact directly with it. Technical details regarding SMARTIF products can
be found at the ocial site17. p
g
17http://www.smartif.com B.6
Benchmarking Equipment ERL benchmarking is based on the processing of data collected in two ways: ERL benchmarking is based on the processing of data collected in two ways: Internal benchmarking data, collected by the robot system under test (see Section C • Internal benchmarking data, collected by the robot system under test (see Sect • External benchmarking data, collected by the equipment embedded into the test bed. External benchmarking data, collected by the equipment embedded into the test bed External benchmarking data is generated by the ERL test bed in dierent ways depending on
their nature. One of the types of external benchmarking data used by ERL are pose data about
robots and/or their constituent parts. To acquire these, ERL uses a camera-based commercial
motion capture system composed of dedicated hardware and software. Benchmarking data has
the form of a time series of poses of rigid elements of the robot (such as the base or a marker
mounted in a known position). Pose data are acquired and logged by a customized external
software system based on ROS (Robot Operating System): more precisely, logged data is saved
as bagles created with the rosbag utility provided by ROS. Other types of external benchmarking data are usually collected using devices that are specic
to the benchmark and they are described in the context of the associated benchmark. Equipment c⃝2018 by ERL Consumer Revision 1.1 47 B. The ERL Consumer Test bed Contents to collect external benchmarking data includes any server which is part of the test bed and that
the robot subjected to a benchmark has to access as part of the benchmark. Communication
between servers and robot is performed via the test bed's own wireless network (see Section C.3). to collect external benchmarking data includes any server which is part of the test bed and that
the robot subjected to a benchmark has to access as part of the benchmark. Communication
between servers and robot is performed via the test bed's own wireless network (see Section C.3). c⃝2018 by ERL Consumer Revision 1.1 48 C. Robots and Teams Contents Robot Specication C.3 (Sensor Subsystems) Any robot used by a team may use any kind of onboard sensor subsystem, provided that
the sensor system is admitted for use in the general public, its operation is safe at all times,
and it does not interfere with other teams or the environment infrastructure. A team may use any kind of sensor system provided as part of the environment,
e.g. the networked camera specied in Section B.5, by correctly using a wireless communica-
tion protocol specied for such purpose and provided as part of the scenario. Sensor systems
used for benchmarking and any other systems intended for exclusive use of the organisers are
not accessible by the robot system. Any robot used by a team may use any kind of onboard sensor subsystem, provided that
the sensor system is admitted for use in the general public, its operation is safe at all times,
and it does not interfere with other teams or the environment infrastructure. A team may use any kind of sensor system provided as part of the environment,
e.g. the networked camera specied in Section B.5, by correctly using a wireless communica-
tion protocol specied for such purpose and provided as part of the scenario. Sensor systems
used for benchmarking and any other systems intended for exclusive use of the organisers are
not accessible by the robot system. Robot Specication C.1 (Type/Class) A competition entry may use a single robot or multiple robots acting as a team. Robot Specication C.2 (Mobility Subsystems) At least one of the robots entered by a team must be mobile and able to visit dierent task-
relevant locations by autonomous navigation. Teleoperation (using touch screens, tablets,
mouse, keyboard, etc.) of robots for navigation is not permitted (except when otherwise
specied, e.g., in particular instances of task and functionality benchmarks). The robot
mobility must work in the kind of environments specied for ERL Consumer and on the kind
of oors dened in the ERL Consumer environment specications. C
Robots and Teams The purpose of this section is threefold: 1. It species information about various robot features that can be derived from the environ-
ment and the targeted tasks. These features are to be considered at least as desirable, if
not required for a proper solution of the task. Nevertheless, we will try to leave the design
space for solutions as large as possible and to avoid premature and unjustied constraints. 1. It species information about various robot features that can be derived from the environ-
ment and the targeted tasks. These features are to be considered at least as desirable, if
not required for a proper solution of the task. Nevertheless, we will try to leave the design
space for solutions as large as possible and to avoid premature and unjustied constraints. 2. The robot features specied here should be supplied in detail for any robot participating
in the competition. This is necessary in order to allow better assessment of competition
and benchmark results later on. 2. The robot features specied here should be supplied in detail for any robot participating
in the competition. This is necessary in order to allow better assessment of competition
and benchmark results later on. 3. It species the benchmarking equipment and data logging facilities required to perform
benchmarking. 3. It species the benchmarking equipment and data logging facilities required to perform
benchmarking. Robot Specication C.4 (Communication Subsystems) Any robot used by a team may internally use any kind of communication subsystem,
provided that the communication system is admitted for use in the general public, its op-
eration is safe at all times, and it does not interfere with other teams or the environment
infrastructure. A robot team must be able to use the communication system provided as part of the
environment by correctly using a protocol specied for such purpose and provided as part
of the scenario. Any robot used by a team may internally use any kind of communication subsystem,
provided that the communication system is admitted for use in the general public, its op-
eration is safe at all times, and it does not interfere with other teams or the environment
infrastructure. A robot team must be able to use the communication system provided as part of the
environment by correctly using a protocol specied for such purpose and provided as part
of the scenario. infrastructure. A robot team must be able to use the communication system provided as part of the
environment by correctly using a protocol specied for such purpose and provided as part
of the scenario. Robot Constraint C.3 (Environmental Aspects) (
p
)
Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other
mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular,
very loud noise as well as well-audible constant noises (humming, etc.) should be avoided. The regulations of the country in which a competition or benchmark is taking place must
be obeyed at all times. The event organizers will provide specic information in advance, if
applicable. Robots, devices, and any apparatus used should not be the cause of eects that are
perceived as a nuisance to the humans in the environment. Examples of such eects in-
clude causing wind and drafts, strong heat sources or sinks, stenches, or sources for allergic
reactions. Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other
mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular, Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other
mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular,
very loud noise as well as well-audible constant noises (humming, etc.) should be avoided. The regulations of the country in which a competition or benchmark is taking place must
be obeyed at all times. The event organizers will provide specic information in advance, if
applicable. Robots, devices, and any apparatus used should not be the cause of eects that are
perceived as a nuisance to the humans in the environment. Examples of such eects in-
clude causing wind and drafts, strong heat sources or sinks, stenches, or sources for allergic
reactions. Robot Specication C.5 (Power Supply) Any mobile device (esp. robots) must be designed to be usable with an onboard power supply
(e.g. a battery). The power supply should be sucient to guarantee electrical autonomy for
a duration exceeding the periods foreseen in the various benchmarks, before recharging of Revision 1.1 c⃝2018 by ERL Consumer 49 C. Robots and Teams Contents batteries is necessary. Charging of robot batteries must be done outside of the competition environment. The
team members are responsible for safe recharging of batteries. If a team plans to use inductive
power transmission devices for charging the robots, they need to request permission from
the event organizers in advance and at least 3 months before the competition. Detailed
specications about the inductive device need to be supplied with the request for permission. Robot Constraint C.2 (Safety and Security Aspects) For any device a team brings into the environment and/or the team area, and which fea-
tures at least one actuator of any kind (mobility subsystems, robot manipulators, grasping
devices, actuated sensors, signal-emitting devices, etc.), a mechanisms must be provided to
immediately stop its operation in case of an emergency (emergency stop). For any device
a team brings into the environment and/or the team area, it must guarantee safe and se-
cure operation at all times. Event ocials must be instructed about the means to stop such
devices operating and how to switch them o in case of emergency situations. Robot Constraint C.1 (Computational Subsystems) Any robot or device used by a team as part of their solution approach must be suitably
equipped with computational devices (such as onboard PCs, microcontrollers, or similar)
with sucient computational power to ensure safe autonomous operation. Robots and other
devices may use external computational facilities, including Internet services and cloud com-
puting to provide richer functionalities, but the safe operation of robots and devices may not
depend on the availability of communication bandwidth and the status of external services. C.3.1
Setup for the Motion Capture System During all task benchmarks, the pose of the robot will be captured by a motion capture system. For this, a Marker Set, similar to the one depicted in Fig. 12, which was used during the RoCKIn
2014 Competition, will be provided by ERL to be tted on the robot. (a) Perspective view
(b) Top view
Figure 12: RoCKIn Marker Set used during the RoCKIn 2014 Competition (the motion
capture markers are illustrated as red spheres) (b) Top view (b) Top view (b) To (a) Perspective view Figure 12: RoCKIn Marker Set used during the RoCKIn 2014 Competition (the motion
capture markers are illustrated as red spheres) As part of robot internal data (see Section C.3.2) Teams must provide the position of the
Marker Set in the test bed reference frame together with the robot estimated pose in the same
reference frame. To do so, the static transformation between the origin of the reference frame of
the base of the robot and the Marker Set, acquired through the motion capture system, will be
provided to the Teams during the setup days. The Marker Set will be provided to the Teams in advance with respect to the competition
and the Teams require to mount it on the robot so to be above the robot and completely visible
from the motion capture system. The robot must avoid collisions between the Marker Set and
other objects (when assessing collisions for scoring, the Marker Set is considered as a part of the
robot). C.3
Benchmarking Equipment and Data Logging on the Robot Whenever teams are required to install some element provided by ERL on (or in) their robots,
such element will be carefully chosen in order to minimize the work required from teams and the
impact on robot performance. C.2
Safety Check and Robot Inspection During the set-up days, all robots will be checked by the TC/OC for compliance with the
specications and constraints described in Section C.1. Teams will be asked to show the safety
mechanisms of their robots and to demonstrate their use. A live demonstration is necessary: for
example, pushing an emergency stop button while the robot is moving and verifying that the
robot immediately stops. If the robot has other mechanical devices (e.g. a manipulator), their
safety must be demonstrated as well. This inspection can be done at any time during the set-up days. When teams are ready for
an inspection, they can request one of the TC/OC members. The inspection can be repeated at
any time during the competition days, upon request of the TC/OC. Referees, TC/OC members,
team members and any other user who is interacting with the robot are always allowed to operate
the safety mechanisms when there is a clear risk for the safety of any person or for the damage
of any part of the environment. c⃝2018 by ERL Consumer c⃝2018 by ERL Consumer 50 Revision 1.1 C. Robots and Teams Contents Robots that are not considered safe by the TC/OC are not allowed to participate
in the competition! Revision 1.1 C.3.2
Internal Data Logging During all task benchmarks, robots are required to log Internal data according to the following
specications. This data must be expressed in the reference frame of the test bed which will be
clearly marked on it. It will be possible for teams to dene such frame in their robot before the
start of the competition. Fig. 13 illustrates one possible position of the test bed reference frame. Only relevant data is expected to be logged (i.e. pointcloud used to recognize an object, more
than one if an algorithm requiring multiple pointclouds is used). There are no restriction about
the framerate: data can be saved, for the relevant parts of the benchmark, at the rate they are
acquired or produced. The log may be a rosbag or the corresponding YAML representation, as c⃝2018 by ERL Consumer Revision 1.1 51 Contents C. Robots and Teams Figure 13: Example of a test bed reference frame for ERL Consumer. The z-axis points
towards the reader. Figure 13: Example of a test bed reference frame for ERL Consumer. The z-axis points
towards the reader. specied in Section C.4, here we refer to the rosbag version, the corresponding YAML translation
should be direct. The list of topics to be logged (i e
for all tasks and functionality benchmarks) is reported specied in Section C.4, here we refer to the rosbag version, the corresponding YAML translation
should be direct. The list of topics to be logged (i.e., for all tasks and functionality benchmarks) is reported
in the following table Topic
Type
Frame Id
Notes
/erlc/robot_pose18
geometry_msgs/PoseStamped
/map
10 Hz
/erlc/marker_pose19
geometry_msgsPoseStamped
/map
10 Hz
/erlc/trajectory20
nav_msgs/Path
/map
Each (re)plan
/erlc/<device>/image21
sensor_msgs/Image
/<device>_frame
/erlc/<device>/camera_info22
sensor_msgs/CameraInfo
/erlc/depth_<id>/pointcloud23
sensor_msgs/PointCloud2
/depth_<id>_frame
/erlc/scan_<id>24
sensor_msgs/LaserScan
/laser_<id>_frame
10-40Hz
tf25
tf
The format for the name of the bag le to be saved by the Teams on their robot is the
following: The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation. 18The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation. 19The 3D pose of the marker in 6 degrees of freedom. 20 Trajectories planned by the robot, referred to the robot base, including when replanning. 20Trajectories planned by the robot, referred to the robot base, including when replanning. 19The 3D pose of the marker in 6 degrees of freedom.
20 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account
the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so
on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range
nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. g
_
_
25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly
connected through the /base_frame which is the odometric center of the robot. Trajectories planned by the robot, referred to the robot base, including when replanning.
21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if
multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on
to the device name: e.g., "rgb 0", "stereo left 2", and so on. 19The 3D pose of the marker in 6 degrees of freedom.
20Trajectories planned by the robot, referred to the robot base, including when replanning.
21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if
multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on
to the device name: e.g., "rgb_0", "stereo_left_2", and so on.
22Calibration info for /erlc/<device>/image.
23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account
the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so
on.
24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range
nders could be present on the robot: e.g., "scan_0", "scan_1", and so on.
25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly
connected through the /base_frame which is the odometric center of the robot. g
j
y
_
_ g
g
multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on
to the device name: e.g., "rgb_0", "stereo_left_2", and so on.
22Calibration info for /erlc/<device>/image.
23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account
the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so
on. 18The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation
19 C.4
YAML Data File Specication The subsequent paragraphs specify the YAML le format that can be converted to ROS bag
les. This closely follows the data items described in D-2.1.7 [3]. The YAML format was chosen
because it is a simple format, easy to produce without using any special library. Furthermore,
the ROS messages format is already dened: as produced by the rostopic echo command. {F|T}BM{H|W}{1|2|3}_YYYYMMDDhhmm_{teamname}.bag {F|T}BM{H|W}{1|2|3}_YYYYMMDDhhmm_{teamname}.bag e.g., FBMH1_201503041356_myteam.bag, TBMH3_201503041156_myteam.bag, etc What data must be saved? Beside the data in the table, additional data the robot must
save is specied in the particular benchmark subsection. Please note that some data streams
(those with the highest bitrate) must be logged only in the time intervals when they are actually
used by the robot to perform the activities required by the benchmark. In this way, system load
and data bulk are minimized. For instance, whenever a benchmark includes object recognition
activities, video and point cloud data must be logged by the robot only in the time intervals
when it is actually performing object recognition. What we do with the data? This data is not used during the competition. In particular,
they are not used for scoring. The data are processed by ERL after the end of the competition
for in-depth analyses and/or to produce datasets to be published for the benet of the robotics
community. Where and when the robot must save the data? Robots must save the data, as
specied in the particular benchmark subsection, on a USB stick provided by ERL. The USB
stick is given to the team immediately before the start of the benchmark, and must be returned
(with the required data on it) at the end of the benchmark. NOTE: while the content of the data les saved by the robot is not used for scoring, the
existence of such les and their compliance to the specications does inuence the
score of the robot. Teams have the responsibility of ensuring that the required data les are
saved, and of delivering them to the referee at the end of the benchmark. These aspects will be
noted on the score sheet and considered for team ranking. C.3.2
Internal Data Logging 21 j
p
y
,
,
g
p
g
21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if
multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on
to the device name: e.g., "rgb_0", "stereo_left_2", and so on. 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account
the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so
on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range
nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range
nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. p
g ,
_
,
_
,
25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly
connected through the /base_frame which is the odometric center of the robot. 25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly
connected through the /base_frame which is the odometric center of the robot. c⃝2018 by ERL Consumer 52 Revision 1.1 C. Robots and Teams Contents Revision 1.1 C.4.1
File Format The YAML le should be composed of a single list of messages. Each message should have four
items: • topic - The topic name. • topic - The topic name. • secs - Timestamp of the message, in number of seconds since 1970. • nsecs - Nanoseconds component of the timestamp. • message - The message, according to the topic type. The message should be formatted in YAML, according to its structure. This is the same as
the output of rostopic echo. However, binary elds may be specied in base 64 encoding for
much smaller les. You can copy the le src/base64.hpp to your project, it depends only on
boost to encode base 64. And example for a le generated according to above specication could look as follow Revision 1.1 c⃝2018 by ERL Consumer 53 Contents C. Robots and Teams - topic: pose2d
secs: 1397024209
nsecs: 156423000
message:
x: 5.5
y: 6
theta: 6.4
- topic: image
secs: 1397024210
nsecs: 53585000
message:
header:
seq: 306
stamp:
secs: 1397024210
nsecs: 53585000
frame_id: ''
height: 4
width: 4
encoding: bgr8
is_bigendian: 0
step: 12
data:
!!binary JaU8JY0kGXUIAZ0UDWzgAXjgAb0kIglwbkGsnkWwoiWUfiGUhi2olhmUgc1YRaUw - topic: pose2d
secs: 1397024209
nsecs: 156423000
message: !!binary JaU8JY0kGXUIAZ0UDWzgAXjgAb0kIglwbkGsnkWwoiWUfiGUhi2olhmUgc1YRaUw C.4.2
YAML-to-ROSbag Conversion Tool D.1
Safety check Every run of each of the task benchmark will be preceded by a safety-check, outlined as follows: 1. The team members must ensure and inform at least one of the Organizing Committee
(OC) or Technical Committee (TC) member, present during the execution of the task,
that they have an emergency stop button on the robot which is fully functional. Any
member of the OC/TC can ask the team to stop their robot at any time which must be
done immediately. 1. The team members must ensure and inform at least one of the Organizing Committee
(OC) or Technical Committee (TC) member, present during the execution of the task,
that they have an emergency stop button on the robot which is fully functional. Any
member of the OC/TC can ask the team to stop their robot at any time which must be
done immediately. 2. A member of the OC/TC present during the execution of the task will make sure if the
robot complies with the other safety-related rules and robot specications presented in C. 2. A member of the OC/TC present during the execution of the task will make sure if the
robot complies with the other safety-related rules and robot specications presented in C. C.4.2
YAML-to-ROSbag Conversion Tool A tool to convert ERL Consumer YAML les into ROS bag les is available at the following
Github repository: https://github.com/rockin-robot-challenge/benchmark_and_scoring_converter c⃝2018 by ERL Consumer Revision 1.1 54 D. General Procedure and Scoring for Task Benchmarks Contents D
General Procedure and Scoring for Task Benchmarks General procedures, as well as scoring methods, are common to all Task Benchmarks. Those are
detailed in this Appendix. D.2
General Procedures This section species the procedures that will be followed for the start, restart or exit of each
TBM. All teams are required to perform each task according to the steps mentioned in the rules
and procedures sections for the tasks. Revision 1.1 D.2.2
Restart Procedure Within the rst 2 minutes after the robot enters the apartment and within the rst 5 minutes
from the start a test, the team can request for a restart. In this case the team is allowed to
enter the apartment, bring the robot outside and perform any operation on the robot. It is not
allowed to work on the robot inside the apartment (even if it is a quick and simple operation). Whenever the robot is ready, it can re-enter the arena and restart the test. The restart can be
done only once for each run of the test. No penalties will be given for a restart. But any score
achieved before the restart will be canceled and the time will not be stopped during the restart
procedure. D.2.1
Start Procedure The robots must be prepared outside of the apartment, in particular in a preparation area outside
at one of the doors that has been designed to start the test. This preparation area is reserved
for the next team in the schedule and can be accessed about 5 minutes before the start of the
test. Any other preparation must be done at the own team area or in any other location that
does not interfere with the competition. The referee will inform the two participating team 2 minutes before the start of the test. After 2 minutes, the referee will start the test, i.e. s/he starts the timer (no delays for any
reason). From this moment on, the robot is allowed to enter the apartment. If the robot is
not ready and team members are still working on it after the test is started, there will be no
penalty. But the time will run on. Whenever the robot enters the apartment, the team is not
allowed to operate the robot in any way (e.g., touching any device, using a mouse, keyboard or
touch screen, also remotely). In some task benchmarks it may be required that a person, e.g. guides the robot through the environment. In such a case the description of the respective task
benchmark will relax the previous rule. Only those actions described in the particular test are
allowed inside the apartment. For each test, a desired location that the robot has to reach inside the apartment will be
communicated to the teams during the set-up days. Entering the apartment must be done with
a natural behavior (no joystick, keyboard, remote control, etc.). Autonomous navigation is the
preferred solution, but following a person (e.g. a team member) is also an alternative way to
guide the robot into the apartment. Using an easy-to-use interface may be considered as a
natural behavior, however this must be approved beforehand by the by TC. In case of non-fully
autonomous behaviors, the teams must verify with the TC in advance that their solution is
suitable. If a team prepares a behavior which is not within the scope for a particular test, it should
contact the TC by e-mail at least one week before the competition. c⃝2018 by ERL Consumer Revision 1.1 55 D. General Procedure and Scoring for Task Benchmarks Contents D.2.3
Exit Procedure After the end of the test, as communicated by the referee(s), the robot must quickly exit the
apartment from the door designated for the test (which is usually dierent from the entrance
door). The team members are allowed to manually drive, push or lift the robot. A penalty (in
terms of an absolute negative score) will be given to the team if the robot is not outside the
arena 2 minutes after the end of the test. D.3
Scoring and Ranking Evaluation of the performance of a robot (a.k.a. scoring) in Task Benchmarks is based on
performance equivalence classes. The criterion dening the performance equivalence class of robots is based on the concept
of tasks required achievements, while the ranking of the robot within each equivalence class is
obtained by looking at the performance criteria. In particular: • The performance of any robot belonging to performance class N is considered as better
than the performance of any robot belonging to performance class M whenever M < N • Considering two robots belonging to the same class, then a penalization criterion (penalties
are dened according to task performance criteria) is used and the performance of the one
which received less penalization is considered as better • If the two robots received the same amount of penalization, the performance of the one
which nished the task more quickly is considered as better (unless not being able to reach
a given achievement within a given time is explicitly considered as a penalty). Performance equivalence classes and in-class ranking of the robots are determined according
o three sets: Performance equivalence classes and in-class ranking of the robots are determined according
o three sets: • A set A of achievements, i.e. things that should happen (what the robot is expected to
do). • A set PB of penalized behaviors, i.e. robot behaviors that are penalized, if they happen,
(e.g., hitting furniture). • A set DB of disqualifying behaviors, i.e. robot behaviors that absolutely must not
happen (e.g. hitting people). oring is implemented with the following 3-step sorting algorithm: Scoring is implemented with the following 3-step sorting algorithm: 1. If one or more of the elements of set DB occur during task execution, the robot gets
disqualied (i.e. assigned to the lowest possible performance class, called class 0), and no
further scoring procedures are performed. c⃝2018 by ERL Consumer 56 Revision 1.1 D. General Procedure and Scoring for Task Benchmarks Contents 2. Performance equivalence class X is assigned to the robot, where X corresponds to the
number of achievements in set A that have been accomplished. 2. Performance equivalence class X is assigned to the robot, where X corresponds to the
number of achievements in set A that have been accomplished. 3. Whenever an element of set PB occurs, a penalization is assigned to the robot (without
changing its performance class). 3. c⃝2018 by ERL Consumer D.3
Scoring and Ranking Whenever an element of set PB occurs, a penalization is assigned to the robot (without
changing its performance class). One key property of this scoring system is that a robot that executes the required task
completely will always be placed into a higher performance class than a robot that executes the
task partially. Moreover the penalties do not make a robot change class (also in the case of
incomplete task). c⃝2018 by ERL Consumer Revision 1.1 57 E. The ISRoboNet@Home Test Bed at IST Contents E
The ISRoboNet@Home Test Bed at IST
Bedroom
Bathroom
O
u
t
s
i
d
e
H
a
l
l
w
a
y
Inside Hallway
Patio
C
o
u
c
h
Center
Table
T
V
Kitchen Table
Kitchen cabinet
Glass-top
Dining Table
L
i
v
i
n
g
c
u
m
d
i
n
i
n
g
r
o
o
m
3.5 m
m
3.0 m
2.0 m
1.0 m
2.5 m
6.0 m
1.0 m
1.75 m
2.50 m
1.5 m
A
B
C
D
E
F
G
H
I
A
B
C
D
E
F
G
H
I
1.75 m
3.50 m
2.50 m
5.00 m
3.50 m
3.00 m
2.00 m
2.50 m
1.50 m
a
b
c
d
a
+ b
+ c
+ d
1.00 m
Width
Height
1.50 m
1.00 m
* Only wall A is the high wall
* A - I in blue are wall segments
* a - d in red are doors
* doors c,b and d should have a minimum
width of 80 cm
Arm
chair
Arm
chair
chairs
chairs
chairs
chairs
Large
Double-Bed
Side
table
Side
table
Wardrobe with mirror
Figure 14: Layout and dimensions of the @Home test bed at ISR/IST, Lisbon. E
The ISRoboNet@Home Test Bed at IST Bedroom
3.5 m
3.0 m
6.0
D
E
c
Large
Double-Bed
Side
table
Side
table
Wardrobe with mirror Figure 14: Layout and dimensions of the @Home test bed at ISR/IST, Lisbon. Based on the general design and specications of the ERL Consumer test bed detailed pre-
viously in this text, in this sub-section we present the exact design specications of the IS-
RoboNet@Home test bed installed at the premises of the Institute for Systems and Robotics
(ISR) of IST, University of Lisbon. D.3
Scoring and Ranking Note that this test bed is not an exact replica of the actual
ERL Consumer Competition test bed but ts its general specications and, as such, can be seen
as a concrete example of using them for an actual implementation. Pictures of this test bed are
presented in Figures 1517. E.1
Environment Structure and Properties • Ensemble of ve spatial areas accessible to the robots and three others inaccessible. Rooms
and spatial areas (accessible to the robot): Living room, dining room, kitchen, inside
hallway, bedroom. Spatial areas (inaccessible to the robot): outside hallway, bathroom,
patio. • Flat with no stairs • Open-plan architecture followed for the living room, dining room and kitchen. The bed-
room is separated by walls. • Open-plan architecture followed for the living room, dining room and kitchen. The bed-
room is separated by walls. • Sizes of spatial areas: Please refer to Figure 14. • Sizes of spatial areas: Please refer to Figure 14. Revision 1.1 58 c⃝2018 by ERL Consumer E. The ISRoboNet@Home Test Bed at IST Contents • Connectivity of spatial areas: Same as depicted in Figure 9. • Connectivity of spatial areas: Same as depicted in Figure 9. • Floor: Parquet, well-leveled and uniform all over the test bed. • Walls: Final version not yet in place will be reported in version 3 of this document. • Ceilings: Uniform false roof made of coated and perforated aluminum segments without
slopes. • Ceilings: Uniform false roof made of coated and perforated aluminum segments without
slopes. • Bedroom specications (and furniture): one open-able and tilt-able window, a double bed,
two side tables, two table lamps and one large wardrobe with mirror. • Bedroom specications (and furniture): one open-able and tilt-able window, a double bed,
two side tables, two table lamps and one large wardrobe with mirror. • Living room specication (and furniture's): contains windows that cannot be opened,
couch, two armchairs, one coee table, one TV table and one large oor lamp. • Living room specication (and furniture's): contains windows that cannot be opened,
couch, two armchairs, one coee table, one TV table and one large oor lamp. • Dining room specication (and furniture's): One glass-top dining table and 2 dining chairs. • Dining room specication (and furniture's): One glass-top dining table and 2 dining chairs. • Kitchen specication (and furniture's): One kitchen table and 2 chairs, kitchen cabinet
with multiple drawers and wash sink, two wall-mounted kitchen shelves. • Kitchen specication (and furniture's): One kitchen table and 2 chairs, kitchen cabinet
with multiple drawers and wash sink, two wall-mounted kitchen shelves. • Hallway: consists of one coat rack. 26www.ikea.pt
27http://www.cisco.com/c/en/us/products/collateral/wireless/aironet-1140-series/data_
sheet_c78-609338.html
28http://www.axis.com/products/cam_p1344 E.2
Objects in the Environment A list of all objects present in the environment of this test bed is given below through Tables 1 to 3. As most of the objects were purchased from the IKEA furniture store, the IKEA-reference code
of the objects are provided to facilitate the readers of this documents. Note that this reference
code is from the Portuguese version of IKEA's homepage26. 26www.ikea.pt ikea.pt
p://www.cisco.com/c/en/us/products/collateral/wireless/aironet-1140-series/data_
78-609338.html
p://www.axis.com/products/cam_p1344 Table 1: List of task-relevant navigation-related objects in the environment E.3
Network Devices The @Home test bed at IST is equipped with network devices capable of opening/closing the
blind and turning on/o the lamps. The network is organized as shown in Figure 11 followed by
a description of each block. • Server: A computer used to manage the network. • Switch: An Ethernet switch used to connect all the devices. • AP: An Access Point where the robot is supposed to connect. This is the only connection
between the robot and the network. Acts as a bridge between WLAN and LAN. The Access
Points used work in Dual-band Standalone 802.11a/g/n. The models used are Cisco AIR
- AP1042N-E-K9 27. • Ethernet Camera: Perspective camera facing the Outside Hallway. The camera can have
its parameters (frame rate, resolution, color gains) changed over Ethernet and it is not
motor controlled (no pan-tilt). The model of the camera can be found here 28. • Devices: Dierent devices may exist in the house. In our test bed the devices are: a motor
to control the window blinds, 3 controlled power plugs, 1 light dimmer, and 1 door bell
button. c⃝2018 by ERL Consumer 59 Revision 1.1 E. E.3
Network Devices The ISRoboNet@Home Test Bed at IST Contents Task-relevant Objects
Navigation-related
Object
Quantity
IKEA Code
Size (cm)
Ref-code
Observations
Double
bed
1
BRUSALI
140x200
702.499.07
bed-frame
1
BRUSALI
140x200
901.245.34
bars
Matress
1
HAFSLO
140x200x18
602.443.64
Slatted
bed base
1
SULTAN
LÖDINGEN
140x200
401.602.37
Bedside ta-
bles
2
BRUSALI
44x36
502.501.57
Wardrobe
+ mirror
1
BRUSALI
131x190
402.501.67
Rug
1
HAMPEN
80x80
502.037.88
green
1
HAMPEN
80x80
102.037.90
red
Coee
ta-
ble
1
LACK
90x55
401.042.94
black
Couch
1
KLIPPAN
100.722.56
couch
1
202.788.55
cover
Armchairs
2
PELLO
500.784.64
Bookshelf
1
BORGSJÖ
75x181 cm
002.209.50
shelf
202.209.54
doors in glass
Dining ta-
ble
1
INGATORP
59/88/117x78
802.214.27
without glass
Dining
Chairs
3
SIGURD
002.522.48
black
1
KAUSTBY
400.441.96
brown
Kitchen
cupboard
FYNDIG
white
1
80x60x86
702.266.80
closet
with
doors
1
126x60.6
502.375.33
top cover
1
40x60x86
702.266.75
closet with 1
door
and
1
drawer
1
70x50
502.021.33
sink
1
SUNDSVIK
800.318.61
tap
2
SATTA
602.700.70
(1 red and 1
transparent)
Coat Rack
1
KROGKIG
128 (height)
201.745.08
multi-color
1
HEMNES
185 (height)
002.468.70
black
TV table
1
BYAS
160x42x45
802.277.97
with drawers
Kitchen
Shelf
2
EKBY JARPEN
/ VALTER
119x28
699.265.93
Glass Din-
ing table
1
GLIVARP
75/110x70
802.423.02
with glass
Table 1: List of task-relevant navigation-related objects in the environment Task-relevant Objects Revision 1.1 c⃝2018 by ERL Consumer 60 E. The ISRoboNet@Home Test Bed at IST Contents Task-relevant Objects
Manipulation-related
Object
Quantity
IKEA Code
Ref-code
Observations
Coee Mugs
8
FÄRGRIK (2) +
OMBYTLIG (1)
+ TECKEN (1)
+ UNGDOM (1
pack of 4)
401.439.93 +
202.099.80 +
702.160.49 +
702.348.97
Coee cups
6
DINERA
001.525.50
Dessert plates
1
ÖVERENS
202.097.20
(1 pack of 6)
Cake plate
1
ARV BRÖLLOP
401.255.50
Small glasses
6
GODIS
800.921.09
Large glasses
6
POKAL
+
KROKETT
102.704.78 +
201.952.52
Water jug
1
LÖNSAM
+
VÄNLIG
202.135.43 +
101.316.99
Table 2: List of task-relevant manipulation-related objects in the environment Task-relevant Objects • SMARTIF IO: This module controls the dierent devices/sensors existing in the house. It
is prepared to add more devices in case of need. • SMARTIF Server: Device responsible for the communication between the SMARTIF IO
mentioned above and the network. It is also where the system congurations (through the
SMARTIF Cong Too) are stored and changed. Technical details regarding SMARTIF
products can be found at the ocial site 29. 29http://www.smartif.com/smarthome/techspecs.html c⃝2018 by ERL Consumer Revision 1.1 E.3
Network Devices In our network, robots are supposed to communicate with the devices by sending a message
to a specic IP and port. A SDK existent on the server will receive that message and transmit
it to the SMARTIF IO witch will then control the device. Images from the Ethernet camera
are also available through the AP. The quick set-up in the SMARTIF Conguration Tool, along
with the possibility of adding/removing more devices, allows us to change the network if needed
and with ease. c⃝2018 by ERL Consumer Revision 1.1 61 E. The ISRoboNet@Home Test Bed at IST Contents Non-task-relevant Objects
Object
Quantity
IKEA Code
Ref-code
Observations
Curtains
1
RITVA
145x300
24 - number in
the curtains' sec-
tion. 1 pack of 2
Table mats
8
102.361.11
Napkins
1
101.012.73
pack of 50
Couch Pillows
3
FJADRAR
400.667.39
inside of the pil-
low
1
STOCKHOLM
302.366.76
cover of the pil-
low (multi-color,
squares)
1
GURLI
202.496.03
cover
(plain
blue)
1
SVARTTALL
002.897.13
cover (spots)
Linien for bed
1
DVALA
401.499.52
1
SVARTTALL
602.911.38
Pillow for bed
2
GOSA VADD
501.291.66
Lamp
(small,
bed side)
2
KVART
601.524.58
Lamp (oor, liv-
ing room)
1
SAMTID
202.865.63
white
Plants
in
pots
(small)
3
FEJKA
702.514.72
Plants
in
pots
(large)
1
FEJKA
302.340.07
Small
picture
frames with pics
6
NYTTJA
601.674.93
Medium
pic
frames
5
NYTTJA
601.170.35
Large paintings
1
102.340.46
each pack con-
tains 3 pics with-
out frame
Decoration bowl
2
901.244.02
bowl
2
902.508.86
stung for the
bowl (dry ow-
ers)
Triples
of
can-
dles
3
FLORERA
302.514.69
Flower Jar
2
BLOMSTER
301.136.18
jar
12
SNARTIG
101.391.91
owers
Table 3: List of Non-task-relevant objects in the environment Table 3: List of Non-task-relevant objects in the environment c⃝2018 by ERL Consumer 62 Revision 1.1 E. The ISRoboNet@Home Test Bed at IST Contents Figure 15: Living room in the @Home test bed at IST Figure 15: Living room in the @Home test bed at IST Figure 16: Living room, kitchen and dining area in the @Home test bed at IST Figure 16: Living room, kitchen and dining area in the @Home test bed at IST c⃝2018 by ERL Consumer Revision 1.1 63 Contents E. The ISRoboNet@Home Test Bed at IST Figure 17: Bedroom in the @Home test bed at IST Figure 17: Bedroom in the @Home test bed at IST c⃝2018 by ERL Consumer Revision 1.1 64 Bibliography [1] (2015) The RoCKIn Wiki. [Online]. Available: http://thewiki.rockinrobotchallenge.eu [2] D. Croce, G. Castellucci, and E. Bastianelli, Structured learning for semantic role labeling.
Intelligenza Articiale, vol. 6, no. 2, pp. 163176, 2012. [3] A. Ahmad, I. Awaad, F. Amigoni, J. Berghofer, R. Bischo, A. Bonarini, R. Dwiputra,
G. Fontana, F. Hegger, N. Hochgeschwender, L. Iocchi, G. Kraetzschmar, P. Lima, M. Mat-
teucci, D. Nardi, V. Schaonati, and S. Schneider, Description of Ground Truth System,
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https://openalex.org/W2027692179 | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0071078&type=printable | English | null | The E3 Ligase AtRDUF1 Positively Regulates Salt Stress Responses in Arabidopsis thaliana | PloS one | 2,013 | cc-by | 7,478 | Introduction (ABA), an important phytohormone that can protect plants from
damage induced by drought, salinity, and pathogenic attack
[16,17]. The accumulation of compatible osmolytes such as
proline under dehydration conditions allow cells to maintain
osmotic balance with the extracellular space and help to protect
the activities of the enzyme activity [18]. Ubiquitination is a mechanism of post-translational regulation. The ubiquitination cascade is catalyzed by ubiquitin-activating
enzyme (E1), ubuiquitin-conjugating enzyme (E2) and ubiquitin
protein ligase (E3). There are .1300 predicted E3 ligases in the
Arabidopsis genome, including .450 RING type E3s [1,2]. The
vast majority of E3 uibiquitin ligases in the Arabidopsis genome
facilitate
the
identification
of
specific
substrates
and
their
subsequent ubiquitination [1,3]. The E3 ubiquitin ligases are a
huge and varied family of proteins and protein complexes which
contain either a HECT domain or a U-box/RING domain. The
HECT domain subfamily of E3s is relatively small in Arabidopsis. The RING domain subfamily of E3s is large in Arabidopsis and can
be further divided into single subunit RING E3s, such as
Constitutive
Photomorphogenesis1
(COP1)
[4],
SEVEN
IN
ABSENTIA IN ARABIDOPSIS THALIANA 5 (SINAT5) [5],
and Arm Repeat-Containing 1 (ARC1) [6], and multisubunit
RING E3s including the SCF, CUL3-BTB, and APC complexes
[7]. The RING E3s typically contain a cross-brace structure
formed of eight Cys and His residues that coordinates two zinc
ions [8,9,10]. E3 ligases are involved in various aspects of plant
biological processes, including growth, development, and protec-
tion from biotic and abiotic stresses [11,12]. AtRDUF1 and AtRDUF2 are homologous proteins with a
domain-of-unknown-function (DUF) 1117 motif in their C-
terminal regions. Both proteins were identified as ABA-, salt-,
and drought-inducible RING finger domain-containing E3 ligases
[19]. A study using knock-out mutations revealed that AtRDUFs
are positive regulators of ABA response and drought tolerance
[19]. Here, through the use of overexpression and knock-out
materials, we show that AtRDUF1 positively participates in the
response of plants to salt stress. Abstract Ubiquitination is an important post-translational protein modification that is known to play critical roles in diverse biological
processes in eukaryotes. The RING E3 ligases function in ubiquitination pathways, and are involved in a large diversity of
physiological processes in higher plants. The RING domain-containing E3 ligase AtRDUF1 was previously identified as a
positive regulator of ABA-mediated dehydration stress response in Arabidopsis. In this study, we report that AtRDUF1 is
involved in plant responses to salt stress. AtRDUF1 expression is upregulated by salt treatment. Overexpression of AtRDUF1
in Arabidopsis results in an insensitivity to salt and osmotic stresses during germination and seedling growth. A double
knock-out mutant of AtRDUF1 and its close homolog AtRDUF2 (atrduf1atrduf2) was hypersensitive to salt treatment. The
expression levels of the stress-response genes RD29B, RD22, and KIN1 are more sensitive to salt treatment in AtRDUF1
overexpression plants. In summary, our data show that AtRDUF1 positively regulates responses to salt stress in Arabidopsis. Citation: Li J, Han Y, Zhao Q, Li C, Xie Q, et al. (2013) The E3 Ligase AtRDUF1 Positively Regulates Salt Stress Responses in Arabidopsis thaliana. PLoS ONE 8(8):
e71078. doi:10.1371/journal.pone.0071078 Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Copyright: 2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Program from the Chinese Ministry of Agriculture (2011ZX0 8009-003-002), the Natural Science Foundation of China
for the innovation team (31121065) and the Innovation Grant of CAS (KSCX2-EW-N-07-3). The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: xuyy@ibcas.ac.cn Competing Interests: The authors have declared that no competing interests exist. * E-mail: xuyy@ibcas.ac.cn . These authors contributed equally to this work. unhua Li1,2., Yingying Han1,4., Qingzhen Zhao3, Chunhua Li1, Qi Xie3, Kang Chon Junhua Li1,2., Yingying Han1,4., Qingzhen Zhao3, Chunhua Li1, Qi Xie3, Kang Chong1, Yunyuan Xu1*
1 Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China, 2 College of Life Sciences, Henan Normal University,
Xinxiang, Henan, China, 3 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China, 4 Key Laboratory of Molecular Biology, College of 1 Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China, 2 College of Life Sciences, Henan Normal University,
Xinxiang, Henan, China, 3 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China, 4 Key Laboratory of Molecular Biology, College of
Life Sciences, Heilongjiang University, Harbin, Heilongjiang, China Expression pattern of AtRDUF1 p
p
To investigate the tissue-specific expression pattern of AtR-
DUF1, a fusion gene comprising the native AtRDUF1 promoter, a
1.3-kb fragment upstream of the start codon of AtRDUF1 CDS,
and the b-glucuronidase (GUS) gene [26] coding sequence as the
reporter gene were constructed and transformed into wild-type
Arabidopsis. Histochemical staining showed that AtRDUF1 ex-
pressed abundantly in seeds, but was also locally detectable in
flowers, hypocotyls, leaves and roots (Figure 2). The staining was
strong in immature seeds (Figure 2A), whereas in intact desiccated
seeds, the GUS expression was only detectable at the funiculus
attachment region (Figure 2B). In broken seeds, GUS staining was
uniformly presented throughout the seed (Figure 2C), indicating
that the limitation of GUS staining in intact seeds was due to
blocking by the seed coat. To exclude possible false observations
caused by the diffusion of the soluble intermediate of GUS
substrates [27,28], seeds were dissected and stained separately. The GUS staining signal could be observed uniformly throughout
the embryo, but only in the funiculus attachment region of the
seed coat (Figure 2D). During germination, a reduction in GUS
staining was detectable early on (Figure 2E–H), which is consistent
with the decrease of AtRDUF1 expression detected by real-time
qRT-PCR (Figure S2 in File S1). In 4-d-old seedlings, the GUS
expression was mainly detected in the junction of the root and
hypocotyl, in leaf tips, and around the meristem (Figure 2H). In 2-
week old seedlings, the GUS staining was only detectable in leaf
tips and root tips (Figure 2I and 2J). In reproductive tissue, The AtRDUF1 protein contains a conserved C3H2C3-type
RING domain, which shows similarity with many known proteins
in Arabidopsis (Figure 1A), including several proteins known to be
involved in ABA and/or stress signaling pathways, such as ABI3-
interacting protein 2 (AIP2) [21], SALT- AND DROUGHT-
INDUCED RING FINGER 1 (SDIR1) [22] and ATLs [23,24]. One of these homologous proteins, RING finger protein for
embryogenesis (RIE1), is required for normal development of
seeds [25]. Subcellular studies using a 35S::AtRDUF1:GFP fusion protein
in Arabidopsis leaf protoplast cells showed that the fusion protein
was mainly found in the cytosol and in the nuclei (Figure 1B). We
examined whether AtRDUF1 is an E3 ligase using in vitro methods. E3 Ligase Positively Regulates Salt Responses At5g59550 and At3g46620 were up-regulated 5.5 and 2.9-fold,
respectively, after salt treatment for 6–24 h. At5g59550 and
At3g46620 were previously designated as AtRDUF2 and AtRDUF1,
respectively [19]. Characterization of AtRDUF1 protein Characterization of AtRDUF1 protein In order to identify stress-related genes, we analyzed several
publicly available databases of Arabidopsis microarray experiments. A gene family with three genes (At5g59550, At3g46620 and
At2g39720) that encode DUF1117 containing RING finger
proteins from stress-specific expression profiles in Genevestigator
[20] attracted our interest. The microarray data showed that the
expression of these genes was up-regulated by several kinds of
abiotic stresses. Of particular interest were the data showed that To adapt to stressful conditions such as drought, cold, and
salinity, plants have developed redundant and sophisticated
response strategies which function throughout their life cycle
[13,14,15]. Plants subjected to stress often accumulate abscisic acid August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 1 E3 Ligase Positively Regulates Salt Responses Expression pattern of AtRDUF1 As shown in Figure 1C, in the presence of E1 and E2,
autoubiquitination of MBP:AtRDUF1 can be detected in the
presence of E1 and E2 by both nickel-horseradish peroxidase as
well as by anti-MBP antibody assay, indicating that AtRDUF1 is
an active E3 ligase. A mutant allele with substitution of metal
ligand positions Cys-3, His-4, and His-5 of the RING motif with
Tyr (CH/Y) was completely inactive (Figure 1C), indicating that
an intact RING motif is essential for the E3 ligase activity of
AtRDUF1. Figure 1. Analysis of the AtRDUF1 protein. (A) Alignment of the RING finger domains of the AtRDUF1 homologs in Arabidopsis. Black and gray
indicate 100% and $50% identities, respectively. (B) Subcellular localization of AtRDUF1:GFP fusion protein in Arabidopsis leaf protoplast cells. Bars
represent 20 mm. The green and blue fluorescenece are GFP and 49,6-diamidino-2-phenylindole (DAPI) signals, respectively. (C) Verification of E3
ligase activity of AtRDUF1 by in vitro autoubiquitination assay. CH/Y represents the mutant form of the MBP:AtRDUF1 fusion protein, with
substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr. The numbers at left denote the molecular masses of marker
proteins in kilodaltons. Nichel-HRP (Ub), the nickel-horseradish peroxidase used to detect His-tagged ubiquitin. Anti-MBP, the anti-MBP antibody to
detect maltose fusion proteins. doi:10.1371/journal.pone.0071078.g001 Figure 1. Analysis of the AtRDUF1 protein. (A) Alignment of the RING finger domains of the AtRDUF1 homologs in Arabidopsis. Black and gray
indicate 100% and $50% identities, respectively. (B) Subcellular localization of AtRDUF1:GFP fusion protein in Arabidopsis leaf protoplast cells. Bars
represent 20 mm. The green and blue fluorescenece are GFP and 49,6-diamidino-2-phenylindole (DAPI) signals, respectively. (C) Verification of E3
ligase activity of AtRDUF1 by in vitro autoubiquitination assay. CH/Y represents the mutant form of the MBP:AtRDUF1 fusion protein, with
substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr. The numbers at left denote the molecular masses of marker
proteins in kilodaltons. Nichel-HRP (Ub), the nickel-horseradish peroxidase used to detect His-tagged ubiquitin. Anti-MBP, the anti-MBP antibody to
detect maltose fusion proteins. doi:10.1371/journal.pone.0071078.g001 August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 2 E3 Ligase Positively Regulates Salt Responses Figure 2. Histochemical localization of GUS activity in AtRDUF1::GUS transgenic plants. (A) Developing seed at 12 days after pollination. (B)
Desiccated mature seed. (C) Broken mature seed. (D) Dissected seed after imbibition. Expression pattern of AtRDUF1 (E–H) Germinating seedlings at 1-day (E), 2-days (F), 3-days (G),
and 4-days (H) after germination. (I) Leaf. (J) Root. (K) Flower. (L) Pollen. (M) Siliques. Bars represent 0.25 mm in A-D; 0.1 mm in J; 10 mm in L; and
1 mm in E-I, K, and M. doi:10.1371/journal.pone.0071078.g002 Figure 2. Histochemical localization of GUS activity in AtRDUF1::GUS transgenic plants. (A) Developing seed at 12 days after pollination. (B)
Desiccated mature seed. (C) Broken mature seed. (D) Dissected seed after imbibition. (E–H) Germinating seedlings at 1-day (E), 2-days (F), 3-days (G),
and 4-days (H) after germination. (I) Leaf. (J) Root. (K) Flower. (L) Pollen. (M) Siliques. Bars represent 0.25 mm in A-D; 0.1 mm in J; 10 mm in L; and
1 mm in E-I, K, and M. doi:10.1371/journal.pone.0071078.g002 (CaMV) 35S promoter. Six transgenic lines of AtRDUF1 were
obtained (Figure S1D and S1E in File S1). The 35S::AtRDUF1
plants showed a wild-type growth phenotype under normal
conditions. AtRDUF1::GUS activity was observed at the junction of carpels and
pedicels, as well as in stigma, anthers, and pollen, and low levels
were detected in the vascular tissues of sepals and petals
(Figure 2K–M). The expression of the AtRDUFs had been shown to be induced
by salt treatment [19]. We therefore tested whether AtRDUF1
plays a role in plant responses to salt. Seeds of wild-type (WT),
atrduf1atrduf2, atrduf1, and AtRDUF1 overexpression lines were
germinated vertically in 1/2 MS medium. 3-day-old seedlings
were transferred to 1/2 MS medium supplemented with 110, 120
or 150 mM NaCl. In the control condition, no significant
difference in the length of primary roots was observed among
any of the materials (Figure 3A and 3D). Under salt stress
conditions, the primary roots of 35S::AtRDUF1 seedlings grew
faster than did wild-type seedlings, and the atrduf1atrduf2 double
mutants showed inhibited growth (Figure 3A and 3D). AtRDUF1 positively regulates plant salt and osmotic
stress responses To investigate the function of AtRDUFs, mutants with T-DNA
insertions within the exons of the AtRDUFs were obtained and
verified (Figure S1A–B in File S1). Expression of the mutant genes
was not detected by RT-PCR with primers spanning the T-DNA
in the respective homozygous mutants (Figure S1C in File S1). The mutants for AtRDUF1 and AtRDUF2 were named atrduf1-2
and
atrduf2-1,
respectively
(hereinafter
called
‘‘atrduf1’’
and
‘‘atrduf2’’). The double mutant atrduf1atrduf2 was generated by
crossing. Germinated atrduf1atrduf2, atrduf1 and 35S::AtRDUF1 lines were
transplanted to soil for two weeks, and watered with 200 mM We generated transgenic Arabidopsis plants with constitutive
expression of AtRDUF1, driven by cauliflower mosaic virus August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org August 2013 | Volume 8 | Issue 8 | e71078 3 E3 Ligase Positively Regulates Salt Responses Figure 3. Salt tolerance of AtRDUF overexpression plants and mutants. (A) WT, atrduf1atrduf2, atrduf1, RDUF1-L1 (Line 1 of 35S::AtRDUF1
transgenic plants), RDUF1-L2 and RDUF1-L3 seedlings with or without salt treatment. 3-day-old seedlings were transferred to 1/2 MS medium
containing 0, 110, 120 or 150 mM NaCl, and vertically cultured for 6 days. Bars represent 1 cm. (B) Soil-grown plants under salt treatment. 2-week-old
soil-grown plants were treated with 200 mM NaCl for 15 days. (C) Germination of seeds at 10 days after imbibition on medium supplemented with 0,
200, or 250 mM NaCl, respectively. (D-F) Primary root length (D), survival rates (E) and germination rates (F) of materials under the conditions
described in (A), (B), and (C), respectively. Data are presented as means 6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g003 Figure 3. Salt tolerance of AtRDUF overexpression plants and mutants. (A) WT, atrduf1atrduf2, atrduf1, RDUF1-L1 (Line 1 of 35S::AtRDUF1
transgenic plants), RDUF1-L2 and RDUF1-L3 seedlings with or without salt treatment. 3-day-old seedlings were transferred to 1/2 MS medium
containing 0, 110, 120 or 150 mM NaCl, and vertically cultured for 6 days. Bars represent 1 cm. (B) Soil-grown plants under salt treatment. 2-week-old
soil-grown plants were treated with 200 mM NaCl for 15 days. (C) Germination of seeds at 10 days after imbibition on medium supplemented with 0,
200, or 250 mM NaCl, respectively. (D-F) Primary root length (D), survival rates (E) and germination rates (F) of materials under the conditions
described in (A), (B), and (C), respectively. Data are presented as means 6 SD. PLOS ONE | www.plosone.org Discussion In the course of our investigation of likely stress-related genes,
we identified AtRDUFs from in silico data. Their putative proteins
contain both RING finger and DUF1117 domains, and represent
a novel E3 ligase family in plants. Real time qRT-PCR and
promoter-GUS analyses confirmed that the transcription of
AtRDUF1 was indeed salt inducible (Figure 5B). We analyzed
the phenotypes of wild-type as well as overexpression and loss-of-
function mutants of AtRDUFs following salt treatment. Our results
showed that AtRDUF1 positively regulates plant responses to salt
treatment during both germination and post-germination growth
(Figure 3). Furthermore, AtRDUF1 also positively regulates plant
tolerance to osmotic and dehydration stress (Figure 4). The
fluorescence
of
AtRDUF1:GFP
fusion
protein
was
detectable in our subcellular localization study (Figure 1B), and
35S::AtRDUF1 transgenic plants showed obvious tolerance to salt,
osmotic, and water loss stresses (Figure 3 and 4). In a similar
report, a fusion protein approach was used to develop transgenic
plants that overexpressed AtRDUF1. However, the authors were
unsuccessful in detecting significant accumulation of the fusion
protein, in spite of expression of significant amounts of AtRDUF1
mRNA, so the plants were not extensively analyzed [19]. The
discrepancy of detection may be attributable to distinctions in
vector efficiency or differences in the sensitivity of the assay
methods employed in these independent studies. In addition to the results reported here, AtRDUF1 and AtRDUF2
are also known to be up-regulated by chitin treatment [32]. Among the homologous proteins of the AtRDUFs subfamily, the
E3 ligases KEG [12] and AIP2 [21] are negative regulators of
ABA signaling, acting by targeting and degrading ABI5 and ABI3,
respectively. The E3 ligase SDIR1 positively regulates ABA
signaling, and the sdir1 mutant is resistant to salt and drought stress
[22]. Therefore,
it
is
apparent
that
AtRDUFs
and
their
homologous proteins are widely involved in plant adaptations to
stress. We were able to confirm that AtRDUF1 has E3 ligase activity
by ubiquitination assays (Figure 1C). Ubiquitination has been
shown
to
play an
important
role
in the
perception
and
transduction of various internal and external environmental
signals [33,34]. To test whether AtRDUF1 affects the expression
of known stress pathway genes, several marker genes in the stress-
responsive pathways were analyzed, RD29B, RD22, and KIN1
showed a hypersensitive salt response in transgenic plants
(Figure 5A). RD29B is a cold-, high salt-, and dessication-inducible
gene with two ABA-responsive elements (ABREs) present in its
promoter region [35]. E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses Water-loss rate is calculated as the ratio between water loss and plant
initial fresh weight (FW), expressed in %. Data are presented as means
6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g004 Water-loss rate is calculated as the ratio between water loss and plant
initial fresh weight (FW), expressed in %. Data are presented as means
6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g004 2 MS agar plates were sprayed with 200 mM NaCl solution, the
seedlings were harvested after 1 h and 2 h, for extraction of total
RNA. The result showed that in RDUF1-L1 seedlings, the
transcription levels of RD29B, RD22, and KIN1 increased more
than those of the WT after 2 h of salt treatment (Figure 5A),
suggesting that AtRDUF1 may directly or indirectly interact with
known abiotic stress response pathways. When the AtRDUF1::GUS
transgenic plants were subjected to salt treatment, the GUS
staining was enhanced compared with control plants (Figure 5Ba–
5Bd), which is consistent with the real-time qRT-PCR results
(Figure 5Be). AtRDUF1 positively regulates plant salt and osmotic
stress responses Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g003 NaCl solution for 15 days to induce salt stress. 35S::AtRDUF1
seedlings exhibited higher survival rates than did WT seedlings. Contrastingly, the survival rate of the salt treated atrduf1atrduf2
double mutant seedlings was lower than the WT control seedlings
(Figure 3B and 3E). NaCl solution for 15 days to induce salt stress. 35S::AtRDUF1
seedlings exhibited higher survival rates than did WT seedlings. Contrastingly, the survival rate of the salt treated atrduf1atrduf2
double mutant seedlings was lower than the WT control seedlings
(Figure 3B and 3E). known to be used as an osmotic agent in some studies [29,30,31]. The root growth of 35S::AtRDUF1 seedlings was less severely
inhibited by mannitol than that of WT seedlings (Figure 4A and
4B). Therefore, the tolerance of 35S::AtRDUF1 seedlings to salt
treatment is at least partly osmotic in nature. After imbibition on 1/2 MS medium containing NaCl and
transfer to a growth chamber for 10 days, the germination rates of
35S::AtRDUF1 seeds were higher than that of WT seeds (Figure 3C
and 3F). Therefore, the germination ability of AtRDUF1 overex-
pression seeds is insensitive to salt treatment. In our salt tolerance
tests, no significant difference was observed between WT and the
atrduf1 mutant. In contrast with the accelerated water loss in detached leaves of
the atrduf1 mutant [19], the water loss of rosette leaves in the
overexpression lines was slower than that of WT leaves (Figure 4C). The overexpression plants also showed a sensitive response to ABA
in terms of primary root length (Figure S3 in File S1). Our results
support that AtRDUF1 positively participates in ABA-mediated
dehydration stress responses. Salinity causes ionic and osmotic stresses in plant cells. Germinated transgenic seedlings were transferred to MS medium
supplemented with mannitol, a nonmetabolizable sugar, which is We investigated the expression profiles of several stress-
responsive genes in the AtRDUF1 overexpression lines grown
under salt stress conditions. 10-day-old seedlings grown on 1/ August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org August 2013 | Volume 8 | Issue 8 | e71078 4 Discussion Compared with the mock treated plants (a
and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial
regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated
with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1
overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated
with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks
indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. Compared with the mock treated plants (a
and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial
regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated
with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control
TUBULIN. Asterisks indicate significance (*, P,0.05 versus 0 h control). doi:10.1371/journal.pone.0071078.g005 The vegetative tissues of 35S::RDUF1 seedlings contained a higher
content of triglycerides (the ester of glycerol) than did WT control
tissues (Figure S4C in File S1). Finally, the oleosin maker gene
OleS3 and triglycerides content change in response to salt stress
(Figure S4D and S4E in File S1). We speculate that a mechanism
by which AtRDUF1 increases salt tolerance is through the
positively regulation of either the delayed catabolism or the
increased accumulation of the storage lipids. region [22,36]. KIN1, which contains the C repeat/dehydration-
responsive element (CRT/DRE) motif in its promoter, can be
induced by cold, ABA and dehydration treatment [37]. Discussion According
to our data and published results [19], AtRDUF1 may be involved
in the up-regulation of stress responses in Arabidopsis seedlings, in
this respect, AtRDUF1, may be similar to SDIR1 and AtSAP5,
both of which have been shown to be E3 ligases and are known in
promoting stress gene expression and stress tolerance [22,38,39]. The vegetative tissues of 35S::RDUF1 seedlings contained a higher
content of triglycerides (the ester of glycerol) than did WT control
tissues (Figure S4C in File S1). Finally, the oleosin maker gene
OleS3 and triglycerides content change in response to salt stress
(Figure S4D and S4E in File S1). We speculate that a mechanism
by which AtRDUF1 increases salt tolerance is through the
positively regulation of either the delayed catabolism or the
increased accumulation of the storage lipids. Glycerol, a compatible osmolyte, is used in defending against
dehydration stresses in yeast, marine algae, insects, and amphib-
ians [40,41,42,43]. Accumulation of intracellular glycerol was
observed during the salt adaptation processes of many microor-
ganism such as Aspergillus nidulans [44] and Aureobasidium pullulans
[45]. In Arabidopsis, the results from studies in mutants with defects
in storage lipid accumulation prior to seed maturation or lipid
catabolism following germination [29,30,31] suggest that glycerol
or glycerol-derived lipids could serve as compatible osmolytes in
dehydration stress conditions in plants. As AtRDUF1 expressed
primarily in embryos of matured seeds (Figure 2), we tested the
correlation of AtRDUF1 expression with storage lipids (Text S1 in
File S1). In young seedlings, the staining of GUS driven by the
AtRDUF1 promoter partially coincided with staining of Sudan red
7B, a fat-soluble dye that stains lipids red, and the Sudan red 7B
staining was darker in the 35S::RDUF1 seedlings (Figure S4A in
File S1). The levels of triacylglycerol (TAG), the primary seed oil
in Arabidopsis were higher in seeds and young seedlings of
35S::AtRDUF1 lines than in WT seedlings (Figure S4B in File S1). In conclusion, our data show that AtRDUF1 is a functional E3
ligase and a positive regulator of the Arabidopsis response to salt
stress. This study contributes to our understanding of the
molecular factors involved in the responses of plants to abiotic
stresses. Plant materials All Arabidopsis plants used in this study were of the Columbia (Col-
0) ecotype. T-DNA insertion lines SALK_131634 (for AtRDUF1)
and N471914 (for AtRDUF2) were obtained from ABRC [46] and
NASC [47], respectively. Seedlings were grown under long-day
conditions (16 h light/8 h dark) at 22uC, 40 to 60% RH and
63 mE?s21?m22 light intensity. Discussion RD22 transcription is induced by salt and
ABA treatment, but no ABRE was identified in its promoter Figure 4. Osmotic tolerance and detached leaf water-loss rates
of AtRDUF1 overexpression plants. (A) WT, atrduf1atrduf2, atrduf1,
RDUF1-L1, RDUF1-L2 and RDUF1-L3 with or without osmotic stress
treatment. 3-day-old seedlings were transferred to 1/2 MS medium
containing 0, 200, or 350 mM mannitol, and vertically cultured for 6 d. Bars represent 1 cm. (B) Statistical comparison of root lengths of
seedlings under the conditions described in (A). (C) Water loss rates of
detached leaves. Detached rosette leaves from wild-type and AtRDUF1
overexpression seedlings were incubated for 6 h at room temperature. August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 5 E3 Ligase Positively Regulates Salt Responses Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1
overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated
with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks
indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. Compared with the mock treated plants (a
and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial
regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated
with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control
TUBULIN. Asterisks indicate significance (*, P,0.05 versus 0 h control). doi:10.1371/journal.pone.0071078.g005
E3 Ligase Positively Regulates Salt Responses Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1
overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated
with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks
indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses promoter. The primers used for AtRDUF1 overexpression were
R1BamHIF and R1KpnIR (all primer sequences used in this study
are listed in Table S1 in File S1). The 1.3 kb promoter sequence
of
AtRDUF1
was
amplified
with
primers
R1PKpnIF
and
R1PBamHIR, and cloned into the pGUS1301 vector [49]. The
constructed plasmid was introduced into Agrobacterium tumefaciens
strain C58. Arabidopsis was transformed using the floral dip method
[50]. Transgenic plants were first screened on medium containing
40 mg/l hygromycin and subsequently transferred to soil. To
produce a AtRDUF1:GFP fusion gene driven by 35S promoter, the
AtRDUF1 CDS sequence with the stop codon deleted was
amplified with primers R1GXhoIF and R1GKpnIR, and cloned
in frame into pBI121GFP. To generate the MBP:AtRDUF1
fusion, the AtRDUF1 CDS was cloned in frame into pMAL-c2
(NEB, Berverly, MA, USA) with primers R1MBamHIF and
R1MSalIR. A mutant allele with substitution of metal ligand
positions Cys-3, His-4, and His-5 of the RING motif with Tyr
(CH/Y) was introduced with primers R1mF and R1mR. DpnI
mediated site-directed mutagenesis in the plasmid was performed
as described previously [51]. promoter. The primers used for AtRDUF1 overexpression were
R1BamHIF and R1KpnIR (all primer sequences used in this study
are listed in Table S1 in File S1). The 1.3 kb promoter sequence
of
AtRDUF1
was
amplified
with
primers
R1PKpnIF
and
R1PBamHIR, and cloned into the pGUS1301 vector [49]. The
constructed plasmid was introduced into Agrobacterium tumefaciens
strain C58. Arabidopsis was transformed using the floral dip method
[50]. Transgenic plants were first screened on medium containing
40 mg/l hygromycin and subsequently transferred to soil. To
produce a AtRDUF1:GFP fusion gene driven by 35S promoter, the
AtRDUF1 CDS sequence with the stop codon deleted was
amplified with primers R1GXhoIF and R1GKpnIR, and cloned
in frame into pBI121GFP. To generate the MBP:AtRDUF1
fusion, the AtRDUF1 CDS was cloned in frame into pMAL-c2
(NEB, Berverly, MA, USA) with primers R1MBamHIF and
R1MSalIR. A mutant allele with substitution of metal ligand
positions Cys-3, His-4, and His-5 of the RING motif with Tyr
(CH/Y) was introduced with primers R1mF and R1mR. DpnI
mediated site-directed mutagenesis in the plasmid was performed
as described previously [51]. The water loss assay was performed as described previously
[54]. Eight rosette leaves per plant were detached from 3-week-old
plants. 2. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, et al. (2005) Functional
analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol
137: 13–30. Stress and ABA treatment After surface sterilization, seeds were imbibed at 4uC for 3 d in
the dark. The seeds were sown on half-strength Murashige and
Skoog medium [53] supplemented with 1% sucrose and 0.7%
agar. 3-day-old seedlings were transferred to 1/2 MS medium
containing NaCl, mannitol, or ABA. Primary root length was
measured after 6 d. 4-day-old seedlings were transplanted to soil
and cultured for two weeks, and treated with 200 mM NaCl for
15 days to induce salt stress. For the germination test, all seeds
were harvested simultaneously and stored for 5 weeks after
harvest. Germination was determined as penetration of the radicle
through the seed coat 10 days after imbibition. Each assay was
repeated three times. The data in the graphs (Figure 3D-F, 4B–
C, S3B, S4C and S4E in File S1) were subjected to analysis of
variance (ANOVA) and means were compared by t-test at the 5%
level. All analyses were performed with version 13.0 of SPSS
software. Acknowledgments We thank Jia Zhao for plant care and Huanhuan Liu for help with
microscope. The authors would like to thank two anonymous reviews for
their valuable comments and suggestions for improving the quality of this
paper. 1. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic
pathway. Annu Rev Plant Biol 55: 555–590. E3 Ligase Positively Regulates Salt Responses The leaves were exposed to air and the fresh weights were
measured at the indicated time points shown in Figure 4C. Water-
loss rate is calculated as the ratio between water loss and plant
initial fresh weight, expressed in %. GUS histochemical assays Tissues of transgenic seedlings harboring AtRDUF1::GUS at
various growth stages were used for the GUS activity assays. Fixation of the tissues by acetone and incubation in staining
solution was performed as described by Sieburth and Meyerowitz
[55]. For staining of pollen, the pollen was isolated from stamens
by vortexing in acetone and enriched using centrifugation at rcf
3000. E3 ubiquitin ligase activity assay The MBP:AtRDUF1 fusion protein was expressed in Escherichia
coli strain BL21 (DE3), and subsequently purified using amylose
resin (NEB). The in vitro E3 ubiquitin ligase activity assay was
performed as described previously [5]. Following the assay
reactions, proteins were separated by SDS-PAGE, blotted, and
probed by either HisDetector Nickel-HRP (KPL company, USA)
for the detection of His-tagged ubiquitin or antibody to MBP
(antiserum; NEB) for detection of the MBP-tagged AtRDUF1
protein. Results were visualized using chemiluminescence as per
the instructions of the manufacturer (ECL; Amersham Pharmacia,
Amersham, UK). Author Contributions Conceived and designed the experiments: QX KC YX. Performed the
experiments: JL YH QZ CL. Analyzed the data: JL YH QZ CL QX KC
YX. Contributed reagents/materials/analysis tools: QZ QX CL. Wrote
the paper: JL QZ KC YX. Conceived and designed the experiments: QX KC YX. Performed the
experiments: JL YH QZ CL. Analyzed the data: JL YH QZ CL QX KC
YX. Contributed reagents/materials/analysis tools: QZ QX CL. Wrote
the paper: JL QZ KC YX. Subcellular localization Plasmid 35S::AtRDUF1:GFP and 35S::GFP were purified by
the use of Tiangen kits according to the manufacturer’s protocols. Arabidopsis protoplasts transformations were performed as de-
scribed previously [52]. For detection of nuclei, samples were
stained with DAPI at a final concentration of 1 mg/mL. Expression analysis Total RNA was extracted from tissues with Trizol reagent
(Invitrogen, Carlsbad, CA, USA), and treated with RNase-free
DNase (Takara, Dalian, China) according to the manufacturer’s
instructions. 2 mg of total RNA was used for cDNA synthesis with
avian myeloblastosis virus (AMV) reverse transcriptase (Promega,
Madison, WI, USA) according to the manufacturer’s protocol. Real-Time qRT-PCR was performed as described previously [56]. Three independent experiments were performed. The relative
quantification method (Delta-Delta CT) was used to evaluate
variation in expression. Significance of differences was determined
by x2-test. The primer sets for PCR were: R1realtimeF and
R1realtimeR for AtRDUF1; RD29BF and RD29BR for RD29B;
RD22F and RD22R for RD22; KIN1F and KIN1R for KIN1;
TubulinF and TubulinR for TUBULIN; OleS3F and OleS3R for
OleS3; ACTINF and ACTINR for ACTIN. Supporting Information File S1
Text S1, lipid detection. Figure S1, verification of
T-DNA insertion mutants of AtRDUFs and AtRDUF1 overexpres-
sion
lines. Figure S2,
relative
quantification
of
AtRDUF1
transcription during germination assayed by real-time qRT-
PCR. Figure S3, response of AtRDUF1 overexpression plants to
ABA. Figure S4, effects of AtRDUF1 and salt treatment on plant
lipids. Table S1, sequences of the oligonucleotides used in this
study. (DOC) Vector construction and Arabidopsis transformation The cDNA of AtRDUF1 was amplified and cloned into the
pSN1301 expression vector [48] driven by the CaMV 35S August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 6 E3 Ligase Positively Regulates Salt Responses p
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https://openalex.org/W4361873294 | https://figshare.com/articles/journal_contribution/Supplementary_Figure_2_from_Bcl3_Selectively_Promotes_Metastasis_of_ERBB2-Driven_Mammary_Tumors/22400061/1/files/39845820.pdf | English | null | Supplementary Figure 6 from Bcl3 Selectively Promotes Metastasis of ERBB2-Driven Mammary Tumors | null | 2,023 | cc-by | 64 | Supplementary Figure 2 Bcl3-/-/MMTV/N2
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Bcl3-/- N2
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Bcl3+/N2
Ki67
B
Cl. Casp.3
Neu
185kda
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Bcl3+/N2
Bcl3-/N2
Tubulin
EGFR
175kda
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Bcl3+/+/MMTV/N2
Bcl3+/-/MMTV/N2
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Bcl3+/+ N2
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https://openalex.org/W4308834190 | https://www.biorxiv.org/content/biorxiv/early/2022/11/10/2022.11.09.515817.full.pdf | English | null | Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin expression in osteocytes to promote bone formation in mice | bioRxiv (Cold Spring Harbor Laboratory) | 2,022 | cc-by | 17,130 | .
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bioRxiv preprint Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin
expression in osteocytes to promote bone formation in mice Yishu Wang1#, Jianmei Huang1#, Sixiong Lin2,1#, Lei Qin3, Dingyu Hao1, Peijun
Zhang1, Shaochuan Huo1,4, Xuenong Zou2, Di Chen3,5, Guozhi Xiao1*
1Department of Biochemistry, School of Medicine, Guangdong Provincial Key
Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key
Laboratory of Cell Microenvironment, Southern University of Science and
Technology, Shenzhen, 518055, China. 2Department of Spine Surgery, Orthopedic Research Institute, The First Affiliated
Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of
Orthopedics and Traumatology, Guangzhou 510080, China. Orthopedics and Traumatology, Guangzhou 510080, China. 3Department of Orthopedics, Huazhong University of Science and Technology Union
Shenzhen Hospital, Shenzhen 518000, China. 4Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese
Medicine, Shenzhen 518000, China. 5Research Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China. #These authors contributed equally to this work. *Address correspondence to: G. X. (email: xiaogz@sustech.edu.cn). . CC-BY 4.0 International license
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bioRxiv preprint Keywords: focal adhesion; vinculin; Mef2c; sclerostin; bone formation. Running title: Vinculin regulation of bone formation. . CC-BY 4.0 International license
perpetuity. It is made available under a
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bioRxiv preprint Abstract The focal adhesion (FA) is the structural basis of the cell-extracellular matrix The focal adhesion (FA) is the structural basis of the cell-extracellular matrix
crosstalk and plays important roles in control of organ formation and function. Here
we show that expression of FA protein vinculin is dramatically reduced in osteocytes
in patients with aging-related osteoporosis. Deleting vinculin using the mouse 10-kb
Dmp1-Cre transgenic mice causes a severe osteopenia in both young and aged mice
by impairing osteoblast function without affecting bone resorption. Vinculin loss
impairs the anabolic response of skeleton to mechanical loading in mice. At the
molecular level, vinculin knockdown increases, while vinculin overexpression
decreases, sclerostin expression in osteocytes without impacting expression of Mef2c,
a major transcriptional regulator of the Sost gene, which encodes sclerostin. Vinculin
interacts with Mef2c and vinculin loss enhances Mef2c nuclear translocation and
binding to the Sost enhancer ECR5 to promote sclerostin production in osteocytes. Deleting Sost expression reverses the osteopenic phenotypes caused by vinculin loss
in mice. We demonstrate that estrogen is a major regulator of vinculin expression in
osteocytes and that more importantly vinculin loss mediates estrogen deficiency
induction of bone loss in mice. Thus, we demonstrate a novel mechanism through
which vinculin inhibits the Mef2c-driven sclerostin expression in osteocytes to
promote bone formation. . CC-BY 4.0 International license
perpetuity. It is made available under a
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bioRxiv preprint Introduction The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a
process during which the osteoclast-mediated bone resorption is closely coupled with
the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in
osteoporosis characterized with low bone mass and bone fracture (Einhorn &
Gerstenfeld, 2015; Wawrzyniak & Balawender, 2022). Understanding the mechanisms
behind bone remodeling will advance bone biology research and identify new targets
for treating metabolic bone diseases (Wong, Chin, Suhaimi, Ahmad, & Ima-Nirwana,
2016). The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a
process during which the osteoclast-mediated bone resorption is closely coupled with
the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in
osteoporosis characterized with low bone mass and bone fracture (Einhorn &
Gerstenfeld, 2015; Wawrzyniak & Balawender, 2022). Understanding the mechanisms
behind bone remodeling will advance bone biology research and identify new targets
for treating metabolic bone diseases (Wong, Chin, Suhaimi, Ahmad, & Ima-Nirwana,
2016). The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a
process during which the osteoclast-mediated bone resorption is closely coupled with
the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in
osteoporosis characterized with low bone mass and bone fracture (Einhorn & The focal adhesion (FA), which consists of integrins, extracellular matrix (ECM),
cytoskeleton, kindlin-2, talin, vinculin and other proteins, mediates communication
between cells and their environment and plays a central role in regulation of the
cell-ECM adhesion, migration, differentiation, survival and mechanotransduction
(Calderwood, Campbell, & Critchley, 2013; Larjava, Plow, & Wu, 2008; Ma, Qin, Wu,
& Plow, 2008; Montanez et al., 2008; Qin, Liu, Cao, & Xiao, 2020; Qin, Yang, Yi,
Cao, & Xiao, 2021; Ussar, Wang, Linder, Fässler, & Moser, 2006; H. Xu, Cao, &
Xiao, 2016). Abnormalities in expression and activation of the FA proteins are
involved in the pathogenesis and metastasis of cancers (Guo & Wu, 2019, 2020; Lin
et al., 2017; Theodosiou et al., 2016; Xue, Xue, Wan, Li, & Shi, 2020; Zhan & Zhang,
2018). More recent studies reveal that FA proteins are critical for control of formation
and organs and tissues, including skeleton (Cao et al., 2020; S. Chen et al., 2022; Fu . Introduction CC-BY 4.0 International license
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bioRxiv preprint 2016; Y. Wang et al., 2019; C. Wu et al., 2015; X. Wu, Cao, & Xiao, 2021; X. Wu et al., 2022), heart (Liang, Sun, & Chen, 2009; Qi et al., 2019; Zhang et al., 2016), 1980; Geiger, 1979). Vinculin is critical for the FA formation and maintenance. Cells overexpressing vinculin assemble large FAs (Janssen et al., 2006; Rodríguez Fernández, Geiger, Salomon, & Ben-Ze'ev, 1993), whereas vinculin-deficient cells form smaller and fewer FAs (Peng, Maiers, Choudhury, Craig, & DeMali, 2012; W. . CC-BY 4.0 International license
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bioRxiv preprint Gao et al., 2017). However, the function of vinculin in bone has not been explored. In this study, we demonstrate that mice lacking vinculin in the dentin matrix
protein 1 (Dmp1)-positive cells (i.e., osteocytes and mature osteoblasts) display a
severe bone loss with impaired bone formation, fail to properly respond to mechanical
loading, and do not show further bone loss on estrogen deficiency. Vinculin interacts
with Mef2c and vinculin loss increases Mef2c nuclear translocation and binding to the
Sost enhancer ECR5 to promote sclerostin production in osteocytes and thereby
inhibit bone formation. Results Vinculin is downregulated in osteocytes in human osteoporotic bones and Vinculin is downregulated in osteocytes in human osteoporotic bones and
vinculin loss impairs osteocyte adhesion and spreading. vinculin loss impairs osteocyte adhesion and spreading. As an initial attempt to explore the potential involvement of alteration in expression
of FA protein vinculin in the pathogenesis of osteoporosis, we collected human bone
tissue samples from young (from 29 to 32 years old) and aged individuals (from 78 to
88 years old) and performed immunofluorescence (IF) staining of these bone sections
to determine the expression level of vinculin protein. The results showed that
osteocytes embedded in the trabecular bone matrix in the young bone samples
expressed a high level of vinculin protein, which was drastically decreased in the aged
bones (Fig. 1a, b). To gain insights into the function of vinculin in osteocytes, we
utilized the CRISPR-Cas9 technology to delete the Vcl gene, which encodes vinculin,
in MLO-Y4 osteocyte-like cells. We found that MLO-Y4 cells with deletion of two . CC-BY 4.0 International license
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bioRxiv preprint alleles of the Vcl gene did not grow and die in culture (data not shown). We therefore
knocked down (KD) vinculin expression by deleting one allele of the Vcl gene in
MLO-Y4 cells. Note: vinculin KD did not markedly affect the expression levels of
other FA proteins, such as integrinb1, kindlin-2, talin and pinch1 (Fig. 1c, d), as
measured by IF staining and western blotting analyses. Vinculin KD greatly altered
the distribution and orientation of filamentous actin (Fig. 1e) and impaired cell
spreading in MLO-Y4 cells (Fig. 1f). Deleting vinculin expression in Dmp1-expressing cells causes a low bone mass in
mice. To investigate potential role of vinculin in bone, we deleted its expression in the
dentin matrix protein 1 (Dmp1)-expressing cells (primarily osteocytes and mature
osteoblasts) by breeding the floxed Vcl mice (Vclfl/fl) with the 10-kb mouse Dmp1-Cre
transgenic mice (Dmp1-Cre; Vclfl/fl, referred as cKO hereafter). The results from
qRT-PCR and western blotting analyses showed that vinculin mRNA and protein
expression was significantly reduced in cKO cortical bones compared to that in
control bones (Fig. 2a, b). Micro-computed tomography (µCT) analysis of distal
femurs from 3- and 14-mo-old male control and cKO mice showed that vinculin loss
caused a severe osteopenia at both ages. Vinculin loss significantly decreased the bone
mineral density (BMD) (Fig. 2c, d) and bone volume fraction (BV/TV) (Fig. 2c, e)
without affecting the cortical thickness (Ct.Th) (Fig. 2f). Consistent with results from
µCT analyses, results from H/E staining of tibial sections showed much less . CC-BY 4.0 International license
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bioRxiv preprint trabecular bone mass in cKO mice than that in control mice (Fig. 2g). Similar
reductions in BMD (Fig. 2h, i) and BV/TV (Fig. 2h, j) were observed in 3-mo-old
male cKO spine (L4-5) compared to those in control mice (Fig. 2h-j). Note: vinculin
loss did not affect the bone mass in skull (Fig. 2k). trabecular bone mass in cKO mice than that in control mice (Fig. 2g). Similar Vinculin loss mainly impairs bone formation without markedly impacting bone To investigate mechanism through which vinculin loss causes a low bone mass, we
determined the osteoblast and osteoclast formation and function in control and cKO
long bones. Results from the double calcein labeling experiments showed that the
mineralization apposition rate (MAR) and bone formation rate (BFR) in the femur
metaphyseal cancellous bones from 3-mo-old male cKO mice were significantly
decreased compared to those in control mice (Fig. 3a-c). The serum level of the
procollagen type 1 amino-terminal propeptide (P1NP), a marker of in vivo bone
formation(D'Oronzo, Brown, & Coleman, 2017), was significantly lower in cKO
mice than that in control mice (Fig. 3d). To determine the effects of vinculin loss on
the osteoid production and mineralization, we performed the von Kossa staining of
femur sections of control and dKO mice and found that the osteoid volume/tissue
volume (OV/TV) and mineralized bone volume/tissue volume (mBV/TV) were
decreased in cKO mice relative to those in control mice (Fig. 3e-g). We next
performed the colony forming unit-fibroblast (CFU-F) assay and colony forming performed the colony forming unit-fibroblast (CFU-F) assay and colony forming performed the colony forming unit-fibroblast (CFU-F) assay and colony forming . CC-BY 4.0 International license
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bioRxiv preprint unit-osteoblast (CFU-OB) assay. The results showed that the number of CFU-OB,
but not that of CFU-F, was reduced in cKO group compared to that in control group
(Fig. 3h, i). We further measured the osteoclast formation and bone-resorbing
activity in control and cKO mice. The serum levels of collagen type I cross-linked
C-telopeptide (CTX), degradation products from type I collagen during in vivo
osteoclastic bone resorption(D'Oronzo et al., 2017), were not significantly different
between the two genotypes (Fig. 3j). Vinculin loss mainly impairs bone formation without markedly impacting bone Results from TRAP staining of tibial sections
showed that the osteoclast surface/bone surface (Oc.S/BS) and osteoclast
number/bone perimeter (Oc.Nb/BPm) in both primary and secondary cancellous
bones were not markedly altered in cKO mice relative those in control mice (Fig. 3k-o). 3k-o). Vinculin loss increases, while vinculin overexpression decreases, sclerostin
expression without affecting the level of Mef2c protein in osteocytes. Sclerostin is encoded by Sost and mainly secreted by osteocytes. Sclerostin decreases
osteoblast and bone formation via inhibiting the Wnt/b-catenin signaling. Sclerostin
loss or pharmacological neutralization greatly increases bone formation and bone
mass (Reid & Billington, 2022). Because the osteoblast and bone formation was
severely impaired by vinculin loss in the cKO mice, as demonstrated above, we next
determined whether vinculin loss increased sclerostin production in mice. Results
from by IHC, RT-qPCR and western blotting analyses revealed that the expression . CC-BY 4.0 International license
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bioRxiv preprint levels of sclerostin mRNA and protein were strikingly increased in cKO versus
control osteocytes and bones (Fig. 4a-e). It should be noted that vinculin loss did not
markedly alter the level of Mef2c protein in bone extracts (Fig. 4d, e), a major
transcriptional regulator of the Sost gene. In contrast, overexpression of vinculin
decreased the level of sclerostin in MLO-Y4 cells (Fig. 4f, g). Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear
translocation and binding to the Sost enhancer ECR5 in osteocytes. Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear
translocation and binding to the Sost enhancer ECR5 in osteocytes. We found that siRNA knockdown (KD) of Mef2c in MLO-Y4 cells reversed the
sclerostin upregulation caused by vinculin loss (Fig. 4h, i). Furthermore, vinculin KD
decreased the level of cytoplasmic Mef2c and, in the meantime, increased that of its
nuclear protein in MLO-Y4 cells, which were reversed by vinculin overexpression
(Fig. 4j, k). IF staining revealed that vinculin and Mef2c colocalized in MLO-Y4
cells and that vinculin KD increased Mef2c nuclear translocation in these cells,
which was reversed by vinculin overexpression (Fig. 4l). Results from
co-immunoprecipitation (Co-IP) experiments demonstrated interactions of
endogenous or overexpressed vinculin and Mef2c proteins in MLO-Y4 cells (Fig. 4m-o). Results from ChIP assay using the MLO-Y4 cells revealed that vinculin KD
dramatically increased the binding of Mef2c to the Sost enhancer ECR5 (Fig. 4p). Consistent with the fact that sclerostin is a potent inhibitor of the Wnt/b-catenin
pathway, the level of active b-catenin, but not that of its total protein, was
dramatically reduced in cKO BMSC cultures relative to that in control BMSC dramatically reduced in cKO BMSC cultures relative to that in control BMSC . CC-BY 4.0 International license
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bioRxiv preprint cultures (Fig. 4q). .
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bioRxiv preprint Deleting Sost expression in Dmp1-expressing cells reverses the osteopenia
induced by vinculin loss. Deleting Sost expression in Dmp1-expressing cells reverses the osteopenia
induced by vinculin loss. Above results suggest that the sclerostin upregulation by vinculin loss may play a
role in causing the bone loss in cKO mice. To determine if this is the case, we next
determined the effects of Sost deletion in Dmp1-expressing cells on the osteopenic
phenotypes caused by vinculin loss in mice. We bred the Dmp1-Cre; Vclfl/fl (cKO)
mice with Sostfl/fl mice and generated Dmp1-Cre; Vclfl/fl; Sostfl/fl and Dmp1-Cre;
Sostfl/fl mice. We performed µCT analyses of the femurs of the indicated groups (Fig. 5a). As expected, Sost loss increased the BMD, BV/TV and Ct.Th (Fig. 5b-d). Importantly, Sost deletion largely reversed the osteopenia of cKO mice (Fig. 5b, c). H/E staining of the tibial sections revealed that Sost ablation reversed the low bone
mass in vinculin-deficient mice (Fig. 5e). Sost inactivation similarly reversed the
osteopenic phenotypes in spine (L4-L5) in vinculin cKO mice (Fig. 5f-h). Because it
is known that sclerostin reduces bone formation by inhibiting Wnt/b-catenin pathway,
we measured the bone-forming activity of osteoblasts in vivo by performing the
double calcein labeling experiments. As expected, we observed significant increases
in the MAR and BFR after Sost inactivation (Fig. 5i-k). Importantly, deleting Sost
expression largely restored the impairment in bone formation in cKO mice (Fig. 5i-k). Results from the TRAP staining of tibial sections showed no marked
differences in osteoclast formation between the control and cKO mice with and . CC-BY 4.0 International license
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bioRxiv preprint without Sost deletion (Fig. 5l-p). Vinculin loss impairs the anabolic responses of skeleton to mechanical loading It is now widely believed that osteocytes embedded in the mineralizing matrix are the
major mechanosensors of bone (Lewis, 2021; Qin et al., 2020). We next examined
whether vinculin is involved in the bone mechanotransduction by performing the
tibial loading experiments in control and cKO mice (Qin et al., 2022). Results from
µCT analyses showed that 2 weeks’ mechanical loading caused significant increases
in the BMD, BV/TV and Ct.Th in control tibiae, which were essentially abolished in
cKO tibiae (Fig. 6a-d). Results from H/E staining of the tibial sections showed that
mechanical loading markedly increased the trabecular volume in control but not cKO
mice (Fig. 6e). Mechanical loading significantly increased the values of MAR and
BFR in control but not cKO tibiae (Fig. 6f-h). Finally, tibial loading decreased the
Oc.Nb/BPm, but not the OC.N/BPm, in control mice, which was lost in cKO mice
(Fig. 6i-m). Estrogen loss reduces vinculin expression in osteocytes and ovariectomy no
longer causes bone loss in vinculin-deficient mice. Estrogen loss reduces vinculin expression in osteocytes and ovariectomy no
longer causes bone loss in vinculin-deficient mice. We next determined vinculin expression in osteocytes in mice with ovariectomy
(OVX), which mimics the postmenopausal osteoporosis in humans. Surprisingly, we
found that the expression level of vinculin protein was strikingly decreased in . CC-BY 4.0 International license
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bioRxiv preprint osteocytes embedded in the bone matrix in OVX mice (Fig. 7a, b). We next osteocytes embedded in the bone matrix in OVX mice (Fig. 7a, b). We next
determined whether estrogen can directly regulate vinculin expression in cultured
osteocytes and found that estrogen increased the level of vinculin protein in MLO-Y4
cells in a dose-dependent manner (Fig. 7c, d). In contrast, fulvestrant, an estrogen
receptor antagonist, decreased the level of vinculin protein in MLO-Y4 cells (Fig. 7c,
e). We next compared the effects of OVX on reduction of bone mass in control and
vinculin cKO mice. To this end, 3-month-old control and vinculin cKO female mice
were subjected to sham or OVX surgery, as we previously described (Fu et al., 2020). At two months after surgery, the bone mass was reduced in control mice, which is
expected. Shockingly, the OVX-induced trabecular bone loss was dramatically
reduced (BV/TV) or completely abolished (BMD) in cKO mice (Fig. 7f-i). While
OVX did not markedly impact the MAR and BFR in both control and cKO mice (Fig. 7k-m), it caused dramatic increases in the OC.S/BS and OC.N/BPm in control mice,
which were lost in vinculin cKO mice (Fig. 7n-r). Discussion We summarize the main findings of the present study as follows. First, the expression
of FA protein vinculin is drastically reduced in osteocytes in patients with age-related
osteoporosis and in mice with estrogen deficiency. Second, deleting vinculin in
Dmp1-expressing cells, i.e., primarily osteocytes and mature osteoblasts, causes a
severe bone loss in both young and aged mice. Third, vinculin deletion impairs the
bone mechanotransduction in mice. Fourth, vinculin expression in osteocytes is . CC-BY 4.0 International license
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bioRxiv preprint critically involved in estrogen control of bone mass in mice. Finally, vinculin
regulates osteocyte adhesion and inhibits sclerostin expression to promote bone
formation. critically involved in estrogen control of bone mass in mice. Finally, vinculin
regulates osteocyte adhesion and inhibits sclerostin expression to promote bone
formation. In this study, we demonstrate that vinculin increases bone mass and BMD by
primarily promoting bone formation. Thus, vinculin loss in osteocytes and mature
osteoblasts dramatically decreased the values of serum P1NP, BFR, MAR, OV/TV
and mBV/TV, all osteoblastic parameters. These impairments lead to reduced bone
formation and severe osteopenia. Of note, vinculin loss does not markedly alter
osteoclast formation (OC.S/BS and OC.N/BPm) and bone resorption (serum CTX-1). This result on osteoclast formation is similar to that in mice lacking the other FA
proteins pinch1/2 in Dmp1-expressing cells (Y. Wang et al., 2019), but in contrast to
those in mice with deletion of FA protein kindlin-2 in the same cell type, which
displayed increased osteoclast formation and bone resorption in part due to enhanced
Rankl production in osteocytes (Cao et al., 2020). The reason(s) for this discrepancy
are not clear. Our findings from this study strongly suggest that vinculin inhibits sclerostin
expression in osteocytes and mature osteoblasts to promote the osteoblast-mediated
bone formation. Our in vitro and in vivo results demonstrate that vinculin-deficient
osteocytes produce a large amount of sclerostin protein, which inhibits binding of
Wnt ligands to the LRP5/6 receptors and, thereby, the Wnt/b-catenin signaling. The
latter is a major player in control of the bone mass accrual in vertebrates. Consistently,
vinculin loss reduces the level of active b-catenin protein and CFU-OB formation in . CC-BY 4.0 International license
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bioRxiv preprint bone marrows and bone formation in mice. Of particular significance, deleting Sost
expression in Dmp1-expressing cells essentially reverses the low bone mass caused
by vinculin loss. Thus, we provide important genetic evidence that FA protein
vinculin plays a critical role in promoting bone formation by facilitating the
Wnt/b-catenin signaling in osteoblastic cells. critically involved in estrogen control of bone mass in mice. Finally, vinculin
regulates osteocyte adhesion and inhibits sclerostin expression to promote bone
formation. At the molecular level, we provide intriguing evidence that vinculin loss
promotes Sost expression through, at least in part, Mef2c, a major transcriptional
regulator of the Sost gene (Collette et al., 2012; Kramer, Baertschi, Halleux, Keller, &
Kneissel, 2012). Importantly, upregulation of sclerostin expression induced by
vinculin loss is largely reversed by Mef2c KD in osteocytes. While vinculin loss does
not alter the expression level of total Mef2c protein in osteocytes, it increases the
Mef2c nuclear translocation and binding to the Sost enhancer ECR5. It is known that
Mef2c binding to this enhancer is critical for Sost expression in osteocytes (Leupin et
al., 2007). Our results suggest that binding of vinculin to Mef2c prevents the Mef2c
nuclear translocation by retaining it in the cytoplasm. While estrogen deficiency causes the postmenopausal osteoporosis, its
mechanism(s) remain incompletely understood. We demonstrate that OVX mice
express an extremely low level of vinculin protein in osteocytes in bone. Of particular
significance, mice lacking vinculin in osteocytes are resistant to OVX-induced bone
loss. We find that estrogen directly increases vinculin expression in osteocytes. While estrogen deficiency causes the postmenopausal osteoporosis, its
mechanism(s) remain incompletely understood. We demonstrate that OVX mice
express an extremely low level of vinculin protein in osteocytes in bone. Of particular
significance, mice lacking vinculin in osteocytes are resistant to OVX-induced bone
loss. We find that estrogen directly increases vinculin expression in osteocytes. Collectively, these results suggest that estrogen signaling favors bone formation by in
part inducing vinculin expression in osteocytes. This knowledge improves our Collectively, these results suggest that estrogen signaling favors bone formation by in
part inducing vinculin expression in osteocytes. This knowledge improves our . CC-BY 4.0 International license
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bioRxiv preprint understanding of the molecular mechanism(s) underlying the postmenopausal
osteoporosis. understanding of the molecular mechanism(s) underlying the postmenopausal
osteoporosis. Mechanical force is the most potent anabolic stimulus for bone formation. Mechanical force is the most potent anabolic stimulus for bone formation. Osteocytes, the most abundant ed cells embedded in the mineralizing matrix in bone,
are now believed to be the major sensor and mediator of mechanotransduction in bone
(Qin et al., 2020). In this study, we demonstrate that vinculin expression in osteocytes
is essential for skeletal response to mechanical loading to increase bone formation. It
should be noted that loss of other FA proteins Kindlin-2 or pinch in osteocytes caused
a similar defect in the anabolic effects of mechanical loading on bone in mice (Qin,
Fu, et al., 2021; Y. Wang et al., 2019). Collectively, these results suggest a critical
role of the FA signaling pathway in mediation of the mechanotransduction in bone. Notably, previous studies demonstrate that mechanical force promotes vinculin
activation through conformational changes and a loss of tension causes vinculin to be
rapidly inactivated (Carisey et al., 2013). Finally, we propose a working model regarding how FA protein vinculin
expression in osteocytes embedded in the bone matrix controls bone formation (Fig. 8). In young and adult animals, vinculin is highly expressed in osteocytes where it,
probably together other FA proteins, such as talin and actin, forms a complex with
Mef2c in the cytoplasm. Complex formation prevents the nuclear translocation of
Mef2c, leading to reduced expression and production of sclerostin and, thereby,
increased bone formation. In contrast, in the presence of vinculin deficiency in
osteocytes, which is related to aging and estrogen deficiency, the nuclear translocation . CC-BY 4.0 International license
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bioRxiv preprint of Mef2c and its binding to the Sost enhancer ECR5 are enhanced, thus stimulating
Sost expression and inhibiting bone formation. understanding of the molecular mechanism(s) underlying the postmenopausal
osteoporosis. In summary, in this study, we
demonstrate that vinculin plays an important role in control of bone formation and
may be a useful target for the prevention and treatment of aging and estrogen
deficiency induced osteoporosis. Tissue samples Human cancellous tissues and their corresponding adjacent normal controls were
collected from the Shenzhen Hospital of Guangzhou University of Chinese Medicine. Written informed consent was obtained from all patients. The study has been
approved by the Shenzhen Hospital of Guangzhou University of Chinese Medicine,
China (NO. GZYLL(KY)-2022-027). Specimens were collected and stored in
formaldehyde after surgery. Animal studies Dmp1-Cre mice were generously provided by Dr. Jian Q Feng (Baylor College of
Dentistry) (J. Q. Feng et al., 2003). Vcl fl/fl mice were purchased from the Jackson
Laboratory. The experimental animals used current studies were obtained using a
2-step breeding strategy. Homozygous Vcl fl/fl mice were first crossed with Dmp1-Cre
transgenic mice to generate Dmp1-Cre; Vcl fl/+ mice. These offspring were then
crossed with Vcl fl/fl to generate Dmp1-Cre; Vcl fl/fl mice. The generation of the
Dmp1-Cre; Vcl fl/fl; Sost fl/fl mice was as follow: Dmp1-Cre; Vcl fl/fl mice were first
crossed with Sostfl/fl mice to generate Dmp1-Cre; Vcl fl/+; Sost fl/+ mice. These
offspring were then intercrossed with Vcl fl/fl; Sost fl/fl mice to generate the Dmp1-Cre;
Vcl fl/fl; Sost fl/fl mice and other genotypes. In vivo tibial loading experiments were
performed as previously described (Qin, Fu, et al., 2021). All animal experiments in
this study were approved by the Institutional Animal Care and Use Committees
(IACUC) of the Southern University of Science and Technology. . CC-BY 4.0 International license
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bioRxiv preprint Micro-computerized tomography (µCT) analysis Fixed non-demineralized femur, tibia, spine or skull were used for µCT analysis in the
Experimental Animal Center of Southern University of Science and Technology using
a Bruker µCT (SkyScan 1176 Micro-CT, Bruker MicroCT, Kontich, Belgium)
following the standards of techniques and terminology recommended by the
American Society for Bone and Mineral Research (ASBMR) (Bouxsein et al., 2010). BMSC culture Primary bone marrow stromal cells (BMSC) were isolated from femurs of
3-month-old male mice as previously described (Yan, Gao, Yao, Ling, & Xiao, 2022). Briefly, bone marrow cells were cultured on 60-mm cell culture dishes in a-MEM
(Hyclone, USA) containing 15% FBS. After 48 h, the non-adherent cells were
removed. On the seventh day, the cells trypsinized for subsequent experiments. Colony forming unit-fibroblast (CFU-F) assay and colony forming unit-osteoblast
(CFU-OB) assay were performed as we previously described (Lei et al., 2020). Histological evaluation and bone histomorphometry For histology, bone tissues were fixed in 4% paraformaldehyde (PFA) at 4oC for 24 h,
decalcified in 10% EDTA (pH 7.4) for 21 d, and embedded in paraffin after
dehydration. Bone sections were used for hematoxylin and eosin (H/E) and
tartrate-resistant acid phosphatase (TRAP) staining using our standard protocols (Y. Wang et al., 2019; C. Wu et al., 2015). . CC-BY 4.0 International license
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bioRxiv preprint Immunohistochemistry (IHC) and immunofluorescence (IF) staining For IHC staining, 5-µm sections were stained with antibodies or control IgG using
the EnVision+System-HRP (DAB) kit (Dako North America Inc, Carpinteria, CA,
USA) as previously described (Cao et al., 2020). IF staining of bone sections and
MLO-Y4 cells was performed as we previously described (Zhu et al., 2020). Western blot analysis Western blot analysis was performed as previously described (Y. Wang et al., 2021). Briefly, whole-cell lysates were prepared in RIPA lysis buffer (Sigma, USA) and
aliquots of 15 µg protein were separated by SDS-PAGE and blotted onto a
polyvinylidene fluoride (PVDF) membrane (Millipore, MA, USA). Membranes were
blocked at room temperature for 15 min in QuickBlock™ Western (Beyotime), Western blot analysis was performed as previously described (Y. Wang et al., 2021). Briefly, whole-cell lysates were prepared in RIPA lysis buffer (Sigma, USA) and
aliquots of 15 µg protein were separated by SDS-PAGE and blotted onto a
polyvinylidene fluoride (PVDF) membrane (Millipore, MA, USA). Membranes were
blocked at room temperature for 15 min in QuickBlock™ Western (Beyotime),
followed by an overnight incubation at 4 °C with specific antibodies. After incubation
with appropriate HRP-conjugated secondary antibodies (ZSGB-bio), blots were
developed using an enhanced chemiluminescence (ECL Kit, BIORAD) and exposed
in ChemiDoc XRS chemiluminescence imaging system. Antibodies used in this study
are listed in Supplementary Table 2 followed by an overnight incubation at 4 °C with specific antibodies. After incubation
with appropriate HRP-conjugated secondary antibodies (ZSGB-bio), blots were
developed using an enhanced chemiluminescence (ECL Kit, BIORAD) and exposed
in ChemiDoc XRS chemiluminescence imaging system. Antibodies used in this study
are listed in Supplementary Table 2 RNA extraction and qRT-PCR analysis RNA isolation and quantitative real-time RT-PCR analysis were performed as we
previously described (H. Gao et al., 2019). The specific primers for gene expression
analysis were listed in Supplementary Table 1. ELISA assays Serum levels of P1NP were measured using the RatLaps EIA Kit (cat# AC-33F1)
according to the manufacturer’s instruction (Immunodiagnostic Systems Limited). Serum levels of CTX, degradation products from type I collagen during osteoclastic
bone resorption, were measured using the RatLaps EIA Kit (cat# AC-06F1) according
to the manufacturer’s instruction (Immunodiagnostic Systems Limited). . CC-BY 4.0 International license
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bioRxiv preprint Co-immunoprecipitation (Co-IP) assay Co-IP assay was performed as previously described (Fu et al., 2020). Briefly, cells
were incubated for 10 min at 4 °C in RIPA buffer (Sigma, USA). After a
centrifugation at 12,000 × g for 10 min at 4 °C, the supernatant was first incubated
with corresponding primary antibody overnight and then with Protein A/G Magnetic Co-IP assay was performed as previously described (Fu et al., 2020). Briefly, cells
were incubated for 10 min at 4 °C in RIPA buffer (Sigma, USA). After a . CC-BY 4.0 International license
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bioRxiv preprint Beads at room temperature for 1 h. DynaMag™-2 Magnet (Thermo Fisher) was used
to collect dynabeads-antigen-antibody complex. The complex was washed with IP
buffer three times and resuspended with 60 µl 1× loading buffer and cooked at 95 °C
for 5 min, followed by SDS-PAGE and western blotting. Chromatin immunoprecipitation (ChIP) assay ChIP assay was performed using the ChIP Kit (Abcam, ab500) as previously
described (X. Wang et al., 2020). Briefly, 1 × 107 cells were collected in lysis buffer
and sonicated to generate chromatin samples with average fragment sizes of
100–500 bp. Cell lysates were incubated with the indicated antibodies or IgG
overnight at 4°C. Then, the supernatants were mixed with the blocked Protein A/D
sepharose beads to collect the antibody–chromatin complexes. After washing 4 times,
the immunoprecipitated DNA was eluted and purified for the subsequent qPCR
analysis. Statistical Analyses The sample sizes for all experiments conducted in this study were determined based
on our previous experience on similar studies. Mice used in this study were randomly
grouped. The IF, IHC and histology were conducted and analyzed under double-blind
conditions. Statistical analyses were completed using the Prism GraphPad. Two-way
ANOVA and unpaired two-tailed Student’s t-test was used as indicated. P < 0.05 was
considered statistically significant. . CC-BY 4.0 International license
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bioRxiv preprint Data availability All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures. . CC-BY 4.0 International license
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bioRxiv preprint Acknowledgments The authors acknowledge the assistance of Core Research Facilities of Southern
University of Science and Technology. This work was supported, in part, by the
National Key Research and Development Program of China Grant
(2019YFA0906004), the National Natural Science Foundation of China Grants
(82230081, 82250710175, 81991513, 81630066, 81870532, 82004395), the China
Postdoctoral Science Foundation (2021M691435) and the Guangdong Provincial
Science and Technology Innovation Council Grant (2017B030301018). Author contributions: Study design: GX and YW. Conducting study, data collection
and analyses: YW, JH, SL, LQ, DH, PZ and SH. Data interpretation: GX, YW, XZ
and DC. Drafting the manuscript: GX and YW. YW and GX take the responsibility for
the integrity of the data analysis. Competing interests: The authors declare that they have no competing financial
interests. . CC-BY 4.0 International license
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bioRxiv preprint Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in osteocytes in human osteoporotic bones. a, b Immunofluorescence (IF) staining and
hematoxylin and eosin (H/E) staining. Sections of human cancellous samples from
young (29-32-yrs-old) and old 78-88-yrs-old) subjects were subjected to H/E and IF
staining with a vinculin antibody. Scale bars: 50 µm. Quantitative data (b). Results
were expressed as mean ± s.d. N = 3 biologically independent replicates per group,
**P < 0.01 versus young, unpaired two-tailed Student’s t test. c Western blot analysis. Protein extracts isolated from MLO-Y4 osteocyte-like cells with and without vinculin
knockdown (KD) by CRISPR-Cas9 technology were subjected to western blotting
using the indicated antibodies. d IF staining. MLO-Y4 cells with and without vinculin
KD were subjected to IF staining using phalloidin or DAPI. e IF staining. MLO-Y4
cells with and without vinculin KD were subjected to IF staining using the indicated
antibodies. f Cell adhesion assay. MLO-Y4 cells with and without vinculin KD were
seeded in a 96-well plate at a density of 1×105 cells/well. The absorbance was
measured at the time points of 0.5h, 1h, 3h, 6h and 12h, respectively. Results were
expressed as mean ± s.d., **P < 0.01, ***P < 0.001 versus controls, unpaired
two-tailed Student’s t test. two-tailed Student’s t test. Figure 2. Vinculin loss in Dmp1-expressing cells causes severe osteopenia by
impairing bone formation in mice. a Real-time RT-PCR (qPCR) analyses. Total
RNAs isolated from the indicated tissues of 3 mo-old male control (con) and cKO . CC-BY 4.0 International license
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bioRxiv preprint mice were used for qPCR analysis for expression of Vcl gene, which was normalized
to Gapdh mRNA. Results were expressed as mean ± s.d., N = 3 biologically
independent replicates per group, **P < 0.01 versus controls, unpaired two-tailed
Student’s t test. b Western blot analysis. Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in Protein extracts were isolated from the
indicated tissues of the control and cKO mice were subjected to western blotting
analysis for vinculin expression. Gapdh was used for loading control. c Three-dimensional (3D) reconstruction from micro-computerized tomography (µCT)
scans of distal femurs from male control and cKO mice with the indicated ages. d-f
Quantitative analyses of the bone volume/tissue volume (BV/TV), cortical thickness
(Ct.Th) and bone mineral density (BMD) of distal femurs from male control and cKO
mice with the indicated ages. Results were expressed as mean ± s.d., N = 6
biologically independent replicates per group, *P < 0.05, **P < 0.01, ***P < 0.001
versus controls, unpaired two-tailed Student’s t test. g H/E staining of tibial sections
of 3-mo-old male control and cKO mice with the indicated ages. h 3D reconstruction
from µCT scans of spine (L4, L5) from 3-mo-old male control and cKO mice. i, j Quantitative analyses of the bone volume/tissue volume (BV/TV) and bone mineral
density (BMD) of spine from male control and cKO mice. Results were expressed as
mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P <
0.01 versus controls, unpaired two-tailed Student’s t test. k 3D reconstruction from
µCT scans of skull. . CC-BY 4.0 International license
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bioRxiv preprint affecting the osteoclast formation and bone resorption. a-c Calcein double labeling affecting the osteoclast formation and bone resorption. a-c Calcein double labeling. Representative images of 3-mo-old male control and cKO femur sections (a). Sections
of non-demineralized femurs of 3-mo-old male control and cKO mice were used for
measurements of the mineral apposition rate (MAR) and bone formation rate (BFR). Quantitative MAR (b) and BFR (c) for the metaphyseal trabecular bones of the two
genotypes. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6
biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls,
unpaired two-tailed Student’s t test. d Serum level of procollagen type 1
amino-terminal propeptide (P1NP). Sera harvested from 3-mo-old male control and
cKO mice were subjected to ELISA assay for P1NP. Results were expressed as mean
± s.d., N = 6 biologically independent replicates per group, **P < 0.01 versus controls,
unpaired two-tailed Student’s t test. e-g von Kossa staining. Undecalcified sections of
femora from 3-mo-old male control and cKO mice were subjected to von Kossa
staining (e). Quantitative OV/TV (osteoid volume/tissue volume) (f) and mBV/TV
(mineralized bone volume/tissue volume) (g) data for the cancellous bones from distal
femora were measured by bone morphometry. Scale bar, 50 µm. Results were
expressed as mean ± s.d., N = 5 biologically independent replicates per group, *P <
0.05, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. h Colony
forming unit-fibroblast (CFU-F) assays. Bone marrow nucleated cells from 3-mo-old
male control and cKO mice were seeded in a 6-well plate with a cell density of 2x106 . CC-BY 4.0 International license
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bioRxiv preprint 14 days, followed by Giemsa staining. i Colony forming unit-osteoblast (CFU-OB)
assays. affecting the osteoclast formation and bone resorption. a-c Calcein double labeling Bone marrow nucleated cells from 3-mo-old male control and cKO mice were
seeded in a 6-well plate with a cell density of 4x106 per well and cultured in
osteoblast differentiation medium (complete a-MEM containing 50 µg/ml L-ascorbic
acid and 2.0 mM b-glycerophosphate) for 21 d and media were changed every 48h,
followed by alizarin red staining. j Serum level of collagen type I cross-linked
C-telopeptide (CTX). Sera collected from 3-mo-old male control and cKO mice were
subjected to ELISA assay for CTX. Results were expressed as mean ± s.d., N = 6
biologically independent replicates per group, *P < 0.05 versus controls, unpaired
two-tailed t test. k-o Tartrate-resistant acid phosphatase (TRAP) staining. Tibial
sections of 3-mo-male control and cKO mice were used for TRAP staining (k). Osteoclast surface/bone surface (Oc.S/BS) (l, m) and osteoclast number/bone
perimeter (Oc.N/BPm) (n, o) of primary and secondary cancellous bones were
measured using Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as
mean ± s.d., N = 7 biologically independent replicates per group, *P < 0.05 versus
controls, unpaired two-tailed Student’s t test. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases
Mef2c nuclear translocation and binding to the Sost enhancer ECR5 to promote
sclerostin expression in osteocytes. a, b Immunohistochemical (IHC) staining. Tibial sections of 3-mo-old male control and cKO mice were stained with an
anti-sclerostin antibody. Quantitative data (b). N = 5 biologically independent Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases . CC-BY 4.0 International license
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bioRxiv preprint replicates per group, **P < 0.01, versus controls, unpaired two-tailed Student’s t test. c qPCR analyses. Total RNA isolated from cortical bone of 3 mo-old male mice was
used for qPCR analysis for expression of Sost gene, which was normalized to Gapdh
mRNA. Results were expressed as mean ± s.d., N = 5 biologically independent
replicates per group, ***P < 0.001 versus controls, unpaired two-tailed Student’s t
test. d, e Western blot analyses. Protein extracts isolated from cortical bones of 3
mo-old male mice were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., N = 3 biologically independent replicates per
group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. f, g Vinculin
overexpression. Protein extracts isolated from MLO-Y4 cells transfected with
control or vinculin-expressing plasmid were subjected to western blotting using the
indicated antibodies. Results were expressed as mean ± s.d., **P < 0.01, ***P <
0.001 versus veh, unpaired two-tailed Student’s t test. h, i Whole cell extracts from
MLO-Y4 cells with and without vinculin or Mef2c siRNA knockdown (KD) were
subjected to western blotting using the indicated antibodies. Results were expressed
as mean ± s.d., *P < 0.05, **P < 0.01 versus veh, two-way ANOVA. j,k Mef2c
nuclear translocation. Cytoplasmic (CE) and nuclear extracts (NE) from MLO-Y4
cells with and without vinculin KD and with and without vinculin overexpression
(OE) were subjected to western blotting with the indicated antibody. Quantitative
data (k). Results were expressed as mean ± s.d., N = 3 biologically independent
replicates per group, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed
Student’s t test. l Vinculin-Mef2c colocalization. MLO-Y4 cells treated as in h were replicates per group, **P < 0.01, versus controls, unpaired two-tailed Student’s t test. c qPCR analyses. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases Total RNA isolated from cortical bone of 3 mo-old male mice was
used for qPCR analysis for expression of Sost gene, which was normalized to Gapdh
mRNA. Results were expressed as mean ± s.d., N = 5 biologically independent
replicates per group, ***P < 0.001 versus controls, unpaired two-tailed Student’s t
test. d, e Western blot analyses. Protein extracts isolated from cortical bones of 3
mo-old male mice were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., N = 3 biologically independent replicates per
group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. f, g Vinculin
overexpression. Protein extracts isolated from MLO-Y4 cells transfected with
control or vinculin-expressing plasmid were subjected to western blotting using the
indicated antibodies. Results were expressed as mean ± s.d., **P < 0.01, ***P <
0.001 versus veh, unpaired two-tailed Student’s t test. h, i Whole cell extracts from
MLO-Y4 cells with and without vinculin or Mef2c siRNA knockdown (KD) were
subjected to western blotting using the indicated antibodies. Results were expressed
as mean ± s.d., *P < 0.05, **P < 0.01 versus veh, two-way ANOVA. j,k Mef2c
nuclear translocation. Cytoplasmic (CE) and nuclear extracts (NE) from MLO-Y4
cells with and without vinculin KD and with and without vinculin overexpression
(OE) were subjected to western blotting with the indicated antibody. Quantitative
data (k). Results were expressed as mean ± s.d., N = 3 biologically independent . CC-BY 4.0 International license
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bioRxiv preprint subjected to IF staining with the indicated antibody. Scale bars: 50 µm. m-o
Co-immunoprecipitation (co-IP) assay. Protein extracts from MLO-Y4 cells with and
without overexpression of HA-vinculin and Flag-Mef2c were incubated with the
indicated antibodies or IgG, and the immunocomplexes were separated by
SDS-PAGE, followed by western blotting with the indicated antibodies. p
CHIP-qPCR analysis. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
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bioRxiv preprint (i-m) Tartrate-resistant acid phosphatase (TRAP) staining. Tibial sections of
3-mo-male mice were used for TRAP staining with indicated genotype. (i). Osteoclast
surface/bone surface (Oc.S/BS) (j, k) and osteoclast number/bone perimeter
(Oc.N/BPm) (l, m) of primary and secondary cancellous bones were measured using
Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6
biologically independent replicates per group, *P < 0.05 versus controls, unpaired
two-tailed Student’s t test. p 3D reconstruction from µCT scans of spine (L4, L5)
from 3-mo-old male mice with indicated genotype. q, r Quantitative analyses of bone
volume/tissue volume (BV/TV) and bone mineral density (BMD) of spine. Results
were expressed as mean ± s.d., N = 6 biologically independent replicates per group,
*P < 0.05, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t
test. test. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases The expression of Sost enhancer ECR5 combined with Mef2c
antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P <
0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot
analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and
cKO mice were subjected to western blotting using the indicated antibodies. subjected to IF staining with the indicated antibody. Scale bars: 50 µm. m-o
Co-immunoprecipitation (co-IP) assay. Protein extracts from MLO-Y4 cells with and
without overexpression of HA-vinculin and Flag-Mef2c were incubated with the
indicated antibodies or IgG, and the immunocomplexes were separated by
SDS-PAGE, followed by western blotting with the indicated antibodies. p
CHIP-qPCR analysis. The expression of Sost enhancer ECR5 combined with Mef2c
antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P <
0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot
analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and
cKO mice were subjected to western blotting using the indicated antibodies. CHIP-qPCR analysis. The expression of Sost enhancer ECR5 combined with Mef2c
antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P <
0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot
analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and
cKO mice were subjected to western blotting using the indicated antibodies. Figure 5. Deleting sclerostin in Dmp1-expressing cells reverses the osteopenia
induced by vinculin loss. a 3D reconstruction from µCT scans of tibia from
3-mo-old male control and cKO mice treated with or without tibial loading
experiment. Scale bar, 250 µm. b H/E staining of tibial sections of 3-mo-old control
and cKO mice were treated with or without tibial loading experiment. Scale bar, 200
µm. c-e Quantitative analyses of BV/TV Ct.Th and BMD. Results were expressed as
mean ± s.d., N = 7 biologically independent replicates per group, *P < 0.05, **P <
0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. f-h Calcein
double labeling. Representative images of femur sections (f). Sections were used for
measurements of mineral apposition rate (MAR). Quantitative MAR data for
metaphyseal trabecular bones (g) and bone formation rate (BFR) (h). Scale bar, 50 µm. . CC-BY 4.0 International license
perpetuity. Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone formation in mice. a 3D reconstruction from µCT scans of tibiae from 3-mo-old
male control and cKO mice treated with or without tibia loading experiment. Scale
bar, 100 µm. b H/E staining of tibial sections of 4-mo-old control and cKO mice were
treated with or without tibia loading experiment. Scale bar, 200 μm. c-e Quantitative
analyses of BV/TV, Ct.Th and BMD. Results were expressed as mean ± s.d., N = 7
biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls,
two-way ANOVA. f-h Calcein double labeling. Representative images of tibial
sections (f). Sections were used for measurements of MAR and BFR for metaphyseal . CC-BY 4.0 International license
perpetuity. It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
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bioRxiv preprint trabecular bones. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 5
biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls,
two-way ANOVA. i-m TRAP staining. Tibial sections of 4-mo-male control and cKO
mice were used for TRAP staining (i). Oc.S/BS) (j, k) and Oc.N/BPm (l, m) of
primary and secondary cancellous bones were measured using Image-Pro Plus 7.0. Scale bar, 50 μm. Results were expressed as mean ± s.d., N = 6 biologically
independent replicates per group, *P < 0.05 versus controls, two-way ANOVA. Figure 7. Estrogen controls vinculin expression in osteocytes and vinculin cKO
mice are resistant to OVX-induced bone loss. a, b IF staining. Tibial sections of
sham and OVX mice with an anti-vinculin antibody, Scale bars: 50 µm. Qauntitative
data (b). N = 6 biologically independent replicates per group, **P < 0.01, versus
controls, two-way ANOVA. c-d Western blot analysis. MLO-Y4 cells were treated
with increasing concentration of estrogen or fulvestrant (an estrogen receptor
antagonist) for 24 h. Gapdh was used as a loading control. Quantitative data from
three biologically independent replicates. Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone ;
https://doi.org/10.1101/2022.11.09.515817
doi:
bioRxiv preprint Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers
Name
5’ primer
3’ primer
Vcl
GCTTCAGTCAGACCCATACTCG
AGGTAAGCAGTAGGTCAGATGT
Gapdh
CAGTGCCAGCCTCGTCCCGTAG
A
CTGCAAATGGCAGCCCTGGTGAC
Sost
AGCCTTCAGGAATGATGCCAC
CTTTGGCGTCATAGGGATGGT
Supplementary Table 2: Antibody information
Antibody
Company
Catalog #
Application/Dilution
Mef2c
Proteintech
10056-1-AP
WB (1:2000) IF (1:200)
talin-1
Proteintech
14168-1-AP
WB (1:1000) IF (1:200)
vinculin
Proteintech
66305-1-Ig
WB (1:1000) IF (1:200)
active b-catenin
CST
8814S
WB (1:2000)
b-catenin
CST
9562S
WB (1:1000)
lamin b1
CST
13435s
WB (1:1000)
Flag-Tag
CST
14793S
WB (1:1000)
HA-Tag
CST
3724S
WB (1:1000)
pinch1
Abcam
ab108609
WB (1:1000), IF (1:200)
b1 integrin
Abcam
ab95623
WB (1:1000), IF (1:200)
sclerostin
Abcam
Ab63097
WB (1:1000), IHC (1:200)
phalloidin-488
Invitrogen™
A12379
IF (1:500)
tubulin
ZSGB-BIO
TA-10
WB (1:1000)
Gapdh
ZSGB-BIO
TA-08
WB (1:1000) Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone Results were expressed as mean ± s.d., *P <
0.05 versus control. f 3D reconstruction from µCT scans of femurs from 5-mo-old
control and cKO female mice performed with sham or OVX surgeries. Scale bar, 250
µm. g-i Quantitative analyses of the BV/TV, Ct.Th and BMD. Results were expressed
as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P <
0.01 versus controls, two-way ANOVA. g H/E staining of tibial sections. Scale bar,
200 μm. k-m Calcein double labeling. Representative images of 3-mo-old male femur . CC-BY 4.0 International license
perpetuity. It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
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bioRxiv preprint . CC-BY 4.0 International license
perpetuity. It is made available under a
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bioRxiv preprint sections (k). Sections of non-demineralized femurs were used for measurements of
MAR and BFR for the metaphyseal trabecular bones. Scale bar, 50 µm. Results were
expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P <
0.05 versus controls, two-way ANOVA. n-r TRAP staining. Tibial sections of
3-mo-male control and cKO mice were used for TRAP staining (n). Oc.S/BS (o, p)
and Oc.N/BPm (q, r) of primary (o, q) and secondary (p, r) cancellous bones were
measured using Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as
mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P <
0.01 versus controls, two-way ANOVA. . CC-BY 4.0 International license
perpetuity. It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
The copyright holder for this
this version posted November 10, 2022. ;
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doi:
bioRxiv preprint . CC-BY 4.0 International license
perpetuity. It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
The copyright holder for this
this version posted November 10, 2022. Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers
Name
5’ primer
3’ primer
Vcl
GCTTCAGTCAGACCCATACTCG
AGGTAAGCAGTAGGTCAGATGT
Gapdh
CAGTGCCAGCCTCGTCCCGTAG
A
CTGCAAATGGCAGCCCTGGTGAC
Sost
AGCCTTCAGGAATGATGCCAC
CTTTGGCGTCATAGGGATGGT Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers
Name
5’ primer
3’ primer
Vcl
GCTTCAGTCAGACCCATACTCG
AGGTAAGCAGTAGGTCAGATGT
Gapdh
CAGTGCCAGCCTCGTCCCGTAG
A
CTGCAAATGGCAGCCCTGGTGAC
Sost
AGCCTTCAGGAATGATGCCAC
CTTTGGCGTCATAGGGATGGT Supplementary Table 2: Antibody information
Antibody
Company
Catalog #
Application/Dilution
Mef2c
Proteintech
10056-1-AP
WB (1:2000) IF (1:200)
talin-1
Proteintech
14168-1-AP
WB (1:1000) IF (1:200)
vinculin
Proteintech
66305-1-Ig
WB (1:1000) IF (1:200)
active b-catenin
CST
8814S
WB (1:2000)
b-catenin
CST
9562S
WB (1:1000)
lamin b1
CST
13435s
WB (1:1000)
Flag-Tag
CST
14793S
WB (1:1000)
HA-Tag
CST
3724S
WB (1:1000)
pinch1
Abcam
ab108609
WB (1:1000), IF (1:200)
b1 integrin
Abcam
ab95623
WB (1:1000), IF (1:200)
sclerostin
Abcam
Ab63097
WB (1:1000), IHC (1:200)
phalloidin-488
Invitrogen™
A12379
IF (1:500)
tubulin
ZSGB-BIO
TA-10
WB (1:1000)
Gapdh
ZSGB-BIO
TA-08
WB (1:1000) Figure 1 vinculin
DAPI
Merged H&E
MLO-Y4(WT) KD-1 KD-2
talin
intergrin β1
Phalloidin
DAPI
Merged
KD-2 KD-1 MLO-Y4(WT)
vinculin/DAPI
Aged Aged
Young Young
a
c
b
d
e
f
vinculin
talin
integrin β1
Gapdh
pinch1
con KD-1 KD-2
**
**
***
**
NS
NS
100kD
pinch1
310kD
75kD
35kD
45kD MLO-Y4(WT) KD-1 KD-2
talin
intergrin β1
vinculin/DAPI
d
pinch1 vinculin
DAPI
Merged H&E
Aged Aged
Young Young
a d d a KD-2 Aged b c
b
e
vinculin
talin
integrin β1
Gapdh
pinch1
con KD-1 KD-2
**
100kD
310kD
75kD
35kD
45kD Phalloidin
DAPI
Merged
KD-2 KD-1 MLO-Y4(WT)
e Phalloidin
DAPI
Merged
MLO-Y4(WT)
e c e e f
**
***
**
NS
NS f
**
***
**
NS
NS f Figure 2 3m/male
14m/male
con cKO
con cKO
con cKO
a
b
e
14m 3m
con cKO
g
h
i
k
con cKO
f
**
***
**
***
**
**
NS
NS
Vinculin
Gapdh
Heart
Liver
Spleen
Lung
Kidney
con cKO
con cKO con cKO con cKO
con cKO con cKO
***
NS
NS
NS
NS
Cortical
bone
j
con
cKO
L5 L4
c
d
Figure 2
100kD
55kD
40kD
130kD a
b
Vinculin
Gapdh
Heart
Liver
Spleen
Lung
Kidney
con cKO
con cKO con cKO con cKO
con cKO con cKO
***
NS
NS
NS
NS
Cortical
bone
Figure
100kD
55kD
40kD
130kD b a 3m/male
14m/male
con cKO
con cKO
e
14m 3m
g
h
i
k
f
**
***
**
***
**
**
NS
NS
Vinculin
Gapdh
con cKO
con cKO con cKO con cKO
con cKO con cKO
***
NS
NS
NS
NS
j
con
cKO
L5 L4
c
d
100kD
55kD
40kD
130kD 3m/male
14m/male
con cKO
con cKO
e
i
f
**
***
**
***
NS
NS
j
con
cKO
c
d 14m/male
con cKO e
f
**
***
con
cKO
d d c 3m/male f f e e
i
f
**
***
NS
NS
j con cKO i **
j con cKO
14m 3m
con cKO
g
h
i
k
con cKO
**
**
j
L5 L4 h 14m 3m
g
h
con cKO
L5
L4 g k cKO cKO **
O
d
Figure 3 Figure 3 Figure 3 14m 3m
con cKO
a
b
c
**
**
**
**
**
con
cKO
con cKO
e
f
**
*
NS
cKO
con
cKO
con
CFU-F
CFU-OB
3m-con 3m-cKO 14m-con 14m-cKO
Primary cancellous
Secondary
cancellous
Primary
cancellous
Secondary cancellous
k
l
m
o
NS
NS
NS
NS
NS
NS
NS
NS
n
con
cKO
d
g
h
i
j
Figure 3 14m 3m
con cKO
a
b
c
**
**
**
**
**
con
cKO
con cKO
e
f
**
*
NS
cKO
con
cKO
con
CFU-F
CFU-OB
d
g
h
i
j
g b
c
**
**
**
**
**
con
cKO
e
d
g b d 14m 3m
con cKO
a a e con cKO
con cKO
e
f
**
*
NS
cKO
con
FU-F
CFU-OB
g
i
j con cKO
e
f
**
g *
g f g 14m cKO
con
CFU-F
h cKO
NS
j i j l l l
m
o
NS
NS
NS
NS
n
con
cKO k 3m-con 3m-cKO 14m-con 14m-cKO
Secondary
cancellous
Primary
cancellous
k m o n Secondary cancellous
o
NS
NS sclerostin
Gapdh
con cKO
Mef2c
vinculin
sclerostin
Gapdh
con Vcl-OE
a
b
c
d
f
g
IHC: sclerostin
e
Con
Vcl-OE
**
***
**
**
***
NS
con cKO
vinculin
Mef2c
sclerostin
Gapdh
WT si-NC
WT si-Mef2c
KD-1 si-NC
KD-1 si-Mef2c
KD-2 si-NC
KD-2 si-Mef2c
h
i
********
NS
NS
**
****
**
***
NS
j
vinculin
Mef2c
tubulin
lamin b1
WT CE
WT NE
KD-1 CE
KD-1 NE
KD-2 CE
KD-2 NE
KD-1CE
KD-1 NE
KD-2 CE
Vcl-OE
KD-2 NE
***
**
**
**
**
NS
l
Merged DAPI Mef2c vinculin
WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE
k
input
IgG
Mef2c
IP: Mef2c
IB: Mef2c
IB: vinculin
Flag
Flag-Mef2c
HA-Vcl
+
+
-
-
+
+
+
+
-
-
+
+
+
-
+
-
+
+
+
-
+
-
+
+
Input
IP(Flag)
IP(HA)
Input
IB:HA
Flag
Flag-Mef2c
HA-Vcl
IB:HA
n
o
p
**
*
Figure 4
m
NS
NS
NS
75kD
25kD
45kD
140kD
100kD
35kD
25kD
170kD
100kD
70kD
25kD
25kD
70kD
70kD
70kD
70kD
55kD
70kD
100kD
100kD
130kD
100kD
130kD
130kD Figure 4 sclerostin
Gapdh
con cKO
Mef2c
b
c
d
f
g
e
**
***
Figure 4
75kD
25kD
45kD b IHC: sclerostin d c a Con
Vcl-OE
**
***
D
D f vinculin
sclerostin
Gapdh
con Vcl-OE
f
g
e
C
V
**
**
***
NS
140kD
100kD
35kD
25kD e g sclerostin
Gapdh
***
NS
con cKO
vinculin
Mef2c
sclerostin
Gapdh
WT si-NC
WT si-Mef2c
KD-1 si-NC
KD-1 si-Mef2c
KD-2 si-NC
KD-2 si-Mef2c
h
i
********
NS
NS
**
****
**
***
NS
j
vinculin
Mef2c
tubulin
lamin b1
WT CE
WT NE
KD-1 CE
KD-1 NE
KD-2 CE
KD-2 NE
KD-1CE
KD-1 NE
KD-2 CE
Vcl-O
KD-2
***
**
**
**
**
NS
l
Merged DAPI Mef2c vinculin
WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE
k
input
IgG
Mef2c
IP: Mef2c
IB: Mef2c
IB: vinculin
Flag
Flag-Mef2c
HA-Vcl
+
+
-
-
+
+
+
+
-
-
+
+
+
-
+
-
+
+
+
-
+
-
+
+
Input
IP(Flag)
IP(HA)
Input
IB:HA
IB:Flag
Flag
Flag-Mef2c
HA-Vcl
IB:HA
IB:Flag
n
o
p
**
*
con cKO
active
β-catenin
β-catenin
Gapdh
q
m
NS
NS
NS
35kD
25kD
170kD
100kD
70kD
25kD
25kD
70kD
100kD
100kD
130kD
70kD
55kD
100kD
130kD
70kD
55kD
75kD
75kD
45kD
130kD i
********
NS
NS
**
****
**
***
NS j
vinculin
Mef2c
tubulin
lamin b1
WT CE
WT NE
KD-1 CE
KD-1 NE
KD-2 CE
KD-2 NE
KD-1CE
KD-1 NE
KD-2 CE
Vcl-OE
KD-2 NE
70kD
70kD
70kD
70kD
55kD vinculin
Mef2c
sclerostin
Gapdh
WT si-NC
WT si-Mef2c
KD-1 si-NC
KD-1 si-Mef2c
KD-2 si-NC
KD-2 si-Mef2c
h
170kD
100kD
70kD
25kD
25kD i h l ***
**
**
**
**
NS
l
Merged DAPI Mef2c vinculin
WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE
k
input
IgG
Mef2c
IP: Mef2c
IB: Mef2c
IB: vinculin
m
NS
NS
NS
25kD
70kD
100kD
130kD l ***
**
**
**
**
NS
k
NS
NS
NS k Merged DAPI M
input
IgG
Mef2c
IP: Mef2c
IB: Mef2c
IB: vinculin
m
70kD
100kD
130kD input
IgG
Mef2c
IP: Mef2c
IB: Mef2c
IB: vinculin
m
70kD
100kD
130kD m Flag
Flag-Mef2c
HA-Vcl
+
+
-
-
+
+
+
+
-
-
+
+
+
-
+
-
+
+
+
-
+
-
+
+
Input
IP(Flag)
IP(HA)
Input
IB:HA
IB:Flag
Flag
Flag-Mef2c
HA-Vcl
IB:HA
IB:Flag
n
o
p
100kD
130kD
70kD
55kD
100kD
130kD
70kD
55kD +
-
+
-
+
+
+
-
+
-
+
+
IP(Flag)
Input
Flag
Flag-Mef2c
HA-Vcl
IB:HA
IB:Flag
o
p
100kD
130kD
70kD
55kD
100kD
130kD
70kD
55kD o n p
**
* p con cKO
active
β-catenin
β-catenin
Gapdh
q
75kD
75kD
45kD con cKO
active
β-catenin
β-catenin
Gapdh
q
75kD
75kD
45kD q b
c
d
*
*
*
**
NS
**
***
***
**
*
fl
Figure 5 Figure 5 a
e
b
c
d
*
*
*
**
NS
**
**
**
**
***
NS
***
*
**
**
NS
*
NS
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl
Dmp1-Cre
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vcl fl/fl Sostfl/fl
*
**
*
**
NS
**
**
**
**
**
NS
***
i
*
*
*
**
NS
**
*
**
*
**
NS
**
Primary
cancellous
Secondary
cancellous
Primary cancellous
Secondary cancellous
l
p
n
o
m
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl
f
g
h
Figure 5
j
k a
b
*
*
*
**
NS
**
***
**
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl
Figure 5 b a
b
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl a Dmp1-Cre d c
d
**
**
**
***
NS
***
*
**
**
NS
*
NS e
Dmp1-Cre Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl c Dmp1-Cre Vclfl/fl e Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl **
**
**
**
NS
***
h f *
**
*
**
NS
**
**
**
**
**
NS
***
g
h h *
**
*
**
NS
**
g Dmp1-Cre
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vcl fl/fl Sostfl/fl
f g Sostfl/fl
mp1-Cre Vcl fl/fl Sostfl/fl f Dmp1-Cre
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vcl fl/fl Sostfl/fl Dmp1-Cre
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vcl fl/fl Sostfl/fl *
*
*
**
NS
**
*
**
*
**
NS
**
j
k j *
**
*
**
NS
**
k Dmp
i
Dmp1-Cre
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl k i p1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl Primary
cancellous
Secondary
cancellous
l
Dmp1-Cre Dmp1-Cre Vcl
Dmp1-Cre Sost
Dmp1-Cre Vcl
Sost
Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/ l p
n
o
m
NS
NS
NS
NS
NS
NS m o p p
NS
NS
NS p
o
NS
NS
NS
l/fl P i
Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl
Dmp1-Cre Sostfl/fl
Dmp1-Cre Vclfl/fl Sostfl/fl Figure 6 Figure 6 Primary cancellous
Secondary cance
con
cKO
sham loading
con+sham
cKO+sham
cKO+loading
con+loading
Primary
cancellous
Secondary
cancellous
con+sham
con+loading
cKO+sham
cKO+loading
con+Sham
con+loading
cKO+sham
cKO+loading
a
e
b
c
d
f
g
h
i
j
k
l
m
sh
loa
**
*
*
*
NS
NS
*
*
*
NS
NS
NS
*
**
*
*
NS
*
NS
NS
NS
NS
NS
NS b
sham
loading
*
*
NS b a con+sham
con+loading
cKO+sham
cKO+loading
con+Sham
con+loading
cKO+sham
cKO+loading
a
e
b
c
d
*
*
*
NS
NS
*
*
*
NS a c
d
*
NS
*
* c d e d
*
*
NS con
cKO
sham loading
f
g
h
**
NS
NS
*
**
* h
NS
**
* f h g Primary cancellous
Secondary cancellous
sham loading
con+sham
cKO+sham
cKO+loading
con+loading
Primary
cancellous
Secondary
cancellous
i
j
k
l
m
*
NS
*
NS
NS
NS
NS
NS
NS Prim
g
con+sham
cKO+sham
cKO+loading
con+loading
Primary
cancellous
Secondary
cancellous
i
j
l
*
N i j k j
k
l
m
*
NS
NS
NS
NS Secondary cancellous
m
NS
NS Secondary cancellous Estrogen
Control
10 -10
10 -9
10 -8
10 -7
vinculin
Gapdh
Fulvestrant
Control
10 -9
10 -8
10 -7
10 -6
c
b
d
e
**
**
**
130kD
100kD
40kD
35kD
Figure 7 Estrogen
Control
10 -10
10 -9
10 -8
10 -7
vinculin
Gapdh
Fulvestrant
Control
10 -9
10 -8
10 -7
10 -6
c
130kD
100kD
40kD
35kD
Figure 7 Figure 7 Estrogen
Control
10 -10
10 -9
10 -8
10 -7
vinculin
Gapdh
sham
con+Sham
con+OVX
cKO+Sham
cKO+OVX
con+OVX
con+sham
cKO+sham
cKO+OVX
Fulvestrant
Control
10 -9
10 -8
10 -7
10 -6
vinculin
DAPI
Merged
con+Sham
con+OVX
cKO+sham
cKO+OVX
Secondary
cancellous
Primary
cancellous
a
c
b
f
OVX
h
sham
OVX
k
l
n
o
p
q
r
d
g
e
**
**
**
** *
*
** **
NS
** **
NS
NS
*
*
** **
NS
j
m
NS
NS
NS
NS
NS
NS
NS
NS
i
130kD
100kD
40kD
35kD
Figure 7 sham
vinculin
DAPI
Merged
a
OVX a a c c d b
d
e
**
**
** b e f g h
sham
OVX
g
** *
*
i con+Sham
con+OVX
cKO+Sham
cKO+OVX
con+Sham
con+OVX
cKO+sham
cKO+OVX
f
h
sham
OVX
g
** *
*
** **
NS
j
NS
NS
i cKO+OVX
cKO+OVX h
** **
NS h
** **
NS
N
i h
** **
NS
NS
NS
i h j i l
m
NS
NS
NS
NS l k m o
p
q
r
** **
NS o
p
q
r
** **
NS
** **
NS p
r
** **
NS Con+OVX
Con+Sham
cKO+Sham
cKO+OVX
Secondary
cancellous
Primary
cancellous
n p o n q r q
r
NS
*
*
Primary cancellous r
NS
NS
Secondary cancellous Secondary
cancellous Figure 8 Vinculin (+) Bone formation
Bone formation
Vinculin (+)
Vinculin ( ) Bone formation Bone formation Bone formation Bone formation Bone formation |
W2032190068.txt | http://informesdelaconstruccion.revistas.csic.es/index.php/informesdelaconstruccion/article/download/1062/1139 | en | Un nuevo camino en Santiago, el periférico de Compostela | Informes de la construcción | 1,995 | cc-by | 4,473 | UN NUEVO CAMINO EN SANTIAGO, EL PERIFÉRICO
DE COMPOSTELA
(A NEW ROAD IN SANTIAGO, THE COMPOSTELA RING ROAD)
Angel González del Rio
Ingeniero Director de las obras de la Demarcación de Carreteras del Estado en Galicia. MOPTMA
ESPAÑA
Fecha de recepción: 12-VI-95
511-3
RESUMEN
SUMMARY
Se presentan los planteamientos de planificación, proyecto y
obra del nuevo periférico de Santiago recientemente puesto en
The article presents the approaches to planning, design and
work execution of the new Santiago ring road, recently open
for traffic.
Las peculiaridades históricas, artísticas, culturales y
medioambientales de la ciudad, han exigido desarrollar un
proyecto especialmente respetuoso con su entorno humano,
urbano y natural.
The historical, artistic, cultural and environmental
peculiarities of Santiago called for the development of a
project that would respect with particular care the city's
human, urban and natural surroundings.
1. Aspectos más destacables del marco institucional
Las bases fundamentales del Convenio son las siguientes:
El 18 de noviembre de 1991 sefirmael Convenio entre el
Ministerio de Obras Públicas, Transportes y Medio
Ambiente y el Ayuntamiento de Santiago de Compostela.
Se trata del punto de partida para un ambicioso plan
sectorial y urbanístico que de una forma integrada sienta
las bases para un profunda transformación de la ciudad de
Santiago de Compostela.
a) Ejecución del nuevo periférico de la ciudad en 7 tramos
que han de conectar las carreteras nacionales N-550 (La
Coruña-Vigo y Tuy), N-634 (Santiago-San Sebastián) y
N-525 (Zamora-Orense-Santiago), así como los tres enlaces de la Autopista A-9 con la ciudad.
Dentro del período 91-99 en el que se desarrolla la
planificación existen dos años clave que enmarcan las
actuaciones, los Años Jubilares 93 y 99.
Las especiales connotaciones históricas y culturales, el
crecimiento que experimenta la ciudad al convertirse en
capital de Galicia y el año Santo Jacobeo 1993 conforman
referencias obligadas al concertar actuaciones.
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b) Desarrollo de acciones de ampliación y remodelación
del Aeropuerto de Labacolla.
c) Ejecución de la Autovía Santiago-Aeropuerto
d) Coordinación entre administraciones para la correcta
acomodación de las nuevas infraestructuras al planeamiento urbanístico en vigor.
e) Desarrollo del Convenio RENFE-Ayuntamiento, bajo
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20
Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
tutela del MOPTMA, desarrollándose diversas actuaciones
de remodelación en las estaciones de Cornes y La Sionlla.
f) Actuaciones en materia de rehabilitación de la ciudad
histórica y programas medioambientales.
g) Tratamientos de borde de las nuevas infraestructuras,
al objeto de acomodarlas e integrarlas en el tejido urbano.
El 11 de octubre de 1993 se firma un protocolo entre la
Secretaría General para las Infraestructuras y el
Ayuntamiento de Santiago que desarrollaba este último
punto concretando actuaciones urbanísticas de borde urbano que afectaban a distintos barrios de Santiago, que de este
modo se integraban al nuevo eje de comunicación y desarrollo que constituye el Periférico de la ciudad.
nuevas viviendas, el pabellón deportivo del Sar y los
barrios tradicionales de Porto, Poza Real, Rocha Vella,
Conxo, Castifíeirifío, Lamas de Abad, Viso, San Lázaro y
Amio.
Santiago se articula ya, en torno a su periférico. La nueva
vía de 10,5 km con 15 enlaces y 700 m de distancia media
entre enlaces, que permite a Santiago, por un lado, superar
sus límites tradicionales, abriendo nuevos espacios y
perspectivas y, por otro, recoge e integra en la ciudad sus
barrios periféricos y sus nuevos equipamientos culturales
y deportivos.
En la figura 1 se detalla el modo en el que se implanta el
trazado del periférico en el territorio. Su alineación,
formando un gran arco al este de la ciudad, constituye un
tercer eje infraestructural, sumándose así a la autopista del
Atlántico y al ferrocarril La Coruña-Santiago-Vigo.
2. Antecedentes del periférico
Los antecedentes del periférico de Santiago han sido dos
básicamente.
1.- La Red Arterial del MOP de 1972
2.- El Plan General de Ordenación Urbana de 1989
La red arterial del MOP planteada en 1972, partía de
viarios y planificaciones urbanísticas que difieren
sustancialmente de las actuales, con algunos aspectos
comunes, como sucedía con el trazado del tramo CornesChoupana (Ronda Sur) que enlaza N-525 y N-550. La
encendida polémica que surgió entre el planeamiento
sectorial viario y los planes de ordenación de la época,
supuso la inviabilidad de la red arterial propuesta entonces.
El PGOU de 1989 supuso un nuevo marco urbanístico para
Santiago, contemplándose como sistemas generales de
comunicación los suelos destinados a albergar el nuevo
periférico
Fig. ].- El Periférico de Santiago.
3. ¿Qué es el periférico?
El nuevo periférico de Santiago, es una vía segura de alta
capacidad y accesibilidad a la trama urbana, que permite
descongestionar los tráficos que afectan al centro histórico
de la ciudad y conexionar entre sí las carreteras nacionales
N-550, N-634, N-525 y mejorar los accesos de la autopista
A-9 en sus distintos enlaces urbanos.
El nuevo vial viene a resolver además los graves problemas
de accesibilidad que sufrían el polígono industrial del
Tambre, en fiíerte proceso expansivo, el nuevo Palacio de
Congresos con capacidad para L 500 congresistas instalado
en S. Lázaro, el estadio multiusos de S. Lázaro con
capacidad para 12.000 espectadores, el centro de acogida
de peregrinos ubicado en el Monte del Gozo, el polígono de
Fontiñas que alberga un gran centro comercial y 4.000
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%
Fig. 2.- Una vista panorámica de los 3 ejes de infraestructuras: A-9,
ferrocarril y periférico.
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21
Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
En la figura n° 2 se aprecian estos tres grandes ejes de
infraestructuras, que son atravesados por el río Sar en
distintos puntos.
El periférico, es por otra parte susceptible de ser cerrado
completamente por el Oeste como anillo de circunvalación
en un futuro próximo, recogiendo las carreteras autonómicas de Noya (salida hacia las playas) y San Comba, si bien,
existen suelos de especial protección en el entorno del
Monte Pedroso que condicionan las posibles soluciones de
trazado.
'4
Los seis objetivos del periférico son:
1) Creación de una infraestructura segura y cómoda que
mejore la movilidad de Santiago y su entorno para tráficos
internos y externos.
Pig. J.- Enlace del Polígono Industrial del tambre.
2) Permitir un desarrollo urbano planificado y ordenado.
3) Mejorar la calidad-ambiental del casco Histórico,
drenando tráficos hacia la nueva red viaria.
4) Proporcionar conexiones con la malla urbana en los
polígonos industriales, barrios tradicionales, nuevas zonas residenciales y equipamientos culturales, deportivos,
comerciales y sanitarios.
5) Establecer la conexión de la red planificada con el
sistema nacional de carreteras del Estado y Autopistas. De
este modo quedaban interconectadas la N-550 (La Coruña,
Pontevedra, Vigo y Tuy), N-634 (Oviedo), N-547 (Lugo)
y N-525 (Orense), así como los tres enlaces de la A-9 en
Santiago.
6) Lograr que la obra respetase el equilibrio ambiental y
conseguir unos acabados y calidades acordes con la ciudad
en la que se integra.
Fig. 4.- Enlace con la A-9 (Norte).
4. El periférico tramo a tramo
A modo de rápido viaje de Norte a Sur a través de la nueva infraestructura, pasaremos sobre los cinco tramos puestos
en servicio el pasado 31 de enero de 1995 y los dos que
actualmente se hallan en ejecución comentando sus aspectos más singulares.
].- Polígono del Tambre-San Lázaro
El tramo une el polígono industrial del Tambre y la N-550
con el enlace Santiago Norte de la Autopista A-9 y la N-634
(Oviedo, Lugo).
Los aspectos particulares reseñables del tramo son:
-Se produjo una afección parcial de los taludes del antiguo
vertedero municipal de basuras, motivando especiales
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medidas correctoras del impacto visual mediante
plantaciones.
-Enlace periférico- Pohgono del Tambre. Resuelto mediante
un trébol completo.
-Especial tratamiento de los fondos de excavación en la
zona denominada "Brañas del Sar" (zona inundable en la
que nace el río Sar) con sustitución de los dos primeros
metros de fango y aportación de piedra sana a efectos de
cimentar la nueva infraestructura.
-Enlace periférico - A-9 (Norte). Resuelto mediante un
diamante con glorieta superior. Esta tipología de enlace ha
sido la adoptada con carácter general eatodo el periférico,
por las ventajas que presentaba en Guanto a seguridad,
sencillez, capacidad y pequeña demanda de suelo frente a
otras tipologías. De este modo la movilidad sobre el
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22
Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
periférico no queda interrumpida en los enlaces y los
tráficos genuinamente locales se resuelven en laglorieta en
un nivel diferente, quedando así jerarquizado el viario. Las
estructuras son dos losas postesadas de 24,2 m de longitud
y 11,50 m de ancho, cuya planta es una corona circular de
45 m de radio interior.
-El barrio de S. Lázaro es atravesado con una rasante
deprimida entre muros que evita impactos visuales y de
ruidos. El enlace de S. Lázaro, análogo al anterior enlaza
con la N-634 (Oviedo), N-547 (Lugo) y el aeropuerto
internacional de Labacolla.
Fig. 6.- Detalle de los muros ilustrados con motivos Jacobeos.
- Se ha tenido especial atención en el cuidado de la reposición
del Camino de Santiago (Camino Francés) en su paso por
S. Lázaro, disponiendo aceras y acabados de muros con
pizarra de Santiago, que dignifican tan insigne itinerario.
-En los distintos muros ejecutados buscamos lograr una
gran calidad constructiva y estética, compatible con la
rapidez de ejecución. Diseñamos así, sobre la base de los
muros prefabricados texturizados, un sencillo elemento
que es la tradicional concha del peregrino, buscando que el
usuario del periférico tuviera la sensación inequívoca de
hallarse en Compostela.
Además, dicho símbolo, que sirve para señalizar los
distintos Caminos hacia Santiago, cumple esta misma
misión específica sobre los alzados de los muros del
periférico, indicando al usuario como acceder a la universal plaza del Obradoiro
2. - San Lázaro-Fontiñas Sur
El tramo une N-634 y N-550 (Avda. de Lugo),
proporcionando accesibilidad a los nuevos equipamientos culturales y deportivos de la ciudad, así como al polígono residencial de Fontiñas.
Se podrían destacar como aspectos más interesantes del
tramo, los siguientes:
-En cuanto al medio físico y su geología, la traza se asienta en las inmediaciones del cauce del río Sar, con predominio
en el sustrato rocoso de esquistos, anfibolitas y suelos limoarcillosos, procedentes de la alteración de dicho substrato.
Una constante del tramo fue la gran heterogeneidad del
material, pasándose de zonas rocosas a zonas arcillosas sin
material de tránsito. Dicha heterogeneidad se puso de
manifiesto al acometer la cimentación de la estructura del
enlace del estadio de fútbol de la S.D. Compostela, donde
el estribo Sur se ejecutaba con cimentación directa y el
estribo Norte con cimentación indirecta, mediante pilotes
in situ de 1,50 m y 20 m de profundidad, quedando la
cimentación de las pilas intermedias en cotas
aproximadamente interpoladas entre ambos valores.
''-^50
-Dicho enlace, proporciona acceso al estadio de la S.D.
Compostela (S. Lázaro), al nuevo Palacio de Congresos
con capacidad para más de 1.500 personas y al vial que
comunica con el recinto del Monte del Gozo, donde se
ubica el centro de acogida de peregrinos.
Fig. 5.- Enlace de San Lázaro.
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Licencia Creative Commons 3.0 España (by-nc)
En este caso, el tronco del periférico pasa sobre la glorieta
inferior, uniéndose a ella mediante un dimnante completo,
construyéndose una losa postesada de tres vanos y 80 m de
luz total, ejecutándose los dos tableros separados para
http://informesdelaconstruccion.revistas.csic.es
23
Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
Fig. 7.- Tramo San Lázaro-Fontiñas Sur.
realizar, posteriormente, la unión de ambos para que
tengan un comportamiento resistente solidario. En el
acceso al Monte del Gozo se ejecutó una estructura mixta
formada por un cajón metálico de acero corten y losa
superior en un solo vano de 40 m que salva el río Sar y el
Ferrocarril.
-Las arcillas de la traza en este tramo tenían una elevada
plasticidad, lo cual, unido alrigorclimatológico de Santiago,
ha impedido su puesta en obra.
-El enlace de Pontifias, sobre el que D. Pernando da Cunha
Rivas, Ingeniero Autor del Proyecto, ha escrito un artículo
específico dentro de este número especial dedicado a
Santiago, es una bella, diáfana yfiíncionalrealización, que
resuelve con elegancia, en un exiguo espacio entre el
ferrocarril y el propio polígono ,el acceso a Pontifias, donde
se ubican en simbiosis urbana usos residenciales (4.000
viviendas), administrativos (nuevos juzgados y
dependencias de la Xunta), deportivos (nuevo pabellón
deportivo y piscinas del Sar) y comerciales (Área Central).
Fig. 8.- Enlace multiusos de San Lázaro.
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Licencia Creative Commons 3.0 España (by-nc)
Por su ubicación, permeabilidad visual y solución
constructiva, el enlace de Pontifias se convierte en uno de
los elementos singulares del periférico. Su permeabilidad
transversal fue condicionante básico de disefio al efecto de
no introducir labarrera visual que hubiera supuesto ejecutar
muros y terraplenes entre las zonas de^ar (donde se halla
la joya románica de la Colegiata de Sar) y Pontifias. La
http://informesdelaconstruccion.revistas.csic.es
24
Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
estructura de la glorieta superior es una losa pretensada
con planta de corona circular de 18,25 m de radio en el eje
y 11,40 m de anchura transversal. El ramai permeabilizado,
es una losa pretensada de 117 m de longitud total y 7,10 m
de anchura. Los pilares en V, dispuestos perimetralmente,
contribuyen decisivamente al airoso resultado de la
estructura.
-La construcción de las nuevas piscinas y pabellón del Sar
a las que habíamos de proporcionar acceso, unido a la
barrera urbanística que suponía el terraplén existente del
ferrocarril La Coruña-Santiago-Vigo en la zona de Sar,
hizo que nos decantásemos por la solución de construir un
paso inferior de hormigón armado por empuje oleodinámico de grandes dimensiones ( 15 m de gálibo horizontal, 5 m
de gálibo vertical y 24 m de longitud, para salvar el
terraplén RENFE). El empuje lo proporcionaron 24 gatos
de 200 t, con un esfuerzo máximo de empuje de 3.2301 y
el peso propio de la estructura (2.430 t). Fue necesario
sobredimensionar la potencia máxima de empuje para
repartir mejor las cargas y aliviar los esfuerzos en el muro
de reacción, a efectos de no correr riesgos de rotura del
sistema de tuberías existentes de pluviales y saneamiento
de Fontiñas, que estaban bajo el cajón, quedando así,
desafectadas. Se procedió al empuje del cajón, vaciando
simultáneamente el terraplén de la vía, no siendo preciso
alterar los tráficos ferroviarios en ningún momento.
POUGONO DE
Fig. 10.- Cajón empujado bajo FFCC. La Coruña-Vigo.
,^^^^#
FOirriÑAS
Fig. 11.- Enlace avda. de Lugo.
-Finalizaba este tramo con el enlace con la N-550 en su
tramo urbano conocido como avda. de Lugo. El periférico
enlaza así con la antigua ronda, cuya sección transversal
también se remodela y ensancha .
Fig, 9.- Enlace de Fontiñas.
(c) Consejo Superior de Investigaciones Científicas
Licencia Creative Commons 3.0 España (by-nc)
El enlace de la avda. de Lugo, se realiza deprimiendo entre
muros el tronco del periférico, quedando la glorieta en el
plano superior, coincidente con la rasante existente de la
antigua circunvalación. La estructura es^na losa postesada,
con planta de semi-corona circular apoyada en tres estribos.
http://informesdelaconstruccion.revistas.csic.es
25
Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
3.-Ampliaciónde laAvda. de Lugo (Fontiñas Sur-Cornes)
Se trata del único tramo del periférico, en el que se
aprovechael tramo existente, ampliándosey reordenándose
la sección transversal, dotada de tres carriles por sentido,
con aparcamientos y amplias aceras.
Actualmente se halla en fase de ejecución, estando prevista su puesta en servicio en Otoño de 1996. Incluye como
obras singulares:
-Resolver la afección del talud de Bellvis, sobre el que se
halla el Seminario Menor de Santiago ,mediante la técnica
del ''talud claveteado", con bulones de 4-5 m, gunitado y
revestimiento.
Fig. 13.- Glorieta de Conxo.
-Ejecutar en voladizo parte de la calzada y acera en el
entorno de la estación de ferrocarril de Cornes.
-Glorieta en Conxo para conectar dicho barrio con el
periférico.
-Construcción de un nuevo enlace en Sar que permitirá
efectuar un by-pass entre tráficos N-5 25/N-5 5 O desafectando la glorieta de Cornes, que es el punto con mayor carga
de tráfico de Santiago (IMD=45.000), ejecutando un cajón
empujado bajo el haz de vías.
-Se construyen dos importantes permeabilizaciones en el
Pajonal y Torrente resueltas con losas postesadas de 125 m
y 140 m, donde el PGOU desarrollará fiituros viales y zonas verdes.
4. - Comes - Choupana
Finaliza el tramo en el nudo de La Choupana, resuelto
mediante un diamante con glorieta superior. Su amplio
Este tramo del periférico es prácticamente idéntico al que
ya recogía el estudio de la Red Arterial de 1972 del MOP.
Enlaza la N-525 (Zamora-Orense-Vigo) y la N-550
(Pontevedra), atravesando el tradicional barrio de Conxo.
Sus nudos y aspectos más destacables son:
-Nueva glorieta de Cornes que recoge los tráficos de la
antigua N-525 y la c/ Romero Donallo, actual salida hacia
la Universidad, Noya y playas. Hay que significar que la
Xunta de Galicia está desarrollando el proyecto La RochaVidán, nuevo tramo del periférico que permitirá enlazar la
N-550 (Pontevedra) con la C-543 (Noya).
-Nuevo enlace con el tramo del periférico CornesCastifíeiriño que constituirá la nueva salida hacia Orense
(N-525).
Fig. 12.- Glorieta de Comes.
(c) Consejo Superior de Investigaciones Científicas
Licencia Creative Commons 3.0 España (by-nc)
Fig. 14.- Imagen virtual del Enlace de la Choupana (arriba). Enlace de
la Choupana (abajo).
http://informesdelaconstruccion.revistas.csic.es
26
Momies de la Constnicción, Vol. 47, n° 438, julio/agosto 1995
campo visual hizo que estudiásemos muy especialmente el
diseño de este enlace, realizando distintas imágenes virtuales que nos permitieron optimizar la solución.
En este nudo queda prevista con un paso inferior la futura
conexión con la carretera autonómica C-543 a Noya.
-Fue tratada especificamente la reposición del itinerario
peatonal relativo al Camino Portugués hacia Santiago.
5.- Choupana - A-9
Este tramo es una adaptación de la sección tipo de la
antigua carretera de 2 carriles N-550, a la nueva del
periférico.
Las singularidades más destacadas del tramo son las
siguientes:
-Se ha ampliado el antiguo Puente de la Rocha en la N-550
(Pontevedra), que salva una pronunciada vaguada de unos
260 m sobre el río Sar. Es una obra singular dentro del
periférico, que ha precisado idear un original sistema
constructivo para poder ampliar la sección transversal,
desde 10 m a 22 m, sin afectar el tráfico del acceso desde
Pontevedra y Vigo a Santiago (IMD=22.000). En un
articulo especifico dentro de esta misma revista, D. José
Antonio Barbosa Ayúcar, Ingeniero proyectista y Jefe de
Obra de Dragados, explica detalladamente la génesis y
desarrollo de la técnica aplicada en esta obra, realizada con
elementos prefabricados (dinteles, soportes y vigas).
6.- Castiñeiriño-Comes
-Supone el desarrollo del nuevo acceso de laN-525 (OrenseSantiago) a Compostela, totalmente en variante.
-En el nudo de Cornes se dispone un paso inferior para los
vehículos que saldrán hacia Orense.
-Posteriormente, para salvar las vías del tren y la vaguada
existente entre Cornes y el Monte do Xeixo, proyectamos
un gran viaducto de 450 m, que salvaba la vaguada y las
vías del ferrocarril Santiago-Vigo y Santiago-Orense, y
que se bifurcan en este punto, con gran esviaje respecto al
trazado del nuevo vial. La estructura se rechaza en 15 vanos isostáticos de 30 m de longitud, con vigas artesa y
cimentaciones directas, generalmente.
-Finalmente, el tramo llega al Castiñeiriño, barrio
tradicional de Santiago que se salva con un paso inferior,
para evitar impactos visuales y de ruidos en el barrio,
resolviéndose en la glorieta superior los tráficos urbanos.
-Se construyeron también nuevas conexiones con los barrios
de Rocha Vella y Porto, mejorando el control de dichos
accesos.
Fig. 16.- Virtualización del Enlace de Castiñeiriño (N-525).
Fig. 15.- El Puente de la Rocha, tras la colocación de dinteles.
(c) Consejo Superior de Investigaciones Científicas
Licencia Creative Commons 3.0 España (by-nc)
Fig. 17.- Tramo Castiñeiriño -A-9.
http://informesdelaconstruccion.revistas.csic.es
27
Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
7. - Castiñeiriño-A -9
Tramo que concluye el nuevo vial de acceso a Santiago de
laN-525 (Orense - Santiago). Este tramo, continuación de
la Variante Cornes-Castiñeiriño, supuso la readaptación
de la antigua N-525 a la nueva sección del periférico,
resolviendo el control de accesos.
Las peculiaridades del tramo ñieron:
-Generar un enlace en trompeta con el núcleo de Lamas de
Abad y centros escolares de la zona.
-Disponer una nueva conexión con la A-9 (enlace N-525).
-Mejorar el control de accesos, generando vías de servicio.
-Ampliación del puente sobre el ff.cc. Santiago-Orense,
adaptándolo a los gálibos prescritos por RENFE.
5. Aspectos generales
-La cifra de inversión final del periférico se sitúa en 10.000
millones, de los cuales 7.000 millones corresponden a la
ejecución de la infraestructura ( 700 millones/km), 2.000
millones para expropiación (200 millones/km), 1.000
millones para los servicios afectados ( 100 millones/km).
-La sección tipo del periférico es uniforme, incluyendo
firme drenante, barrera rápida y luminarias con báculos
dobles de 9 y 12 m, con lámparas de VASP de 25 OW. En
glorietas hemos preferido la solución de iluminar con
torres de iluminación únicas de gran altura, centradas en
la glorieta frente a la iluminación perimetral, para facilitar
la percepción nocturna de los nudos.
-El capítulo de expropiaciones ha sido especialmente
dificultoso, afectando a 90 edificaciones (70 viviendas y 20
naves y talleres) y a 1.500 fincas, estando precedido de
intensos trabajos y de reuniones con los afectados, para
intentar resolver los problemas de sustitución de viviendas,
reclamaciones legales y económicas, coordinando los
plazos de ocupación de fincas y edificaciones, además de
los programas de trabajo de las distintas obras.
A modo de ejemplo, destacaría la solución adoptada de
forma conjunta para el modo de realojo que ñie adoptado
en el tramo Cornes-Choupana, donde los afectados por la
expropiación de sus casas actuaron con promotores de las
nuevas viviendas de sustitución, y que ñieron construidas
en una pieza de suelo urbanizable programado del barrio
de Conxo. Los expropiados consiguieron el suelo a través
de la firma de un convenio urbanístico que contemplaba la
permuta de superficies, en fiínción de las calificaciones
urbanísticas del PGOU.
-Los servicios afectados por el periférico han sido repuestos
de acuerdo con las secciones y demandas estimadas en el
año horizonte del PGOU. Se han enterrado las líneas para evitar impactos visuales y se han creado galerías de
servicios en los tramos en que se reordenaban y ampliaban
las secciones existentes.
-De los 7 tramos, cuatro de ellos son variantes, con control
total de accesos, y 3 tramos, readaptaciones de la sección
transversal ,en las que se han reordenado y restringido los
accesos.
-Las características geométricas son homogéneas en planta
y alzado con R
= 350 m y pendiente máxima del 5%,
salvo la rampafinal de subida del Polígono del Tambre, que
tiene un 6%.
-Se ha cuidado especialmente la corrección de impa tos
ambientales con plantaciones, hidrosiembras y pantallas
arbóreas, especialmente útiles en un clima como el de
Santiago, y tratamientos específicos de jardinería en cada
enlace o glorieta, siempre con instalaciones de riegos por
aspersión.
Q^y-c^:^-Cí,Q'^.
SECCIÓN TIPO
"•,V;V/-VtVo--:-r.Cv.\Cv.\C J^"*
A- Capa de rodadura drenante
B- Capa intermedia S-20
C- Base asfáltica G-25
D- Zaiiorra artificial
Fig. 18.- Sección tipo del Periférico.
(c) Consejo Superior de Investigaciones Científicas
Licencia Creative Commons 3.0 España (by-nc)
^*\' X, ^ ^ ^ ^ p
Fig. 19.- Viviendas de Conxo.
http://informesdelaconstruccion.revistas.csic.es
28
Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995
-Todos los trazados en planta y alzado fueron almacenados
en el ordenador de la Demarcación de Carreteras de Galicia del MOPTMA, permitiéndonos realizar ajustes, definir
con precisión y agilidad detalles, y lograr una adecuada
coordinación entre tramos.
6. Conclusiones
El recorrido a través del nuevo periférico de Santiago de
Compostela nos ha mostrado una solución de red arterial
urbana singular, que ha tratado de plantearse en consonancia con la propia singularidad de la ciudad.
Los nuevos viales constituyen un nuevo camino en Santiago,
que resolviendo los problemas específicos de accesibilidad
de los barrios periféricos de la ciudad y los nuevos
equipamientos urbanos, vienen también a ahviar las fuertes
tensiones creadas por el tráfico dentro del casco histórico.
Me gustaría significar el alto grado de colaboración entre
instituciones que se ha alcanzado en Santiago, que ha
hecho posible, en muy corto espacio de tiempo, desarrollar todos los estudios previos, proyectos de trazado,
construcción y ejecución de las obras.
Quisiera agradecer al gran equipo humano que ha trabajado en el periférico, en el que se han integrado la Demarcación
de Carreteras de Galicia del MOPTMA, el Ayuntamiento
de Santiago de Compostela y las empresas constructoras y
consultoras adjudicatarias de los distintos tramos, por el
generoso esfuerzo y la gran ilusión depositada al servicio
de la obra.
Publicación del Instituto Eduardo Torroja - CSIC
INSTITUTO DE CIENCIAS DE LA CONSTRUCCIÓN
EDUARDO TORROJA
La revista MATERIALES DE CONSTRUCCIÓN, con periodicidad trimestral y dedicada
con exclusividad a la investigación científica y técnica *de la construcción y sus materiales, está editada por el INSTITUTO EDUARDO TORROJA, Centro dependiente del
Consejo Superior de Investigaciones Científicas. Constituye, desde hace cuarenta y
cinco años, un eficaz vehículo de transmisión de nuevos conocimientos científicos y técnicos en el campo de los materiales de construcción y de otros temas relacionados con
los mismos.
Prestigiosos científicos y técnicos de todo el mundo colaboran en su publicación; no obstante,
MATERIALES ha pretendido tener siempre una especial incidencia en el mundo investigador
y técnico en el ámbito internacional y, muy especialmente, en los países de habla hispana.
M
lATERÜ^LES
DE
C
ONSTRXJCCION
I C S I C l CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS
Conviene resaltar, una vez más, la importancia que tiene el desarrollo de los materiales
de construcción considerados tradicionales: el cemento y el hormigón, no sólo desde el
punto de vista técnico sino por la importancia social y económica que conlleva ese
desarrollo. Como muestra, se pueden recordar unas recientes declaraciones del doctor
Schartz, del Instituto Nacional de Normalización de Estados Unidos, en las que decía:
"La investigación del iiormigón supone un enorme potencial de mejora en ese campo.
Lo que se haya de invertir en los próximos veinticinco años, puede depender de una
pequeña inversión en el quinquenio inmediato."
La indudable interrelación de disciplinas y ámbitos ha aconsejado ampliar la línea editorial de MATERIALES a otros campos del conocimiento que no estaban suficientemente
recogidos. Por lo cual nuestra Revista incluye con mayor frecuencia artículos de investigación —e incluso de divulgación—, temas cuya importancia está siendo objeto de una
atención prioritaria tanto por las autoridades científicas de nuestro país, como por los
propios responsables de la política investigadora europea. Un ejemplo destacado son
los estudios sobre Restauración y Conservación del Patrimonio Histórico y, en general,
del Patrimonio Arquitectónico y de la incidencia del medio ambiente en el comportamiento de los materiales, tanto tradicionales como no tradicionales. Algunos de estos
artículos se publican en versión española e inglesa.
(c) Consejo Superior de Investigaciones Científicas
Licencia Creative Commons 3.0 España (by-nc)
http://informesdelaconstruccion.revistas.csic.es
| |
https://openalex.org/W3198975419 | https://zenodo.org/record/5783070/files/fqab032.pdf | English | null | A data-driven approach to studying changing vocabularies in historical newspaper collections | Digital scholarship in the humanities | 2,021 | cc-by | 12,780 | DigitalScholarshipintheHumanities,Vol.36,Supplement2,2021.
V
C TheAuthor(s)2021.PublishedbyOxfordUniversityPressonbehalfofEADH.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by/4.0/),
which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
doi:10.1093/llc/fqab032 E-mail: use state-of-the-art word embeddings to describe
how this process is reflected in the written use of
four different languages: Dutch, English, Swedish,
and Finnish. Earlier work has focused on words and
concepts relating to nationhood, pointing out the gen-
eral trajectories of word use and the increased levels of
vagueness of ‘nation’ as a concept (Kemila¨inen, 1964; A data-driven approach to studying
changing vocabularies in historical
newspaper collections ata-driven approach to studying
nging vocabularies in historical
wspaper collections
............................................................................................................................................. Simon Hengchen
Spra˚kbanken Text, University of Gothenburg, Sweden and iguano-
don.ai, Belgium
Ruben Ros
Centre for Contemporary and Digital History (C2DH), University of
Luxembourg, Luxembourg
Jani Marjanen
and Mikko Tolonen
Helsinki Computational History Group, University of Helsinki,
Finland
...................................................................................................................................... Abstract
Nation andnationhoodare amongthe mostfrequentlystudiedconcepts in the fieldof
intellectualhistory.Atthesametime,theword‘nation’anditshistoricalusagearevery
vague. The aim in this article was to develop a data-driven method using dependency
parsing and neural word embeddings to clarify some of the vagueness in the evolution
of this concept. To this end, we propose the following two-step method. First, using
linguistic processing, we create a large set of words pertaining to the topic of nation. Second,wetraindiachronicwordembeddingsandusethemtoquantifythestrengthof
the semantic similarity between these words and thereby create meaningful clusters,
which are then aligned diachronically. To illustrate the robustness of the study across
languages, time spans, as well as large datasets, we apply it to the entirety of five
historical newspaper archives in Dutch, Swedish, Finnish, and English. To our know-
ledge, thus far there have been no large-scale comparative studies of this kind that
purport to grasp long-term developments in as many as four different languages in a
data-driven way. A particular strength of the method we describe in this article is that,
by design, it is not limited to the study of nationhood, but rather expands beyond it to
other research questions and is reusable in different contexts. ............................................................................................................................................ Ruben Ros
Centre for Contemporary and Digital History (C2DH), University of
Luxembourg, Luxembourg Abstract Nation andnationhoodare amongthe mostfrequentlystudiedconcepts in the fieldof
intellectualhistory.Atthesametime,theword‘nation’anditshistoricalusagearevery
vague. The aim in this article was to develop a data-driven method using dependency
parsing and neural word embeddings to clarify some of the vagueness in the evolution
of this concept. To this end, we propose the following two-step method. First, using
linguistic processing, we create a large set of words pertaining to the topic of nation. Second,wetraindiachronicwordembeddingsandusethemtoquantifythestrengthof
the semantic similarity between these words and thereby create meaningful clusters,
which are then aligned diachronically. To illustrate the robustness of the study across
languages, time spans, as well as large datasets, we apply it to the entirety of five
historical newspaper archives in Dutch, Swedish, Finnish, and English. To our know-
ledge, thus far there have been no large-scale comparative studies of this kind that
purport to grasp long-term developments in as many as four different languages in a
data-driven way. A particular strength of the method we describe in this article is that,
by design, it is not limited to the study of nationhood, but rather expands beyond it to
other research questions and is reusable in different contexts. Correspondence: Simon
Hengchen, University of
Gothenburg, Gothenburg,
Sweden.
E
il 1 Introduction One of the benefits of our case is
that the words nation and national exist in all four
languages as cognates or, in the case of Finnish, as
neologisms in the 19th century. The historical trans-
latability makes it ideal for comparative study in that it
highlights both similarities as well as differences be-
tween the languages in question. y
The linguistic change relating to ‘national’ consists
of a gradual growth in frequency and an expansion in
language domains over time. Setting up a method-
ology that grasps this development over a long period
of time, does so in different languages, is statistically
robust and does so in a data-driven way, will pave the
way for further historical study that could challenge
and complement earlier qualitative accounts of na-
tion-building. We point out that hypotheses devel-
oped in earlier studies based on limited source
corpora have referred to nations and a shift in focus
from the economy to culture and politics (Viroli,
1995; Ihalainen, 2007; Nurmiainen, 2009; Marjanen,
2013). We further propose that a data-driven cluster-
ing of the vocabulary relating to national allows for a
more fine-grained image of the expansion of the na-
tional imaginary. We show signs of change in the lan-
guage of nationhood that could perhaps be described
as processes of culturalization, de-economization, and
institutionalization, which should be evaluated more
closely in historical research. What this means is that,
over the course of the research period, terminology
related to culture and political institutions became
more commonly labelled as something national (as
in national literature or national party), whereas eco-
nomic terminology became proportionately less dom-
inant in the discourse. Many studies on semantic change of particular
words or concepts over long periods of time tend to
focus on changes in words that shift between two dis-
tinct senses (Recchia et al., 2017; Tahmasebi et al.,
2018). The case of national that we chose for this study
is different in that it relates to historical processes that
are of interest to historians in particular, but it also
provides a challenging case for the use of computa-
tional methods as it is not about detecting polysemy,
but rather about grasping a vague term and its increas-
ing importance in political discourse over time (on
vagueness, see Geeraerts, 1993). 1 Introduction There has been extensive research on the process in
which nation-states become pivotal units for inter-
national politics and crucial categories of belonging
for individuals (O¨ zkırımlı, 2000; Anderson, 2006;
Smith, 2013, 2008). Our aim in this article was to S. Hengchen et al. domains, and that historical actors seem to have cared
a lot about which uses were correct. The vagueness of
key terms for navigating society is inherently tied to
the complexity of the data required to detect shifts in
language use. Historical data have developed in con-
junction with societal processes and events (every-
thing from growing wealth to war and censorship
practices to changing fashions), and therefore form
non-standard data units in terms of computation
(Ma¨kela¨ et al., 2020). More importantly, develop-
ments in the data, in our case, newspapers, are part
of the process in which the terminological changes
took place. This means that these newspapers cannot
be used just to study changes, as the changes in them
also need to be factored into the interpretation of the
analyses. Gschnitzer et al., 1978). Word embeddings are com-
monly used in natural language processing (NLP), but
their application in historical research is still at the
experimental stage. There have been many robust
attempts at evaluation in state-of-the-art research
using embeddings, but in the case of historical data,
the evaluation has to be against historical research. It
therefore remains difficult to determine what the real
object of the modelling is and if the results are trans-
ferable to other languages, different corpora, or time
spans. Gschnitzer et al., 1978). Word embeddings are com-
monly used in natural language processing (NLP), but
their application in historical research is still at the
experimental stage. There have been many robust
attempts at evaluation in state-of-the-art research
using embeddings, but in the case of historical data,
the evaluation has to be against historical research. It
therefore remains difficult to determine what the real
object of the modelling is and if the results are trans-
ferable to other languages, different corpora, or time
spans. Our large-scale comparative perspective demon-
strates changes in the development of nationhood
with greater clarity than before in focusing on the
term ‘national’ and using words associated with it to
analyse domains that were increasingly being concep-
tualized as national. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 1 Introduction This also holds for
most of the key terms of interest in understanding
political, social, and cultural transformation in the
modern period. Words such as state, nation, ideology,
culture, gender, and racism have been extensively
researched as pivotal terms that have been contested
in past debates and whose changing meanings have
been indicative of historical transformation, but have
also been the cause of change in the past (see e.g. Koselleck, 1972–1997; Ball et al. 1989). Although
many of these words are polysemous, the aspect that
makes them interesting politically and culturally is
that they are also vague, at least in one of their senses,
that they are used in rather different language Our method is particularly suited to analysing
complex historical keywords that are usually at the
heart of studying the history of political and social
thought. The development of methods and the
concrete plots we devise in this study relate to the ii110 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021
i110 A data-driven approach to study changing vocabularies All of the above-mentioned studies, in one way or
another, concern long-term trends in the meanings
and uses of the words ‘nation’, ‘national’, and ‘nation-
alism’. However, apart from in a few isolated cases of
resorting to relative frequencies, the use of quantita-
tive methods to trace long-term developments in this
vocabulary is almost completely non-existent. The
one exception is Van den Bos and Giffard’s study,
which focuses on key junctures in Dutch history and
the language of nation (van den Bos and Giffard,
2016). The present study takes a step forward and a
step backward. On the one hand, it engages in earlier
claims about changes in word use being part of the
process in which past expectations and experiences
about nationhood were articulated (Koselleck, 1972,
2011), which on the other hand leads to claims that an
over-arching study of the language of national could,
in a general way, describe the process through which
the national perspective became dominant in how
people saw the world (Anderson, 2006). Although
interpretations such as these already exist, they all
rely on examples of particular texts rather than any
kind of data-driven analysis, which means that they
may be detailed in terms of individual examples, but
they are not even close to capturing the whole story. 1 Introduction vocabulary revolving around the adjective national,
but the aim here is not primarily to make a historical
argument about nation building. We rather purport
to identify ways of using computation to analyse his-
torical trends in past conceptualizations of the world
in a more nuanced way than key-word searches, rela-
tive frequencies, or topic models have made possible. Ultimately, the methods used to address historically
informed questions need some level of tailoring to the
data and the type of questions asked. However, given
that the bulk of large-scale diachronic text data sets
provide possibilities for the study of language in rela-
tion to historical processes, there are good possibilities
of reuse in other research cases. This goes hand-
in-hand with open science and the envisioning of
research data as an ecosystem (Lahti et al., 2019). 2.1 Language and nationalism Nationalism is a widely studied phenomenon and the
role of semantic and lexical change has been noted in
literature that provides overviews of the topic (see, in
particular, Leersen, 2006, p. 15; Burke, 2013; Gilbert,
2018), but the bulk of the literature on nationalism has
still been surprisingly indifferent towards the language
of nationhood. This disinterest in the long-term
changes in language relating to nationhood means
that the analytical distinctions relating to nation-states
and their emergence has been prioritized at the ex-
pense of enhancing understanding of the historical
experience of nationhood. Methods for tracing this kind of change are not a
perfect match for the historical questions posed in
earlier research (Hengchen et al., 2021). It is clear
that earlier abstract claims about the shift in focus in
the language of nationhood remain too broad to be
captured in a meaningful way by methods for tracing
semantic change in that they capture many different
and partly conflicting signals from the data. Human
interpretation has tended to filter them out, and quan-
titative methods for assessing shifting vocabulary ne-
cessarily have to find a good way of balancing detailed
view and a result that is interpretable for human
readers. There are good arguments for claiming
that modelling may in some cases be less transparent
and cannot capture the same things as qualitative
interpretation (Biernacki, 2014), but in terms of
understanding the evolving language of nationhood,
the aspect of modelling and quantification has been
completely missing. Studies focusing on language tend to reflect an
interest in the differences and similarities between pat-
riotism and nationalism (Cunningham, 1989; Dietz,
1989; Viroli, 1995; Hont, 2005, pp. 447–528; Schierle,
2009). Another strongly related strand concerns the
link between nation and fatherland in particular
European languages (Kemila¨inen, 1964; de Bertier
de Sauvigny, 1970; Godechot, 1971; Gschnitzer
et al., 1978; Frautschi, 1993; Van Sas, 1999; Brenner,
2013). A few studies have also paid attention to na-
tionalism as an ism in political discourse (Gschnitzer
et al., 1978; Ba¨renbrinker and Jakubowski, 1995;
Freeden,
2009,
pp. 204–224;
Kettunen,
2018;
Kurunma¨ki and Marjanen, 2018). 2.2 Evolving vocabularies 2.3 Representing meaning in time As noted above, previous attempts at studying an
evolving discourse diachronically made use of com-
putational methods and large corpora. More recent
approaches lean on NLP. In this section, we discuss
the state-of-the-art and illustrate why studying a
specific theme over time is not trivial. Topic modelling is extensively discussed and is
sometimes used in the humanities (Fridlund and
Brauer, 2013; Viola and Verheul, 2019). Although
the soft clustering method is most commonly used
synchronically for exploratory research, there are
also dynamic topic models (DTMs) that take time as
a variable and allow the extraction of topics across
time slices. DTMs (Blei and Lafferty 2006) divide
the data into discrete time slices and infer topics across
them to capture topics evolving over time. A different
approach, Topics over Time (Wang and McCallum
2006), treats time as a continuous variable and the
data are not discretized. Although both approaches
are promising, their major drawback is that the topic
models do not allow for a topic to be defined a priori:
they allow an exploratory look at the data, but there is
no easy way to ensure that a certain topic will be
found. The challenge in analysing vocabulary is to ‘strike a
balance between an adaptive strategy that responds to
changes in vocabulary, and a more conservative ap-
proach that keeps the vocabulary stable’ (Kenter et al.,
2015). The vocabulary must maintain a minimal de-
gree of stability in order for it to be historically rele-
vant and meaningful, but at the same time, it should
solve the problem of different words relating to the
same concept over time (onomasiology). Rather than considering a predefined group of
words over time, distributional methods allow for a
more data-driven approach. Recent scholarship in
history has used word embeddings to identify seman-
tically related words and to follow their development
over time. This requires an initial set of seed terms that
is subsequently expanded by selecting similar words
(Kenter et al., 2015; Recchia et al., 2017). Another
approach is to identify a vocabulary based on features
of single words such as ‘isms’ (Pivovarova et al., 2019,
Marjanen et al., 2020), or sequences of words (n-
grams). The latter approach constructs a vocabulary
based on words that are directly preceded (Wevers,
2017; Van Eijnatten and Ros, 2019) or modified
(Hill et al., 2018) by a common adjective, and subse-
quently focuses on the temporal changes. 2.2 Evolving vocabularies The traditional focus in conceptual history has been
on specific keywords such as ‘democracy’, ‘liberalism’, Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021
ii111 S. Hengchen et al. and ‘nation’, but only to a limited degree has there
been any systematic analysis of semantic and lexical
fields related to these keywords. The concentration on
words has led to extensive discussions about their
exact relationship with concepts (Steinmetz, 2012;
Bolla et al., 2019; La¨hteenma¨ki and Kaukua, 2019;
Bolla et al., 2020). Although we do not assume that
we can grasp the conceptual level behind words as
such, we take a pragmatic approach and use distribu-
tional1 methods to study changing vocabulary. These
methods allow us to broaden the scope from words to
groups of words (that are in some way related to con-
cepts) through time. We are still intent on using words
as proxies and thus remaining on the level of words
and language use, because that will enable us to cap-
ture at least some of the personal experiences of his-
torical actors. When they sought to express certain
concepts, they chose particular words that reflected
their own positions and thus left a trace of their
experiences in the data. Moreover, focusing on
words allows for the relatively easy tallying of their
occurrences. insights into conceptual and distributional change
that would go unnoticed were the focus only on spe-
cific keywords. Our method builds on such previous
work, and in delegating the choice of ‘seed terms’ to
nouns modified by a specific adjective allows for a
more data-driven approach, while at the same time
retaining some ‘topical control’ and harnessing se-
mantic information from word embeddings. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3 Methodology As we point out above, studying the changing vocabu-
lary of a concept is no easy task. Doing so in a way that
informs research in the humanities in a data-driven
way adds a layer of complexity: if a certain, specific
theme is to be studied it has to be defined a priori, and
operational choices must be made5 that might bias
any quantitative method applied to the resulting sub-
set of the data. Our methodological contribution is an
approach that follows the fine line between having a
precise research question and making use—in a data-
driven way—of all the data available. It is a two-step
approach, which we illustrate below in a case study on
the changing vocabulary of nationhood in four coun-
tries and four languages. Thus, there have been robust attempts to evaluate
and sometimes compare systems, but it remains dif-
ficult to determine what is actually being modelled,
and whether the performances are transferable to
other languages, different corpora, or dissimilar time
spans. In short, it is arduous to determine whether
NLP systems can be applied as-is to humanities
data. Indeed, as McGillivray et al. (2019) remark, for
example, despite being promising with regard to
English, SCAN (Frermann and Lapata, 2016) per-
forms poorly on an Ancient Greek corpus with sparse
data and extended time bins, and the performance of
an updated model (Perrone et al., 2019) does benefit
from additional information such as literary genre. To illustrate that the method is robust enough to
tackle different data, languages, and periods, we carry
it out on Dutch, Finnish, Swedish, and British news-
paper data. The newspapers stem from different sour-
ces and countries and are available in different
formats. Massive digitized newspaper collections are
increasingly used to address historical questions
through mining textual data.6 The material, as well
as the pre-processing steps, is laid out below, and
the distribution of the data is available in Figs 1 and 2. The Dutch data are the Delpher open newspaper
archive (Royal Dutch Library, 2017) for the period
1618 until 1876 included. 2.3 Representing meaning in time all time bins) to create
vector representations, and more recently contextual-
ized word embeddings (which have token vectors and
not type vectors2) have been applied to diachronic
corpora. example)4 and through how researchers can process it
electronically (missing, incomplete, or wrong meta-
data, varying OCR quality, etc.) (Piotrowski, 2012). Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 2.3 Representing meaning in time This leads to
the quantification of conceptual extension, and gives Another field in which meaning is studied compu-
tationally across time is that of lexical semantic
change, which is particularly suited for conceptual
change in that it focuses on words and not general
themes (Kutuzov et al., 2018; Tahmasebi et al., 2018;
Tang, 2018). To study meaning change, computation-
al methods proceed in two steps: first, they distribu-
tionally model meaning in different time bins
(subsequent temporal slices of the data at hand). Second, the focus is to detect, for any word w, whether
the signal between time bins changes in a significant
way. In recent years, even laws of semantic change
have been proposed (Dubossarsky et al., 2015;
Hamilton
et
al.,
2016)
and
then
disproved ii112 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies (Dubossarsky et al., 2017). Some methods have been
under rigorous evaluation (Dubossarsky et al., 2019;
Schlechtweg et al., 2019, 2020; Shoemark et al., 2019). At the same time, new methods and paradigms aimed
at diachronically modelling semantic information are
being developed further: DTMs specifically targeting
words (Frermann and Lapata, 2016; Perrone et al.,
2019) use bag-of-words to draw sense distributions
for certain target words over time, dynamic, and con-
tinuous word embeddings (Bamler and Mandt, 2017;
Rosenfeld and Erk, 2018; Rudolph and Blei, 2018; Yao
et al., 2018; Dubossarsky et al., 2019; Gillani and Levy,
2019) differ from static embeddings in that they use
the entirety of the data (i.e. all time bins) to create
vector representations, and more recently contextual-
ized word embeddings (which have token vectors and
not type vectors2) have been applied to diachronic
corpora. (Dubossarsky et al., 2017). Some methods have been
under rigorous evaluation (Dubossarsky et al., 2019;
Schlechtweg et al., 2019, 2020; Shoemark et al., 2019). At the same time, new methods and paradigms aimed
at diachronically modelling semantic information are
being developed further: DTMs specifically targeting
words (Frermann and Lapata, 2016; Perrone et al.,
2019) use bag-of-words to draw sense distributions
for certain target words over time, dynamic, and con-
tinuous word embeddings (Bamler and Mandt, 2017;
Rosenfeld and Erk, 2018; Rudolph and Blei, 2018; Yao
et al., 2018; Dubossarsky et al., 2019; Gillani and Levy,
2019) differ from static embeddings in that they use
the entirety of the data (i.e. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3 Methodology This archive is said to con-
tain all newspapers for that period.7 For the years
1877–1899 included, currently only available through
the API, we queried the API for every item of the
‘artikel’ type (‘article’, the Dutch data have article seg-
mentation and further differentiates between adver-
tisements and articles) category containing the
determiner de (‘the’) at least once. Although this
does not guarantee a 100% recall, de is so frequent
that we are confident the extreme majority of articles
of the necessary length for our tasks are retrieved. For
anything pre-1877, we discarded pages that had any-
thing other than exclusively ‘nl’ or ‘NL’ as language
tags in the metadata. Articles from colonial newspa-
pers were systematically removed. This is motivated As anyone who works with historical material is
aware, language changes over time. To avoid anach-
ronisms, one has to make sure that texts are under-
stood in their own context, rather than through a
contemporary lens. Although historians have been
trained to do this, as the above paragraph shows, cur-
rent NLP methods might not be completely fit for the
task. Additionally, NLP usually focuses on relatively
straightforward cases,3 and it is unclear whether or not
the signal picked up by computational models is use-
ful for humanities research, given that the changes in
meaning being studied may well not be as obvious
(Hengchen et al., 2021). Finally, the computational
processing of humanities data notoriously poses spe-
cific challenges both by its nature (evolving grammar
and orthography, uneven size of data across time, for ii113 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV
g
Downloaded from https://academic.oup.com/dsh/article/36/Supplement by the fact that only the Dutch dataset has an extensive
coverage of colonial newspapers, and including them
would have complicated our comparisons with the
other countries in our study. The newspapers from
Finland comprise two language corpora: we used the
entirety of the Finnish Sub-corpus of the Newspaper
and Periodical Corpus of the National Library of
Finland (National Library of Finland, 2011a) for
articles in Finnish, and the corresponding Swedish
Sub-corpus of the Newspaper and Periodical Corpus
of the National Library of Finland (National Library of
Finland, 2011b).8 Swedish newspapers are available in
Fig. 1. 3 Methodology Distribution of data size over time in token counts for FI, NL, and SV
Fig. 2. Distribution of data size over time in token counts for GB
Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021
ii114
Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV by the fact that only the Dutch dataset has an extensive
coverage of colonial newspapers, and including them
would have complicated our comparisons with the
other countries in our study. The newspapers from
Finland comprise two language corpora: we used the
and Periodical Corpus of the National Library of
Finland (National Library of Finland, 2011a) for
articles in Finnish, and the corresponding Swedish
Sub-corpus of the Newspaper and Periodical Corpus
of the National Library of Finland (National Library of
Fig. 2. Distribution of data size over time in token counts for GB
ment_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 2. Distribution of data size over time in token counts for GB
nt_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Fig. 2. Distribution of data size over time in token counts for GB and Periodical Corpus of the National Library of
Finland (National Library of Finland, 2011a) for
articles in Finnish, and the corresponding Swedish
Sub-corpus of the Newspaper and Periodical Corpus
of the National Library of Finland (National Library of
Finland, 2011b).8 Swedish newspapers are available in by the fact that only the Dutch dataset has an extensive
coverage of colonial newspapers, and including them
would have complicated our comparisons with the
other countries in our study. The newspapers from
Finland comprise two language corpora: we used the
entirety of the Finnish Sub-corpus of the Newspaper Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii114 A data-driven approach to study changing vocabularies the Kubhist 2 corpus digitized by the Royal Library of
Sweden, processed with the Sparv pipeline (Borin
et
al.,
2016),
and
made
available
online9
by
Spra˚kbanken through Korp (Borin et al, 2012). 3 Methodology Finally, the British data consist of the British Library
Newspapers covering especially the 19th century,10 the
17th and 18th Century Nichols collection,11 and the
17th and 18th Century Burney collection.12 nationality’ as it is a noun in its own right,16 and the
Finnish kansalliskirjasto ‘national library’ became kan-
sallinen þ kirjasto. Only modified nouns are kept. For
newspapers in Finnish and in Swedish from Finland,
we used linguistic information made available by the
language bank of Finland,17 and similarly for news-
papers in Swedish published in Sweden we used in-
formation made available by the language bank of
Sweden18—both sets of data were produced by differ-
ent versions of the same pipeline, Sparv (Borin et al.,
2016). Dutch and English datasets were dependency-
parsed using spaCy 2 (Honnibal and Montani, 2017). The large models were chosen for both languages. Unfortunately, no assessment of the quality of the
dependency parsing is available for Finnish and
Swedish.19 The changes in corpus size over time bins poses a
problem for any computational text-mining task. Our
approach creates intermediate data points in separate
time bins of 20 years,13 and it is only the aggregate
information that is compared over time. As such,
common pitfalls related to aspects such as limited
vocabularies or the representativity of the data do
not necessarily apply, as we spell out in our evaluation. The absolute counts of nouns modified by ‘nation-
al’ are displayed in Fig. 3. The relative frequencies
show a similar pattern. A further issue is that our data (historical news-
papers) are not only data in which we study changing
language: the change in corpus size and the growing
importance of newspapers as a medium are parts of
the historical process in which the language of nation-
hood has also changed. Growing amounts of news-
papers created a different habitat in which the
vocabulary of national could flourish; hence, there is
no reasonable way of even trying to achieve a balance
with the corpus used for the purpose of computation. Rather understanding changes in the corpus and the
development of the public sphere in general is a form
of corpus control, which is essential in terms of under-
standing the changing vocabulary of nationhood
(Marjanen et al., 2019; Tolonen et al., 2019). Because the meaning of ‘national’ changes over
time, it is possible that other adjectives referred to
what we now classify as national. 3 Methodology To evaluate the ‘cen-
trality’ of the adjective in the different time periods,
therefore, we aggregated all other adjectives that
modified the nouns modified by national. For ex-
ample, in Dutch, this resulted in adjectives such as
‘public’, ‘Dutch’, ‘royal’, and ‘foreign’. The frequen-
cies of these ‘competing’ adjectives were lower in all
decades, however, as well as in the overall time frame. This shows that the adjective ‘national’ was indeed the
most commonly used to modify these nouns. The
‘competing’ adjectives sometimes perform a supple-
mentary function but, as we will reveal, the discourse
of national had a clear role of its own in all languages. 3.1 Extracting nationhood First, using dependency parsing,14 we utilized the
method proposed by Hill et al. (2018) and extracted
all the nouns modified by the adjective at hand, in our
case ‘national’.15 With regard to the other languages
we extracted nouns modified by nationaal and natio-
nale in Dutch, nationella, nationell, and national in
Swedish, and kansallinen in Finnish. Obviously, dif-
ferent
languages
have
different
properties. We
resorted to splitting the Finnish and Swedish com-
pound nouns starting with kansallis- and national-,
respectively, while making sure they were genuine
compounds, removed the ‘national’, and added the
remaining part to our tally. As an example, Swedish
nationalbiblioteket ‘the national library’ became natio-
nell þ biblioteket, but we discarded nationaliteten ‘the Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021
ii11 3.2 From words to concepts Second, to allow the semantic clustering of all nouns
relating to the concept of ‘nation’, we trained dia-
chronic word embeddings on the entirety of the full
text. Given that there was no conclusive way of deter-
mining what type of embedding was best for our data
and that word embeddings are still poorly understood,
and since we argue that dynamic and continuous
word embeddings models cannot reliably be used
here on account of the extremely uneven distribution
of the data, we experimented with two fairly old archi-
tectures, CBOW and SGNS (Mikolov et al., 2013a,b),
which have been studied more thoroughly.20 For the ii115 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 3. Absolute counts of nouns modified by ‘national’ over time in Dutch, Finnish, Swedish from Finland, and Swedish
from Sweden. Relative frequencies, not plotted, show a similar pattern Fig. 3. Absolute counts of nouns modified by ‘national’ over time in Dutch, Finnish, Swedish from Finland, and Swedish
from Sweden. Relative frequencies, not plotted, show a similar pattern previous work based on the same data (Hengchen
et al., 2019; Pivovarova et al., 2019; Marjanen et al.,
2020). These models are referred to later in this article
as UPDATE. At the same time, we independently
trained word embeddings for all time bins, which we
then aligned post hoc as proposed by Kulkarni et al. (2015). The spaces were aligned by means of orthog-
onal Procrustes analysis, as first done by Hamilton
et al. (2016).22 We refer to these models later in this
article as ALIGN. Aside from the frequency threshold,
which we raised due to the enormous number of
types23 in our corpora, we used the default (hyper)-
parameters.24 We are releasing the models along with
this article.25 same reason, we created diachronic word embeddings
using the two most frequently applied methods,
post hoc alignment and incremental updating
(described in detail below). We chose to train mod-
els on double decades for three reasons: first,
20 years roughly corresponds to a ‘generation’ in
historical sociolinguistics (Sa¨ily, 2016); second, we
needed a certain number of nouns related to the
nation for the clustering to make sense, and bins
of 20 years allow enough to be gathered, especially
in the earlier periods; third, and somewhat echoing
the second reason, it allowed us to have relatively
stable models for the earlier periods. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3.2 From words to concepts produces results that are useful for downstream tasks
and analyses such as the study of a concept across large
time scales. Word embedding models are commonly evaluated
using for example word analogies or word similarities. It should be pointed out that these evaluations are
carried out on present-day data for which ground
truth exists. To take but one example, Pennington
et al. (2014) used the analogy task in Mikolov et al. (2013a) as well as the word similarities available in
WordSim-353 (Finkelstein et al., 2002). However,
ground truth is not available for our data. Were we
to find enough annotators30 to create ground truth
and evaluate our embeddings, creating such ground
truth
would
entail
creating
an
unreasonable
amount,31 given that we are training different models
on different time bins.32 This is well beyond the scope
of this project. Finally, as Chiu et al. (2016) point out,
there is no guarantee that intrinsic evaluations of word
embeddings such as described above indicate better
performance in downstream tasks. Instead, we rely
on
recent
conclusions
reported
by
Hill
and
Hengchen (2019), who point out that, on historical,
OCRed, relatively dirty data (i.e. texts with an F-score
of 0.75 compared with their corresponding keyed-in
ground truth) does not severely impact the perform-
ance of vector space models. g
g
As can be inferred from the previous subsections,
the main strength of our approach is that it allows
researchers to rely on hypotheses stemming from his-
torical research while being data-driven. To a certain
extent, we used the entirety of the data available (for
English, upwards of 50 billion words) while guiding
the process—the only interference, which we admit is
crucial and requires domain expertise, was choosing a
key adjective on which to focus. The final product,
fine-grained on a one-year basis, is refined enough
to be analysed in broad strokes as well as to lead to
deeper dives into specific periods. Through the use of
the entirety of the data, and time-specific meaning
representations of words, the method avoids the com-
mon trap of teleology. Unfortunately, an inherent
weakness to type embeddings is that polysemous
words have a single representation in vector space,
‘ironing out’ the polysemy. 3.2 From words to concepts For each time bin, we trained two types of word
embeddings using gensim (Reh˚urek and Sojka, 2010),
a Python library for vector space modelling. Because
separately trained vector spaces cannot be compared
directly, we used two different methods to make the
spaces comparable, and thus to ensure a sound dia-
chronic approach. On the one hand, we followed Kim
et al. (2014) and initialized the vector space for time
bin t1 with the space from t0,21 and updated the vec-
tors by continuing the training. This differs slightly
from the original approach in setting the learning-
rate value of t1 to that of the end of the previous model
(in this case, t0). The aim was to prevent the models
from diverging too rapidly, as successfully reported in Once the word embeddings were trained, we built,
for each time bin, a similarity matrix between all the
nouns extracted above. In other words, we queried the
word-embedding models for a degree of ‘semantic
similarity’26 between all words at hand and stored
those relations in a table. Semantic clusters can then be created. We used two
hard clustering algorithms, which we describe briefly
below. We created the semantic clusters using k-means clus-
tering (MacQueen, 1967) and affinity propagation
(Frey and Dueck, 2007). The aim in k-means is to group
similar data points together. Its main limitation, in our ii116 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies case, is that the number of clusters needs to be decided a
priori. Our second clustering algorithm, affinity propa-
gation, has the advantage of finding the number of
clusters automatically: it splits the data into exemplars
and instances, exemplars being representative tokens of
their instances, the non-exemplar tokens in the same
cluster. As Pivovarova et al. (2019) point out, ‘Affinity
Propagation has been previously used for several NLP
tasks, including collocation clustering into semantically
related classes (Kutuzov et al., 2017) and unsupervised
word sense induction (Alagic et al., 2018)’. Given that,
just as in the above-cited article, we lacked a gold stand-
ard, we used standard hyperparameters27 as available in
the scikit-learn package (Pedregosa et al., 2011). The
main weakness of affinity propagation remains the
computational and memory costs: its O(n2)28 cost is
limiting in larger datasets. 3.2 From words to concepts This is problematic in
that some words might have a certain meaning in
the context of the topic at hand that is not the main
sense of the word, leading to bad clusters.29 Following this, we performed a manual evaluation
on certain words to make sure that the models output
semantically similar words. The models for all lan-
guages except Swedish output words that were
deemed correct.33 As a result, we retrained the
Swedish word embeddings after performing some
data alteration: we only kept sentences that were at
least ten tokens long and for which the Sparv process-
ing pipeline could find at least 50% of lemmas. Our manual checking confirmed that the word
similarities for all languages and models post-1700
(where available) seemed meaningful, and that OCR
errors were indeed captured and deemed similar.34
Similarly, all clusters—either with k-means or affinity
propagation—were meaningful, as illustrated in the
example in Fig. 4. Plotting clusters and their evolution
across time—clusters are given weight through a fre-
quency
count
of
their
members—showed
the
expected signal. For example, Fig. 435 shows the
1860–1880 situation in Finnish-language Finnish
newspapers. The 1863 peak for the legislative cluster Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 4 Evaluation The method proposed in this article can be evaluated
from two perspectives. First, intrinsically, we show
that choices made in the preparation of the data and
in the creation of the intermediate, aggregate data are
reliable and produce sound output. Second, through a
case study in four languages, we show that the method ii117 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 4. Finnish-language clusters for 1860–1880
Downloaded from https://academic.oup.com/dsh/article/36/Supple Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Fig. 4. Finnish-language clusters for 1860–1880 knowledge of the period. In English, for instance, we
show (in Fig. 5) how affinity propagation produces
only one cluster from the time bins from the 18th
century, indicating that the language of national was
tied to issues related to the military and the economy
(debt in particular). Earlier research focusing on the
history of economic thought has pointed this out
(Hont, 2005), but perhaps because of the focus on
the economy, the point has not been widely accepted
in the literature. Our analysis on the totality of the
material does point to a dominance of economic
and military discourse in the period when conceptu-
alizing things as national started to become more
common. As expected, we also show that the era of
the French revolution heralded a period of gestation in
which national themes were associated with political
and, to a certain extent, sentiment-related themes. This entailed a clear expansion of the conceptualiza-
tion of what could be perceived as national. This pro-
cess
continued
and,
consequently,
affinity
propagation provides many more distinct clusters
for the early 19th century. (hallitus, hallituksen, puolueen, hallitns, sota)36 stems
from content about the 1863–1864 session of the Diet
of Finland,37 the legislative assembly of the Grand
Duchy of Finland. The red cluster exploding in 1871
(kokous—kokouksen—kokouksessa—kokoukselle—
kokoukseen)38 stems largely from texts relating to the
Franco-Prussian War. As we are proposing a method for which there is no
gold standard and to which the notion of ‘absolute
truth’ cannot be applied, the only way to determine
whether the approach serves a purpose is to establish
its usefulness.39 The second, extrinsic, part of our
evaluation is described in the next section. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 5 Findings Harnessing word embeddings to cluster words is a
powerful and useful tool when matched with the right
kind of research questions. In the case of the expand-
ing discourse of ‘national’, for example, our clustering
proves the expansion of the vocabulary of nationhood. This does not as such challenge existing historiog-
raphy, but clusters based on affinity propagation in-
dicate this change in all four languages such that the
clusters make sense to a reader with historical The clustering for Swedish, Finnish, and Dutch
follows a similar pattern, but there are some differ-
ences in the timing and contents. In Finnish, for in-
stance, the word kansallinen (as a translation of the ii118 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Decem Fig. 5. Sankey chart of British clusters, 1740–1820 Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 5. Sankey chart of British clusters, 1740–1820 Fig. 5. Sankey chart of British clusters, 1740–1820 national) did not become really frequent before the
1850s (depending on the threshold), so naturally the
development is different with a much quicker expan-
sion of the vocabulary as established notions of na-
tionhood
readily
translated
into
Finnish
from
Swedish, German, and English. As such, this suggests
that the findings resonate with historical knowledge of
the period and could therefore be used to further ex-
plore national peculiarities with regard to the vocabu-
lary of nationhood. signals in the data than a human reader could. We
may now begin to examine in a data-driven way
how different types of attitudes to nationhood emerge
over time and in different places and languages. Our distributional methods based on affinity
propagation performed well in tracing general devel-
opment with regard to nationhood, but also point
towards more detailed findings that could be eval-
uated from the perspective of historical change. As
such, we come much further from the use of key-
word searches, simple plots of relative frequency, or
even topic models in providing methods for diachron-
ic change that relates to theories of long-term histor-
ical change. It should also be possible to use the
method in analyses of other themes such as (the
changing vocabularies) of secularization, moderniza-
tion, and the process of civilization. 5 Findings One way of looking at the cluster differences in the
case of national is to pay attention to the nature of the
clusters and not only to the linked individual words. Although focusing on the 19th century, such an ap-
proach results in a clear division between sentiment-
based (feeling, spirit, pride, prejudice) and object-
based (bank, schools, council, government) nouns
related to nationhood. When studying nationalism,
this is a crucial division as they direct our attention
to the growth of discourses relating to identity and
affinity on the one hand and state institutions on
the other. As such, they channel attention to the
hypotheses about culturalization and institutionaliza-
tion mentioned in Section 1. The aim in this article
was not to make a full-fledged historical argument;
however, it is enough to observe that, in the study of
nationalism, the clusters produced through affinity
propagation are perhaps more precise than what a
historian reading texts would consider relevant
themes, but at the same time, more detailed clusters
could be thematically grouped and would seem to
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for Swedish. Both links last accessed 4 November 2019. 8 We made use of text files created from the original XMLs by
Prof. Eetu Ma¨kela¨, whom we thank. The complete list of
newspapers is available at https://www.kielipankki.fi/wp-con
tent/uploads/klk-lehdet-fi.pdf for Finnish, and at https://
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4 A data-driven approach to study changing vocabularies Yao, Z., Sun, Y., Ding, W., Rao, N., and Xiong, H. (2018). Dynamicwordembeddingsforevolvingsemanticdiscov-
ery. In Proceedings of the Eleventh ACM International
Conference on Web Search and Data Mining, WSDM’18. ACM, Marina Del Rey, California, pp. 673–681 (https://
doi.org/10.1145/3159652.3159703) 7 https://www.delpher.nl/nl/platform/pages/helpitems? title¼dataþinþdelpher, last accessed 4 November 2019. 8 We made use of text files created from the original XMLs by
Prof. Eetu Ma¨kela¨, whom we thank. Notes 9 To the best of our knowledge, there is no official data
release for this public data. We retrieved the files starting
with ‘kubhist2’ on https://spraakbanken.gu.se/lb/resur
ser/meningsmangder/ (last accessed 1 November 2019)
and, with the help of a Spra˚kbanken researcher, made
sure that the data downloaded were the entirety of the
corpus. S.H. was still affiliated with the University of
Helsinki at that time. 9 To the best of our knowledge, there is no official data
release for this public data. We retrieved the files starting
with ‘kubhist2’ on https://spraakbanken.gu.se/lb/resur
ser/meningsmangder/ (last accessed 1 November 2019)
and, with the help of a Spra˚kbanken researcher, made
sure that the data downloaded were the entirety of the
corpus. S.H. was still affiliated with the University of
Helsinki at that time. 1 The distributional hypothesis (Harris, 1954), popularised
by the sentence ‘a word is characterized by the company it
keeps’ (Firth, 1957) is the idea that words that occur in the
same contexts tend to have similar meanings. 1 The distributional hypothesis (Harris, 1954), popularised
by the sentence ‘a word is characterized by the company it
keeps’ (Firth, 1957) is the idea that words that occur in the
same contexts tend to have similar meanings. 2 A type is a class, whereas a token is an instance of that
class. In the case of textual corpora, a type is a word,
whereas ‘tokens’ denote all instances of that word. As
an example, ‘to be or not to be’ contains four types
(‘to’, ‘be’, ‘or’, and ‘not’) and six tokens. In the case
of embeddings, a type-vector is a vector representation
for all instances of a word (and thus conflates poly-
semy), whereas a token-vector has a distinct vector
representation for all occurrences of all tokens in the
vocabulary. 10 https://www.gale.com/intl/primary-sources/british-li
brary-newspapers (last accessed 1 November 2019). 11 https://www.gale.com/intl/c/17th-and-18th-century-nich
ols-newspapers-collection(lastaccessed1November2019). 12 https://www.gale.com/intl/c/17th-and-18th-century-
burney-newspapers-collection
(last
accessed
1
November 2019). Gale’s British Library Newspapers
collection is large, but it is not comprehensive in the
same sense as the National Library of Finland’s news-
paper coverage, which has certain omissions of individ-
ual issues and even newspaper titles but still be
considered a full run of newspapers. The nineteenth-
century coverage of the British newspaper collection is
more local and regional, missing some of the central-
London-based newspapers in particular. 12 https://www.gale.com/intl/c/17th-and-18th-century-
burney-newspapers-collection
(last
accessed
1
November 2019). Notes Gale’s British Library Newspapers
collection is large, but it is not comprehensive in the
same sense as the National Library of Finland’s news-
paper coverage, which has certain omissions of individ-
ual issues and even newspaper titles but still be
considered a full run of newspapers. The nineteenth-
century coverage of the British newspaper collection is
more local and regional, missing some of the central-
London-based newspapers in particular. 3 Some examples from the NLP literature are: ‘gay’ (cheer-
ful -> homosexual), ‘tweet’ (bird noise -> twitter post),
and ‘broadcast’ (to sow seeds -> to transmit TV/radio). 4 Nonetheless, initiatives to tackle this very problem at the
intersection of NLP and DH are being set up. For example,
the International Workshop on Computational Approaches
to Historical Language Change 2019 (https://language
change.org/events/2019-acl-lcworkshop/, last accessed 3
November 2019) was an NLP workshop specifically aiming
to be ‘an outlet for disseminating cutting-edge research on
topics concerning language change’, to ‘bring together do-
main experts across disciplines’, and to ‘raise fundamental
theoreticalandmethodologicalchallenges’.Anotherexample
is the SemEval 2020 Task 1 on Unsupervised Lexical
Semantic Change Detection (https://competitions.codalab. org/competitions/20948, last accessed 3 November 2019),
which uses unbalanced (except for English) historical data. 4 Nonetheless, initiatives to tackle this very problem at the
intersection of NLP and DH are being set up. For example,
the International Workshop on Computational Approaches
to Historical Language Change 2019 (https://language
change.org/events/2019-acl-lcworkshop/, last accessed 3
November 2019) was an NLP workshop specifically aiming
to be ‘an outlet for disseminating cutting-edge research on
topics concerning language change’, to ‘bring together do-
main experts across disciplines’, and to ‘raise fundamental
theoreticalandmethodologicalchallenges’.Anotherexample
is the SemEval 2020 Task 1 on Unsupervised Lexical
Semantic Change Detection (https://competitions.codalab. org/competitions/20948, last accessed 3 November 2019),
which uses unbalanced (except for English) historical data. 13 We clarify the reasons behind the choice of this size in
the next section. 13 We clarify the reasons behind the choice of this size in
the next section. 14 In NLP, dependency parsing is the task of extracting
syntactic relations between words in a sentence. For a
gentle introduction to dependency grammar and de-
pendency parsing, we recommend Nivre (2005). 14 In NLP, dependency parsing is the task of extracting
syntactic relations between words in a sentence. For a
gentle introduction to dependency grammar and de-
pendency parsing, we recommend Nivre (2005). Notes 15 For the sake of clarity and unless we refer to a specific
instance in another language, we use English words in
the remainder of this article. 15 For the sake of clarity and unless we refer to a specific
instance in another language, we use English words in
the remainder of this article. 5 Such choices include: deciding on a (set of) word(s) to
follow, ‘reading tea leaves’ (Chang et al., 2009) in a topic
model, etc. We discuss the a priori definition of a topic in
the following section. 16 In this precise case, nationaliteten is the singulardefinite
form of nationalitet. 16 In this precise case, nationaliteten is the singulardefinite
form of nationalitet. 16 In this precise case, nationaliteten is the singulardefinite
form of nationalitet. 17 Kielipankki/Spra˚kbanken, https://www.kielipankki.fi/
language-bank/ (last accessed 26 October 2019). 17 Kielipankki/Spra˚kbanken, https://www.kielipankki.fi/
language-bank/ (last accessed 26 October 2019). 18 Spra˚kbanken,
https://spraakbanken.gu.se/en
(last
accessed 18 November 2020). 18 Spra˚kbanken,
https://spraakbanken.gu.se/en
(last
accessed 18 November 2020). 6 For recent examples and further discussion , see for in-
stance Brandtzæg et al.(20182); Buntinx et al.(2017); and
van den Bos and Giffard (2016). For a discussion on the
role of the digitization of newspapers in historical re-
search see Cordell (2016 102) and Milligan (2013). 19 We did not carry out a systematic, large-scale evalu-
ation of the results of dependency parsing on English
or Dutch, as this is well beyond the scope of this paper. 19 We did not carry out a systematic, large-scale evalu-
ation of the results of dependency parsing on English
or Dutch, as this is well beyond the scope of this paper. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii125 ii125 S. Hengchen et al. A manual evaluation of the results for all time bins
indicates relatively high precision (i.e. output is made
up of nouns), but we have no information regarding
recall. For more on dependency parsing on (historical,
OCRed) newspapers, see van Strien et al. (2020). A manual evaluation of the results for all time bins
indicates relatively high precision (i.e. output is made
up of nouns), but we have no information regarding
recall. For more on dependency parsing on (historical,
OCRed) newspapers, see van Strien et al. (2020). Notes 30 In general, between three and five annotators are needed
to be able to calculate satisfactory inter-annotator agree-
ment.SeeSchlechtwegetal.(2018,2020)andSchlechtweg
and im Walde (2018) for a discussion on creating anno-
tated ground-truth in diachronic corpora, and particular-
ly on how domain experts (in that case, historical
linguists) have better agreement scores—reinforcing our
intuition that domain experts are needed. 20 See for example: Antoniak and Mimno (2018) and
Mimno and Thompson (2017). 21 And thus t2 with t1, and t3 with t2, etc. 22 We used the code provided by Ryan Heuser, whom we
thank. A copy is available at: https://gist.github.com/faus
tusdotbe/5a87007aaccc1342608c049af83fc5d2.Asthecode
effectively deletes vectors that are not in all time bins, we
made sure our nation-related nouns were not deleted. 31 Additionally, we echo similar work (Hengchen and
Tahmasebi, 2021) in stating that diachronic word
embedding models finetuned on one task are not ne-
cessarily perfect for other tasks. 32 Even if the OCR tool used is the same across all time
bins, there is still variation in the input data (fonts,
columns, etc.), forcing us to be thorough, and to evalu-
ate all models. 23 As an extreme example: the 1880–1900 time bin of British
newspaperscontains16,853,339,700tokensfor664,897,852
(lower-cased) types. Dropping tokens with a frequency
below100forthetwodecadesleavesuswith2,043,844types
(0.3% of the original), while still retaining 15,661,451,873
tokens(92.9% oftheoriginal).Todrivethepointhome:the
enormous number of types is attributable to OCR errors. 33 A more thorough analysis should be conducted, but
it seemed that the model could not abstract from the
structure of definites and indefinites: for example,
brev ‘letter’ and brevet ‘the letter’ were deemed less
similar than brevet and gardet ‘the guard’—two
tokens that share nothing apart from their suffix. Note: this observation was made on the first version
of the corpus (Kubhist), the final embeddings used
and released were trained on the larger, more recent
version (Kubhist 2). 24 For both strategies and all languages, tokens were lower
cased and the (hyper)parameters were as follows: con-
tinuous bag-of-words (CBOW) for UPDATE and skip-
gram with negative sampling (SGNS) for ALIGN,
epochs ¼ 5, window ¼ 5, min_count ¼ 100, negative
¼ 5 (for SGNS), alpha ¼ 0.025 (for ALIGN and the first
UPDATE model) and sample ¼ 0.001. 34 The reason we do not delve into the difference between
clusters created with ALIGN and UPDATE models is
that we could not find a meaningful difference. 25 https://zenodo.org/record/3585027 (last accessed 18
November 2020). Notes 26 For words w1 and w2, the similarity score is (w1w2)/
(kw1k kw2k), where w1 and w2 are, respectively, the L2-
normalised vectors for w1 and w2 and k k denotes the
Euclidean norm. 35 The clusters were created using k-means with eight
clusters. Different cluster sizes for the same time bin
show the same behaviour. 36 Literally: ‘government’ in the nominative, ‘govern-
ment’ in the genitive, ‘political party’ in the genitive,
‘government’ in the nominative with an OCR error,
‘war’ in the nominative. 27 Although the number of clusters cannot be set, the pref-
erence hyperparameter (which defines the ‘will’ of an
item to be an exemplar) can be tuned. 28 The ‘Big O notation’ is used to describe how calculation
time or space requirements grow as the input of a cer-
tain algorithm grows. In the case of O(n2), this means
that the growth is quadratic: with an input of 10 the
requirement is 102 ¼ 100, with an input of 100 the
requirement is 1002 ¼ 10,000, etc. 37 Note that even if the original noun (waltiopa¨iva¨t, val-
tiopa¨iva¨t, ‘state diet’) is not present as a keyword be-
cause it was not modified by ‘national’, the event is still
present. 37 Note that even if the original noun (waltiopa¨iva¨t, val-
tiopa¨iva¨t, ‘state diet’) is not present as a keyword be-
cause it was not modified by ‘national’, the event is still
present. 38 Literally ‘meeting/assembly’ in different cases. 38 Literally ‘meeting/assembly’ in different cases. 39 For amore extensive discussion on the notion of ‘fitness
for use’, see Boydens (1999). 29 We did not find that to be the case in our case study, and
do not expect it to be a large problem. 29 We did not find that to be the case in our case study, and
do not expect it to be a large problem. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii126 |
https://openalex.org/W4383700592 | https://www.qeios.com/read/36PAZ1/pdf | English | null | Review of: "Is gastrulation the most important time in your life?" | null | 2,023 | cc-by | 198 | Qeios, CC-BY 4.0 · Review, July 10, 2023 Qeios ID: 36PAZ1 · https://doi.org/10.32388/36PAZ1 Review of: "Is gastrulation the most important time in your
life?" Yi Zheng1
1 Syracuse University Yi Zheng1
1 Syracuse University Potential competing interests: No potential competing interests to declare. Potential competing interests: No potential competing interests to declare. The author briefly summarized the evolvement of our understanding on gastrulation in an interesting way, and discussed
neuromesoderm to challenge existing concepts. I agree with the author's perspective that there are still quite some
unknown about embryo development. As a matter of fact, based on the studies of pluripotent stem cells, e.g., embryonic
stem cells, a equivalent of in vivo epiblast, early cell lineages are still very plastic. The cells sometimes do not have to go
through the natural developmental stages to differentiate into certain tissues cells. These cells can even be readily
converted back to cell fates of earlier developmental stages. As we conduct more experiments, we may realize that cells,
e.g., mesoderm, have more diverse sources than the views in the classical text books. To make this article more
comprehensive, the authors could discuss more along this path. Qeios ID: 36PAZ1 · https://doi.org/10.32388/36PAZ1 1/1 |
https://openalex.org/W4240635492 | http://scielo.iics.una.py/pdf/ccv/v8n1/2226-1761-ccv-8-01-5.pdf | Spanish; Castilian | null | null | Compendio de ciencias veterinarias | 2,018 | cc-by | 778 | Prof. Dra. Elizabeth Nuñez Grüner, M.Sc
Directora de la Revista “Compendio de Ciencias Veterinarias” doi: 10.18004/compend.cienc.vet.2018.08.01.5-6 DESAFÍOS DE LA INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA La Facultad de Ciencias Veterinarias de la Universidad Nacional de Asunción está llamada a asumir de
manera impostergable el desafío de imprimir mayor fuerza a la búsqueda de soluciones para la realidad
nacional mediante la investigación científica y tecnológica. Los lineamientos en este ámbito deben orientarse a favorecer el logro de los objetivos estratégicos de la
visión país 2030, de reducción de la pobreza, promoción del crecimiento económico inclusivo e inserción
del país en el mundo. (1) En concordancia con el hecho de que son temas relevantes, el gasto público en
este ítem se ha incrementado de 0,06% del PIB en el año 2008 a 0,13% del PIB en el 2015; aun así,
continúa siendo la más baja inversión per cápita de la región (Br 1,14%, Ar 0,58%, Uy 0,33%). (2) En el contexto al que se hace referencia, nuestra casa de estudios ha tenido progresos. Entre ellos, se ha
creado el Departamento de Investigación Científica y Tecnológica (DICT), definido líneas de
investigación, el lanzamiento en el año 2011 de la revista “Compendio de Ciencias Veterinarias”. Así
también, la FCV cuenta con Docente Investigador de Dedicación Completa (DIDCom) y una veintena de
colegas del plantel docente, que han ingresado como investigadores categorizados del Consejo Nacional
de Ciencia y Tecnología (CONACYT), hecho iniciado en el año 2013 y que al 2018 casi ha duplicado el
número inicial. Por otro lado, se ha incrementado la calidad y cantidad de publicaciones científicas; que
son logros destacables y dan cuenta de un franco avance hacia la internalización del concepto de que si no
hay investigación, no hay conocimiento y si no hay conocimiento, no hay progreso. Por tanto, haciendo una pausa y mirando hacia atrás, es un hecho que el camino se ha iniciado y es preciso
avanzar hacia la construcción de una comunidad educativa capaz de entregar medidas efectivas y eficaces
a la sociedad en materia de generación y transferencia de conocimientos; con una gestión de
investigación basada no solo en la interdisciplinariedad y concurrencia temática; sino que también y
sobre todo, en dar respuestas a problemas trascendentes de la realidad nacional y regional. Prof. Dra. Elizabeth Nuñez Grüner, M.Sc
Directora de la Revista “Compendio de Ciencias Veterinarias” doi: 10.18004/compend.cienc.vet.2018.08.01.5-6 5 ISSN 2226-1761
Compend. cienc. vet. 2018; 08 (01) : 5 - 6 ISSN 2226-1761
Compend. cienc. vet. 2018; 08 (01) : 5 - 6 5 ISSN 2226-1761 Prof. Dra. Elizabeth Nuñez Grüner, M.Sc
Directora de la Revista “Compendio de Ciencias Veterinarias” SCIENTIFIC AND TECHNOLOGICAL RESEARCH CHALLENGES Veterinary Sciences Faculty of the National University of Asunción, it´s called to assume, in an urgent way,
the challenge of strength the search of solutions for national reality through scientific and technological
research. The guidelines, in this area, should be oriented to improve the strategic objectives achievement of the
2030 country vision, poverty reduction, inclusive economic growth promoting and the country's
insertion in the world (1). Consistent with the fact that they are relevant issues, public spending on this
item has increased from 0.06% of GDP in 2008 to 0.13% of GDP in 2015; even so, it continues to be the
lowest investment per capita in the region (Br 1.14%, Ar 0.58%, Uy 0.33%). (2) In the context to which reference are made, our Studies House has made progress. Among them, the
Scientific and Technological Research Department (DICT) has been created, defined research lines and
the "Veterinary Sciences Compendium" magazine was launched in 2011. Likewise, the FCV has full-time
Research Teachers (DIDCom) and about twenty colleagues from the teaching staff, who have entered as
categorized researchers of the Science and Technology National Council (CONACYT), a fact that began in
2013 and that 2018 has almost doubled the initial number. On the other hand, quality and quantity of
scientific publications have increased; which are remarkable achievements and account for a frank
advance towards the internalization of the concept that if there is no research, there is no knowledge and
if there is no knowledge, there is no progress. Therefore, by pausing and looking back, it is a fact that the road has begun and it is necessary to move
towards the construction of an educational community capable of delivering effective measures to
society in terms of knowledge generation and transfer. With a research management based not only on
interdisciplinary and thematic concurrence, but also and above of all, in giving answers to transcendental
problems of the national and regional reality. 6 ISSN
Compend. cienc. vet. 2018; 08 (01) : 5 - 6 Compend. cienc. vet. 2018; 08 (01) : 5 - 6 |
https://openalex.org/W3158344372 | https://iris.unipa.it/bitstream/10447/569585/2/StatisticsInMedicine2021.pdf | English | null | Nowcasting COVID‐19 incidence indicators during the Italian first outbreak | Statistics in medicine | 2,021 | cc-by | 15,819 | Correspondence Correspondence
Pierfrancesco Alaimo Di Loro,
Department of Statistical Sciences,
University of Rome “La Sapienza”, Rome,
Lazio 00185, Italy. Email:
pierfrancesco.alaimodiloro@uniroma1.it K E Y W O R D S 6Department of GEPLI, Libera Universitá
Maria Ss Assunta, Rome, Italy COVID-19, growth curves, Richards’ equation, SARS-CoV-2 COVID-19, growth curves, Richards’ equation, SARS-CoV-2 7Department of Mathematics, University
of Bergen, Bergen, Norway 8IAC - CNR, Institute of Applied
Computing “M. Picone”, Rome, Italy Received: 24 October 2020
Revised: 8 March 2021
Accepted: 8 April 2021 Received: 24 October 2020
Revised: 8 March 2021
Accepted: 8 April 2021
DOI: 10.1002/sim.9004 Revised: 8 March 2021
Accepted: 8 April 2021 Received: 24 October 2020 DOI: 10.1002/sim.9004 R E S E A R C H A R T I C L E Nowcasting COVID-19 incidence indicators during the
Italian first outbreak Pierfrancesco Alaimo Di Loro1
Fabio Divino2
Alessio Farcomeni3
Giovanna Jona Lasinio1
Gianfranco Lovison4,5
Antonello Maruotti6,7
Marco Mingione1,8 Pierfrancesco Alaimo Di Loro1
Fabio Divino2
Alessio Farcomeni3
Giovanna Jona Lasinio1
Gianfranco Lovison4,5
Antonello Maruotti6,7
Marco Mingione1,8 1Department of Statistical Sciences,
University of Rome “La Sapienza”, Rome,
Italy
2Department of Bio-Sciences, University
of Molise, Campobasso, Italy
3Department of Economics and Finance,
University of Rome “Tor Vergata”, Rome,
Italy
4Department of Economics, Management
and Statistics, University of Palermo,
Palermo, Italy
5Department of Epidemiology and Public
Health, Swiss TPH Basel, Basel,
Switzerland
6Department of GEPLI, Libera Universitá
Maria Ss Assunta, Rome, Italy
7Department of Mathematics, University
of Bergen, Bergen, Norway
8IAC - CNR, Institute of Applied
Computing “M. Picone”, Rome, Italy
Correspondence
Pierfrancesco Alaimo Di Loro,
Department of Statistical Sciences,
University of Rome “La Sapienza”, Rome,
Lazio 00185, Italy. Email:
pierfrancesco.alaimodiloro@uniroma1.it 1Department of Statistical Sciences,
University of Rome “La Sapienza”, Rome,
Italy 1Department of Statistical Sciences,
University of Rome “La Sapienza”, Rome,
Italy A novel parametric regression model is proposed to fit incidence data typically
collected during epidemics. The proposal is motivated by real-time monitoring
and short-term forecasting of the main epidemiological indicators within the
first outbreak of COVID-19 in Italy. Accurate short-term predictions, includ-
ing the potential effect of exogenous or external variables are provided. This
ensures to accurately predict important characteristics of the epidemic (e.g.,
peak time and height), allowing for a better allocation of health resources over
time. Parameter estimation is carried out in a maximum likelihood framework. All computational details required to reproduce the approach and replicate the
results are provided. 2Department of Bio-Sciences, University
of Molise, Campobasso, Italy 3Department of Economics and Finance,
University of Rome “Tor Vergata”, Rome,
Italy 4Department of Economics, Management
and Statistics, University of Palermo,
Palermo, Italy K E Y W O R D S
COVID-19, growth curves, Richards’ equation, SARS-CoV-2 K E Y W O R D S
COVID-19, growth curves, Richards’ equation, SARS-CoV-2 © 2021 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. 2 10% of those infected.3 During the outbreak, it was crucial to set up appropriate data collection and modeling systems
quickly. Both were necessary for monitoring, evaluation of policy interventions, and prediction. 10% of those infected.3 During the outbreak, it was crucial to set up appropriate data collection and modeling systems
quickly. Both were necessary for monitoring, evaluation of policy interventions, and prediction. Generally speaking, the nature of epidemics’ spread has nearly always followed the same scenario: first, the growth in
the number of infected people is (close to) exponential; in a second moment, this growth gradually but consistently slows
down as an effect, for instance, of various containment measures. This pattern can cyclically recur until the outbreak is
tamed. So far, in order to explain the spread of epidemics and predict their consequences, a number of mathematical and sta-
tistical models of different complexity levels have been used. The starting point is often the Verhulst logistic equation,4
which can easily capture both the exponential increase in the number of infected people at the initial stage of the epi-
demic development, and the tendency towards a constant value by its ending. In more complex models, people are
divided into different groups: (S) the susceptible class, namely those individuals who are capable of contracting the dis-
ease and becoming infected; (I) the infected class, namely those individuals who are capable of transmitting the disease
to others; (R) the removed class, namely infected individuals who are deceased or have recovered, who are either perma-
nently immune or isolated. This group of mathematical models are called SIR (or compartmental) models.5 References
include,6-9 and several more. However, whilst being potentially very appropriate to model the dynamics underlying any
epidemic, SIR-based models rely on accurate initial estimates of several quantities governing its spreading mechanism
(which are unknown). Poor data input on key features of the pandemic can heavily bias these estimates, jeopardizing
the reliability of any theory-based forecasting effort. SIR models are microsimulation models and we believe that, gen-
erally speaking, they should be used mostly for “scenario evaluation” rather than predicting future outcomes. Indeed,
they rely on several speculations and strict theoretical assumptions, not necessarily met by the analyzed data and, espe-
cially during the first stage of the outbreak, failed in predicting various COVID-19 related outcomes.10 Such specifics lead
the choice of coefficients in the equations defining the SIR model and define its initial conditions. It is well known that
even a slight change in those can lead to large differences in the final results. For instance, at the beginning of the epi-
demic, early data providing estimates for case fatality rate, infection fatality rate, basic reproductive number, and other
key numbers that are essential for the modeling, are often inflated and may cause potentially large overestimation of the
epidemic severity. Similar criticism to using compartmental modeling for nowcasting can also be found in Reference 11,
and references therein. Hence, we have preferred to follow an alternative approach, which involved direct modeling of
the observed counts.12 This encompasses the use of phenomenological models without detailed mechanistic foundations,
but which have the advantage of allowing simple calibrations to the empirical reported data. Such approaches are partic-
ularly suitable when substantial uncertainty tarnishes the epidemiology of an infectious disease, including the potential
contribution of multiple transmission pathways. In these situations, phenomenological models provide a starting point
for obtaining early estimates of the transmission potential and short-term forecasts of the epidemic evolution.13 g
We propose a parametric regression model for the modeling of incidence indicators (defined in Section 2.1) based on the
use of the Richards’ curve (a generalized logistic function) in place of the widely used exponential or polynomial trends. Furthermore, we replace the generally entrenched Gaussian assumption for the distribution of log-counts14,15 by the more
appropriate Poisson or Negative Binomial distributions for counts. In this way we avoid the implausible assumptions
stemming from the more common alternatives: the former allows the underlying counts to potentially grow indefinitely;
the latter neglects the proper specification of dependence between mean and variance under the log-normal distribution. We further propose different ways of including the effect of exogenous information on the response function of counts,
in an extended generalized linear model framework. These models have been implemented during the outbreak with
the aim of modeling the medium to long term evolution of the epidemic wave. 1
INTRODUCTION Italy has been the first European country to be severely hit by the first epidemic wave due to the spread of the SARS-CoV-2
virus. COVID-19 syndrome emerged in northern Italy in February 2020, with a basic reproduction number R0 between
2.5 and 4.1 In its most severe form, COVID-19 has two challenging characteristics:2 it is highly infectious and, despite
having a benign course in the vast majority of patients, it requires hospital admission and even intensive care for about
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the
original work is properly cited. © 2021 The Authors Statistics in Medicine published by John Wiley & Sons Ltd Italy has been the first European country to be severely hit by the first epidemic wave due to the spread of the SARS-CoV-2
virus. COVID-19 syndrome emerged in northern Italy in February 2020, with a basic reproduction number R0 between
2.5 and 4.1 In its most severe form, COVID-19 has two challenging characteristics:2 it is highly infectious and, despite
having a benign course in the vast majority of patients, it requires hospital admission and even intensive care for about wileyonlinelibrary.com/journal/sim Statistics in Medicine. 2021;1–22. 1 ALAIMO DI LORO et al. 2.1
Incidence and prevalence indicators: different mathematical features The epidemiological data provided by CPD can be distinguished into two basic types: 1. incidence indicators (flows) 1. incidence indicators (flows) 2. prevalence indicators (stocks) The use of logistic-based curves is also
widely discussed in the literature.16-18 Logistic growth curves can be seen as a flexible formulation for approximating a
large variety of growth phenomena, especially in biology and in epidemiology.19-23 In particular, highly flexible parametric
models such as Gompertz curves and the unified Richards’ family24 have been proposed in the study of organisms’ growth,
for a review see Reference 25. The article is organized as follows: Section 2 gives a detailed description of the Italian situation and provides a brief
account of the Italian public data made available daily, with some remarks on limitations and flaws in the data collection
process; Section 3 contains a description of our approach to modeling incidence indicators, including remarks on how to
obtain standard errors for parameters and predictions performances; Section 4 illustrates results of our approach applied
to the incidence indicators recorded during first wave of the Italian outbreak of COVID-19. Finally, results are discussed
and commented along with some concluding remarks in Section 5. The methods discussed in this article have also been implemented in a Shiny app, publicly available at https://
statgroup19.shinyapps.io/StatGroup19-Eng/. in this article have also been implemented in a Shiny app, publicly available at https://
tatGroup19-Eng/. ALAIMO DI LORO et al. 3 2
AVAILABLE DATA AND THEIR LIMITATIONS The Italian Civil Protection Department (CPD), starting from February 24th, 2020, has been gathering data at the regional
level every day and making these public in a GitHub repository. During most of the Italian epidemic, data were com-
mented by the department head in an official press release at about 6 pm. The daily updated data are currently stored
at https://github.com/pcm-dpc/COVID-19. For public health service purposes, Italy is divided into 21 regions. There are
19 administrative regions, plus two autonomous provinces (Trento and Bolzano) that form the administrative region of
Trentino-Alto-Adige. In the sequel, we focus on modeling the indicators aggregated at the national level. Nevertheless,
the supplementary material contains graphical and quantitative performances of our model on the 21 single regions. 2.1.1
Incidence indicators (B)
F I G U R E 1
Time series
the Italian daily incidence
indicators: daily positives, A an
daily deceased, B (B) F I G U R E 1
Time series of
the Italian daily incidence
indicators: daily positives, A and
daily deceased, B F I G U R E 1
Time series of
the Italian daily incidence
indicators: daily positives, A and
daily deceased, B (A) (B) (B)
F I G U R E 2
Time serie
the Italian cumulative incide
indicators: cumulative positiv
A and cumulative deceased, B (B) (A) F I G U R E 2
Time series of
the Italian cumulative incidence
indicators: cumulative positives,
A and cumulative deceased, B F I G U R E 2
Time series of
the Italian cumulative incidence
indicators: cumulative positives,
A and cumulative deceased, B (A) (B) By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for
the positives and deceased example). By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for
the positives and deceased example). 2.1.1
Incidence indicators Incidence indicators measure the number of individuals with a particular condition, related with the epidemic, recorded
during a given period. They can be referred to different time periods; in particular, in the CPD dataset, daily incidence
counts are available for the following indicators: • positives, which are subclassified into two subconditions: – hospitalized (either in regular wards or in ICU) – isolated-at-home • deceased • recovered/discharged • recovered/discharged These indicators can be considered, by analogy with the terminology used in econometrics, as flow data, quantifying
the daily input (positives) and output (deceased and recovered/discharged) of the system. The time series of daily positives
and daily deceased aggregated at the national level are shown in Figure 1. From the viewpoint of the following modeling
effort, one important feature of these indicators is that they can be referred to longer time intervals, simply cumulating
them over time. The most interesting cumulative incidence indicators are those referring to the whole history of the pan-
demic, computed from a conventional date of “beginning of the pandemic” (typically, the day the systematic recording of
daily positives began) to the current day: • cumulative positives • cumulative deceased • cumulative recovered/discharged In particular, given Y 0 = 0, we can build the whole series of cumulative counts conditionally on the value of the
cumulative indicator at time (t −1), and the incidence indicators at time t, for each t = 1, … , T: Y c
t = Y c
t−1 + It, where Y c
t represents the cumulative indicator and It represents the inputs in the system, for example: cumulative positives
at time t are the cumulative positives at time (t −1) plus the daily positives at day t. 4
ALAIMO DI LORO et al. (A)
(B)
F I G U R E 1
Time series of
the Italian daily incidence
indicators: daily positives, A and
daily deceased, B
(A)
(B)
F I G U R E 2
Time series of
the Italian cumulative incidence
indicators: cumulative positives,
A and cumulative deceased, B
By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for
the positives and deceased example). 4
(A) ALAIMO DI LORO et al. 2.1.2
Prevalence indicators Prevalence indicators measure the number of individuals with a particular condition, related with the epidemic, at a given
instant in time (or at a given short interval of time, eg, a day). They are typically obtained from simple algebra from other
indicators; in particular, in the CPD dataset, the following indicators are available daily: • current positives; • current intensive care units (ICU) occupancy. These indicators result from the balance between total inputs and outputs of the system, for example: current positives
are the difference between cumulative positives and cumulative deceased plus recovered/discharged. Again, by analogy
with the terminology used in econometrics, they can be considered as stock data. In particular, given Y 0 = 0, we can build
the whole series conditionally on the value of the prevalence indicator at time (t −1), and the incidence indicators at
time t, for each t = 1, … , T: Y p
t = Y p
t−1 + It −Ot, ALAIMO DI LORO et al. 5
F I G U R E 3
Time series of
Italian daily prevalence
indicators: current positive,
A and ICU occupancy, B
(A)
(B)
where Y p
t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for
example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the
sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information
by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling
the indicators individually. Two important features of these indicators are that: 5
(B) ALAIMO DI LORO et al. 2.1.2
Prevalence indicators by their own nature, these indicators are not monotone, since they can increase or decrease as a result of different
trends of the component series. Typically, we expect the series of current positives and ICU occupancy to increase in
the rising phase of an epidemic, reach a peak and then decrease to a lower asymptote (see Figure 3), although more
complex patterns due to resurgence of the epidemic are also plausible. Prevalence indicators are characterized by a strong and tangled dependence structure which is cumbersome to
simplify into a manageable and useful statistical model on the short run. For this reason, the focus of this work concerns only incidence indicators. Our model proposal, from a strictly mathe-
matical point of view, could potentially applied also on prevalence indicators. However, from the statistical point of view,
the modeling assumptions which are assumed to hold (with good approximation) considering the incidence indicators,
are likely to be strongly violated by prevalence indicators and the resulting outcome cannot be considered reliable. A brief
discussion about some possible approaches for the analysis of prevalence indicators is given in Section 5. 2.1.2
Prevalence indicators 5 Time series of
evalence
rent positive,
upancy, B
(A) F I G U R E 3
Time series of
Italian daily prevalence
indicators: current positive,
A and ICU occupancy, B F I G U R E 3
Time series of
Italian daily prevalence
indicators: current positive,
A and ICU occupancy, B (B) (A) where Y p
t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for
example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the
sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information
by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling
the indicators individually. Two important features of these indicators are that: where Y p
t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for
example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the
sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information
by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling
the indicators individually. Two important features of these indicators are that: 1. given their stock nature, they cannot be aggregated (eg,: it does not make sense to compute “cumulative current
positives”); 1. given their stock nature, they cannot be aggregated (eg,: it does not make sense to compute “cumulative current
positives”); 2. by their own nature, these indicators are not monotone, since they can increase or decrease as a result of different
trends of the component series. Typically, we expect the series of current positives and ICU occupancy to increase in
the rising phase of an epidemic, reach a peak and then decrease to a lower asymptote (see Figure 3), although more
complex patterns due to resurgence of the epidemic are also plausible. 2. could be even weeks before. Positive status is also counted on the day that test results are received, with swabs being
processed from one day to weeks after symptoms’ onset. No distinction between actively symptomatic and asymptomatic
patients was made. Swabs and positive cases are not time-aligned. For example, in countries like Singapore (https://www.moh.gov.sg/
covid-19), daily data include information on total swabs tested, total unique persons swabbed as well as total swabs per
1 000 000 total population and total unique persons swabbed per 1 000 000 total population. In Italy, up to April 19th,
2020, only the total number of daily swabs is available, and no linkage between swabs and tested individuals was kept
in the data repository. Hence, it is impossible to make statistically sound use of swabs’ count to model the whole first
pandemic wave. Finally, it is crucial to recall that people diagnosed with COVID-19 disease are only a small fraction of the people
infected by the virus. Moreover, since the tracking was highly symptoms driven, especially in the first phase of the out-
break, the detected number of positives cases can provide only a partial estimate of the true incidence of COVID-19 in the
Italian population. Eventually, we expect this detected fraction to vary wildly over space and time. In our opinion, the most reliable indicator is the count of ICU occupancy. The reason is that the Italian Society for
Emergency Care issued national guidelines (that did not change substantially during the epidemic) for testing patients
with a suspected infection by SARS-CoV-2, who also had top priority for swab access and reporting; and ICU admissions
can be expected to depend on the proportion of infected population susceptible to severe infection, rather than on the
regional strategy for testing and contact tracing. However, while probably reliable, this indicator also presents some draw-
backs. First of all, it provides only a partial snapshot of the epidemic’s current stage, which concerns the most severe cases
of the disease. The latter is a critical issue, especially in the COVID-19 case, which is known to present severe symptoms
only in a small percentage of the currently affected individuals. Second, this snapshot is affected by a constant delay (ie,
the time between catching the disease and manifesting severe symptoms). As mentioned in Section 2.1.2, its daily vari-
ation is obtained as a combination of new incoming patients (+) and the deceased or recovered ones (-), whose effects
blend and are hard to disentangle. As a consequence, incidence indicators, such as daily positives and daily deceased, while
being measured with some error and even more delay in the case of deaths, still represent the critical indicators for timely
and appropriate monitoring of the pandemic. 3
MODEL SPECIFICATION The time series of any of the observed indicators, denoted by z = {zt}T
t=t0, is modeled separately and considered as the
realization of the stochastic process Z = {Zt}T
t=t0. The idea behind this article is to model any of the mentioned indicators
through a Generalized Model with a response function E[Zt] = 𝜇(t) = g−1(t; 𝜽), where g(⋅) is a known link function and
𝜽is a parameter vector, that is appropriate for the specific mathematical features of the epidemic process. This must be
coupled with a response distribution f(Zt; 𝛉) coherent with the domain of such indicators, which are counts and therefore
Natural numbers. 2.2
Data issues COVID-19 public Italian data present several issues that severely affect their quality. The information has been gathered
and reported at a regional level, and each regional healthcare organization has a different transmission and data collection
system*. Measurement errors, and errors in data entry, are expected to be often present. Delays in reporting has been,
sometimes, substantial. Some patients were transferred (eg, from Lombardia to Puglia, and even to Germany) without
notification, and they were counted as hospital patients of the receiving region (or not at all when sent abroad) and posi-
tive cases of the region of residence. Most importantly, counts were updated on the notification day rather than aligned to
a more appropriate date. For example, death is counted on the day of the reporting, not on the day of the outcome, which *see https://www.epiprev.it/materiali/2020/EP2-3/112_edit1.pdf for further details. ALAIMO DI LORO et al. 3.1
Response function for incidence indicators F I G U R E 4
Example of
Richards’ curve, A and derivative
of the Richards’ curve, B
0.0
0.3
0.6
λ
0.9
0
1
2
3
4
5
t
(A)
t F I G U R E 4
Example of
Richards’ curve, A and derivative
of the Richards’ curve, B F I G U R E 4
Example of
Richards’ curve, A and derivative
of the Richards’ curve, B (B) can be expressed as: can be expressed as: E[Y c
t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b +
r
(1 + 10h(p−t))s . (1) E[Y c
t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b +
r
(1 + 10h(p−t))s . (1) b ∈R+ represents a lower asymptote and r > 0 is the distance between the upper and the lower asymptote, hence
b + r would be the final epidemic size; h is known as the hill, and represents the infection/growth rate; p ∈R represents a
lag-phase of the trajectory and determines the peak position (it tells when the curve growth speed slows down); s ∈R is
an asymmetry parameter regulating differences in the behavior of the ascending and descending phase of the outbreak. In
our context, since cumulative incidences are always monotone increasing indicators, it is reasonable to assume h, s > 0 †. An extensive review of the Richards’ curve and other logistic growth models, together with discussion on the proper
interpretation of the parameters, is given in Reference 24. An extensive review of the Richards’ curve and other logistic growth models, together with discussion on the proper
interpretation of the parameters, is given in Reference 24. An Extended Generalized Linear Model with (1) as response function seems to be a natural choice for modeling time
series of cumulative counts, whose monotonically nondecreasing average behaves as the Richards’ curve. Unfortunately,
there is a significant drawback to this choice. As it will be better clarified in Section 3.2, a very useful working assumption
would be that all these counts were stochastically independent, given their mean function 𝜆𝜸(t). However, we cannot
consider this assumption as realistic in the case of cumulative counts, since the constraint on the domain of definition on
subsequent counts (ie, yc
t ≥yc
𝜏, ∀𝜏< t) is not guaranteed to be satisfied. †Conversely, we may assume h, s < 0 3.1
Response function for incidence indicators Let us denote by {yc
t}T
t=0 the time-series of cumulative incidence indicators since the start of the epidemic (t0 = 0, first day
of systematic data recording). Visual inspection of these indicators in Figure 2 suggests that their expected values follow
a logistic-type growth curve. Different example of logistic curves have been proposed in the literature, all representing
solutions to specific differential equations that model the spread of epidemics.26-28 Differently from the more standard
exponential models, these are able to describe the slowdown of the outbreak associated with a decaying transmission
rate just after the number of cases approaches its inflection point. They have been already widely used to describe the
evolution of the COVID-19 pandemic in different states during its early to medium stage.29,30 Here, for all the incidence
indicators, we consider the Generalized Logistic Function, also known as Richards’ curve (see Figure 4 as an example), as
response function for the mean of the process.31 This curve was widely used to describe various biological processes,32
but has been recently adapted also in epidemiology for real-time prediction of outbreak of diseases.33-35 The specialty of
the Richards’ curve lies in its ability to describe a great variety of growing processes, endowed with strong flexibility, that
includes as special cases the standard logistic growth curve,36 the Gompertz growth curve37 and others. It can be expressed
in different forms.38-41 One of its most general formulation depends on the vector of five parameters 𝜸⊤= [b, r, h, p, s] and ALAIMO DI LORO et al. 7
F I G U R E 4
Example of
Richards’ curve, A and derivative
of the Richards’ curve, B
0.0
0.3
0.6
λ
λ
0.9
0
1
2
3
4
5
t
(A)
(B)
t
0.00
0.02
0.04
0.06
0
1
2
3
4
5
t
t
~
can be expressed as:
E[Y c
t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b +
r
(1 + 10h(p−t))s . (1) 7
λ
(B)
0.00
0.02
0.04
0.06
0
1
2
3
4
5
t
t
~ ALAIMO DI LORO et al. 8 ALAIMO DI LORO et al. In addition, we may also consider adding a kink effect/baseline 𝛼to the first differences ̃𝜆𝜸(⋅), which is to say assuming
the following functional form for the mean of the daily counts: ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t),
𝛼≥0,
(2) ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t),
𝛼≥0,
(2) ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t),
𝛼≥0, (2) where 𝜽= (𝛼, 𝜸). This would correspond to the following mean function for the cumulative counts: orrespond to the following mean function for the cumulative counts: 𝜇𝜽(t) = 𝛼⋅(t −1) + 𝜆𝜸(t). 𝜇𝜽(t) = 𝛼⋅(t −1) + 𝜆𝜸(t). In practice, the parameter 𝛼includes the possibility of having a strictly positive baseline rate, which can be interpreted
as the endemic steady state incidence rate. This is in line with the current perspective that SARS-CoV-2 might not be
completely eradicated within the next few years.42 On the other hand, the first differences of the Richards’ curve ̃𝜆𝜸(t) are
(by construction) forced to decrease asymptotically to the value of 0. However, this asymptotic result is not necessarily
observed in real data. In particular, Figure 1 highlights that both time-series do not attain the 0 value, but settle to a low,
constant level. This situation may, potentially, continue indefinitely: new cases will be found as long as people will be
tested. Consequently, the model without a baseline lacks the ability to catch this tail and, because of the curve parametric
form, this may indirectly affect the fit on the whole series. In practice, the parameter 𝛼includes the possibility of having a strictly positive baseline rate, which can be interpreted
as the endemic steady state incidence rate. This is in line with the current perspective that SARS-CoV-2 might not be
completely eradicated within the next few years.42 On the other hand, the first differences of the Richards’ curve ̃𝜆𝜸(t) are
(by construction) forced to decrease asymptotically to the value of 0. However, this asymptotic result is not necessarily
observed in real data. In particular, Figure 1 highlights that both time-series do not attain the 0 value, but settle to a low,
constant level. This situation may, potentially, continue indefinitely: new cases will be found as long as people will be
tested. Consequently, the model without a baseline lacks the ability to catch this tail and, because of the curve parametric
form, this may indirectly affect the fit on the whole series. 8 In the first instance, one solution would be to fit the model, including the kink effect 𝛼. Afterward, if it is estimated not
to be sensibly different from 0, the model without 𝛼can be fitted again to stabilize the estimation procedure and decrease
the uncertainty on the other parameters. 3.2
Response distribution for incidence indicators Before introducing the distributions for the daily incidence counts, we must make some assumptions about the time
dependence structure. In particular, we assume that given the mean function ̃𝜇𝜽(t), the daily incidence counts Y t are
stochastically independent from the previous cumulative counts: Yt⊥Y c
𝜏∀𝜏< t. We denote this hypothesis of indepen-
dence by HI. We also assume the value of the first cumulative count Y c
0 = yc
0 to be known and fixed. Exploiting HI,
we can express the joint density of all the subsequent cumulative counts conditional on Y c
0 = yc
0 as the product of the
univariate densities of the corresponding daily counts {Yt}T
t=1. The equivalence follows from the following conditional
argument: fY c
1, … ,Y c
T(yc
1, … , yc
T|yc
0; 𝜃) =
T
∏
t=1
fY c
t (yc
t|yc
0, … , yc
t−1; 𝜃) =
T
∏
t=1
fY c
t (yt + yc
t−1|yc
0, … , yc
t−1; 𝜃) =
=
T
∏
t=1
fYt(yt|yc
0, … , yc
t−1; 𝜃)
HI=
T
∏
t=1
fYt(yt|𝜃), where the second identity is justified in the light of Y c
t = Yt + Y c
t−1, t = 1, … , T, which is true by definition. From a
practical point of view, this also implies a first-order Markov property for the cumulative counts: where the second identity is justified in the light of Y c
t = Yt + Y c
t−1, t = 1, … , T, which is true by definition. From a
practical point of view, this also implies a first-order Markov property for the cumulative counts: Y c
t |Y c
t−1⊥Y c
1, … , Y c
t−2,
t = 1, … , T Y c
t |Y c
t−1⊥Y c
1, … , Y c
t−2,
t = 1, … , T and mutual independence between the daily counts: and mutual independence between the daily counts: Yt⊥Y𝜏,
∀t, 𝜏, t ≠𝜏. We remark that although these independence structure is just an approximation in the present case, this kind of approach
has provided valid inference for all the available Italian incidence indicators. We remark that although these independence structure is just an approximation in the present case, this kind of approach
has provided valid inference for all the available Italian incidence indicators. 3.1
Response function for incidence indicators On the other hand, the stochastic independence
assumption sounds more reasonable, albeit not necessarily true, for the daily incidence counts {yt}T
t=1, that is, the addenda
of the cumulative counts excluding the starting point y0, which can be defined as: yc
t =
t∑
𝜏=0
y𝜏
⇒
yt = yc
t −yc
t−1,
t = 1, … , T, where y0 = 0 by definition. where y0 = 0 by definition. y0
y
Using Equation (1), and exploiting the additive properties of the expected value, we have: Using Equation (1), and exploiting the additive properties of the expected value, we have: ̃𝜇(t) = E[Yt] = E[Y c
t ] −E[Y c
t−1] = 𝜆𝜸(t) −𝜆𝜸(t −1) =
= r ⋅[(1 + 10h(p−t))−s −(1 + 10h[p−(t−1)])−s] = ̃𝜆𝜸(t) which, in particular, does not depend on the baseline b. Therefore, we shall adopt an extended Generalized Model with
response function given by the first differences of the Richards’ curve ̃𝝀𝜸= { ̃𝜆𝜸(t)}T
t=1 to model the daily expected values
𝝁= {𝜇(t)}T
t=1 of the observed incidence counts y = {yt}T
t=1 (see example in Figure 4). which, in particular, does not depend on the baseline b. Therefore, we shall adopt an extended Generalized Model with
response function given by the first differences of the Richards’ curve ̃𝝀𝜸= { ̃𝜆𝜸(t)}T
t=1 to model the daily expected values
𝝁= {𝜇(t)}T
t=1 of the observed incidence counts y = {yt}T
t=1 (see example in Figure 4). †Conversely, we may assume h, s < 0 3.2.1
Poisson distribution or of daily incidence counts, y = {y1, … , yt}, is composed of independent Poisson realizations Let us assume that the vector of daily incidence counts, y = {y1, … , yt}, is composed of independent Poisson realizations
with expected value ̃𝜇𝜽(t): Yt|𝜽∼Pois( ̃𝜇𝜽(t)),
t = 1, … , T. Hence, the likelihood can be written as: Hence, the likelihood can be written as: Hence, the likelihood can be written as: (𝜽|y) =
T
∏
t=1
Pois(yt| ̃𝜇𝜽(t)) ∝
∝̃𝜇𝜽(t)
∑T
t=1yt ⋅exp
{
−
T
∑
t=1
̃𝜇𝜽(t)
}
and the log-likelihood is given by:
l(𝜃|y) = log (𝜽|y) ∝
T
∑
t=1
yt log( ̃𝜇𝜽(t)) −
T
∑
t=1
̃𝜇𝜽(t). (𝜽|y) =
T
∏
t=1
Pois(yt| ̃𝜇𝜽(t)) ∝ ∝̃𝜇𝜽(t)
∑T
t=1yt ⋅exp
{
−
T
∑
t=1
̃𝜇𝜽(t)
} and the log-likelihood is given by: and the log-likelihood is given by: l(𝜃|y) = log (𝜽|y) ∝
T
∑
t=1
yt log( ̃𝜇𝜽(t)) −
T
∑
t=1
̃𝜇𝜽(t). Remark that, under the assumption of Poisson distribution and the baseline 𝛼= 0 (ie, ̃𝜇(𝛼,𝜸) = ̃𝜆𝜸(⋅)), we can exploit
the well-known Poisson’s additive property ‡ to conclude that each cumulative count Y c
t is still marginally distributed
according to a Poisson, parameterized by the original Richards’ curve function 𝜆𝜸(⋅): Y c
t |𝜸∼Pois
( t∑
𝜏=1
̃𝜆𝜸(𝜏)
)
= Pois(𝜆𝜸(t)). 3.2
Response distribution for incidence indicators For communication purposes, it can be of interest to report the results of analyses and predictions in terms of cumu-
lative, rather than daily, incidence indicators. Clearly, it is possible to model and predict the daily incidence indicators
and, from these estimates and predictions, obtain the relevant cumulative incidence indicators. ALAIMO DI LORO et al. 9 3.3
Response function depending on covariates The trend of any of the considered indicators may also depend on additional exogenous information, which we may
assume to be known a priori either because it is immutable (ie, the day of the week), or because policymakers fixed it
(daily number of tested cases/swabs set by the government). For instance: one might want to correct for possible weekly
seasonality, which is known to affect the daily positives series since many laboratories are closed during the weekend
and cannot evaluate swabs. The latter can be used to disentangle the underlying trend of the epidemic from the obvious
positive correlation between tested cases and daily positives. In general, we may want to include the effect of any set of
k time-varying covariates XT×(k+1) = [x(t)]T
t=1 in the Richards’ framework through the usual linear predictor 𝜂(X) = X𝜷,
where 𝜷is a k + 1-dimensional vector of real valued parameters (including intercept). Let us denote the mean function
of the considered indicator as ̃𝜇𝜃(t) = E[Yt], where 𝜽= (𝛼, 𝜸, 𝜷). In order to respect the positivity of the mean parameter
(which is necessary both in the Poisson and in the Negative Binomial case), we consider the link function g(⋅) = log(⋅), so
that the effect on the mean is expressed as: 𝜇𝜷(X) = exp{𝜂(X)} = exp{X𝜷}. Considering a single time point t, we would get the following functional form: Considering a single time point t, we would get the following functional form: 𝜇𝜷(x(t)) = exp{x(t)𝜷}. The mean term of our model shall take into account both the effect of the covariates through 𝜇𝜷(⋅) and the temporal
behavior induced by the Richards’ curve 𝜆𝜸(⋅). As a matter of fact, these two components may be combined in different
ways. We considered two alternative specifications denoted in the sequel as: additive and multiplicative. 3.3.1
Additive inclusion of covariates The inclusion of an additive effect of covariates implies that the effect of every covariate is constant through-out the
pandemic, notwithstanding the current contagion level: for instance, one may think that an increase of daily tested cases
will always produce the same increase of daily daily positives. If that is the case, we may just express the baseline parameter
𝛼at each time-point t as the linked linear combination of covariates 𝜇𝜷(x(t)) = exp{x(t)𝜷}, which would produce the
following mean function: ̃𝜇𝜃(t) = 𝜇𝜷(x(t)) + ̃𝜆𝜸(t). On the whole vector of observations, this can be expressed as ̃𝝁𝜽= 𝜇𝜷(X) + ̃𝝀𝜸. 10 The Negative Binomial does not satisfy the same additive property as the Poisson, hence we cannot draw the same
conclusion reached in the Poisson case about the marginal distribution of the cumulative count Y c
t when 𝛼= 0. In gen-
eral, the cumulative count in the NB case will follow the distribution stemming from the sum of independent Negative
Binomial r.v. with common dispersion parameter 𝜈but different means ̃𝝁= { ̃𝜆𝜸(t)}T
t=1. 3.2.2
Negative Binomial distribution When counts are overdispersed the Poisson distribution is not a suitable choice. We can model the observed daily inci-
dence counts y = {y1, … , yt} as independent realizations from a Negative Binomial with mean ̃𝜆𝜸(t) and dispersion
parameter 𝜈∈R+: Yt|𝜽∼NB( ̃𝜇𝜽(t), 𝜈),
t = 1, … , T. Hence, the likelihood can be written as: Hence, the likelihood can be written as: (𝜽, 𝜈|d) =
T
∏
t=1
NB(yt| ̃𝜇𝜽(t), 𝜈) ∝
∝
T
∏
t=1
[Γ(𝜈+ yt)
Γ(𝜈)
(
𝜈
𝜈+ ̃𝜇𝜽(t)
)𝜈(
̃𝜇𝜽(t)
𝜈+ ̃𝜇𝜽(t)
)yt] (𝜽, 𝜈|d) =
T
∏
t=1
NB(yt| ̃𝜇𝜽(t), 𝜈) ∝
∝
T
∏
t=1
[Γ(𝜈+ yt)
Γ(𝜈)
(
𝜈
𝜈+ ̃𝜇𝜽(t)
)𝜈(
̃𝜇𝜽(t)
𝜈+ ̃𝜇𝜽(t)
)yt]
and the log-likelihood is:
l(𝜃, 𝜈|y) = log (𝜽, 𝜈|y) ∝
T
∑
t=1
log
(Γ(𝜈+ yt)
Γ(𝜈)
)
+ 𝜈
T
∑
t=1
log
(
𝜈
𝜈+ ̃𝜇𝜽(t)
)
T
(
) (𝜽, 𝜈|d) =
T
∏
t=1
NB(yt| ̃𝜇𝜽(t), 𝜈) ∝
∝
T
∏
t=1
[Γ(𝜈+ yt)
Γ(𝜈)
(
𝜈
𝜈+ ̃𝜇𝜽(t)
)𝜈(
̃𝜇𝜽(t)
𝜈+ ̃𝜇𝜽(t)
)yt]
and the log-likelihood is: l(𝜃, 𝜈|y) = log (𝜽, 𝜈|y) ∝
T
∑
t=1
log
(Γ(𝜈+ yt)
Γ(𝜈)
)
+ 𝜈
T
∑
t=1
log
(
𝜈
𝜈+ ̃𝜇𝜽(t)
)
+
T
∑
t=1
yt log
(
̃𝜇𝜽(t)
̃𝜇𝜽(t) + 𝜈
)
. ‡the sum of independent Poissons is still a Poisson with parameter the sum of the parameters ‡the sum of independent Poissons is still a Poisson with parameter the sum of the parameters 10 ALAIMO DI LORO et al. 3.3.2
Multiplicative inclusion of covariates The inclusion of a multiplicative effect of covariates would imply that the more serious the pandemic situation, the more
severe the impact of any covariate on the indicators’ daily rate. p
y
y
First, let us recall that in Section 2.1.1 we computed the first differences of the Richards’ curve function as: ̃𝜆𝜸(t) = r ⋅[(1 + 10h(p−t))−s −(1 + 10h[p−(t−1)])−s] = r ⋅̃𝜆𝜸,−r(t). On the log-scale, it would return the more familiar: log( ̃𝜆𝜸(t)) = log(r) + log( ̃𝜆𝜸,−r(t)). (3) (3) (3) log( ̃𝜆𝜸(t)) = log(r) + log( ̃𝜆𝜸,−r(t)). ALAIMO DI LORO et al. 11 From Equation (3), it comes natural the idea of expressing log(r) at each time-point t as the linear combination of
covariates 𝜂(x(t)) as in a Generalized Poisson model with log link function. Indeed this provides a multiplicative effect of
the covariates, where the parameter r can be expressed as 𝜇𝜷(⋅) in the following way: r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. (4) r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. (4) (4) r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. Note that the constant r is still present and included in Equation (4) through the intercept 𝛽0. Therefore, the mean at
time t is expressed as: ̃𝜇𝜃(t) = 𝛼+ r𝜷(x(t)) ⋅̃𝜆𝜸,−r(t). Considering the whole vector of observations, we would have the following vector of means ̃𝝁𝜽= 𝜶+ r𝜷(X) ⋅̃𝝀𝜸,−r, where
𝜶= 𝛼⋅1T. Considering the whole vector of observations, we would have the following vector of means ̃𝝁𝜽= 𝜶+ r𝜷(X) ⋅̃𝝀𝜸,−r, where
𝜶= 𝛼⋅1T. 3.4
Model estimation Parameters can be estimated by maximizing the log-likelihood l(𝜽|y), where 𝜽in this case includes all the parameters
the likelihood depends on (eg, includes 𝜈in the Negative Binomial case). This optimization problem does not have an
analytical solution, and numerical maximization must be used. To improve computation, we derived analytical expres-
sions for the gradient and Hessian of the two possible log-likelihoods (ie, Poisson or Negative Binomial counts), making
Fisher-scoring iteration very fast. The expressions are reported in the supplementary material. Given the nonsmooth
shape of the objective function, we are at risk of being trapped by local maxima of the log-likelihood, depending on
the initial conditions. Therefore, in order to strengthen the optimization procedure, a multistart procedure based on a
combination of genetic and gradient descent algorithms has been used.43,44 Once an approximate point of maximum ̂𝜽has been obtained, we could theoretically obtain an estimate of the asymp-
totic variance-covariance matrix of the estimated parameters through inverse of the negative log-likelihood Hessian in ̂𝜽
(which corresponds to the Observed Fisher Information): ̂V𝜽= −H(l(̂𝜽|y))−1, where H denotes the Hessian matrix. Nevertheless, we may want to account for the potential misspecification of our
model potentially arising from the independence assumption HI in Section 3.2. Therefore, we resort to a robust approach
for estimating the standard errors and covariance structure associated with the parameter vector 𝜽. In particular, we
consider the Huber Sandwich Estimator of the variance-covariance matrix,45,46 that can be computed as: where H denotes the Hessian matrix. Nevertheless, we may want to account for the potential misspecification of our
model potentially arising from the independence assumption HI in Section 3.2. Therefore, we resort to a robust approach
for estimating the standard errors and covariance structure associated with the parameter vector 𝜽. In particular, we
consider the Huber Sandwich Estimator of the variance-covariance matrix,45,46 that can be computed as: ̂V
R
𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), ̂V
R
𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), ̂V
R
𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), where ∇l(̂𝜽|y) represents the gradient of the log-likelihood in the point of maximum. Interval estimates for the parameters
are directly derived through the asymptotic distribution of the Maximum Likelihood Estimator, with the corresponding
robust covariance matrix ̂𝜽∼(𝜽, ̂V
R
𝜽). A similar theoretical result for predictions is not as straightforward. Therefore,
these are derived through a parametric double bootstrap procedure,47-49 which accounts for both the uncertainty of
parameter estimation and the randomness of the observations. In practice, resampled trajectories {Yi}B
i=1 are obtained
by simulating B sets of parameters from their asymptotic distribution and computing B mean functions trajectories
{𝜇𝜽i(t)}B
i=1. An artificial time series of counts is then simulated for each of the B trajectories and 95% confidence intervals
are obtained by computing the pointwise 2.5% and 97.5% quantiles. The dispersion parameter 𝜈, being a poorly identifi-
able nuisance parameter of no impact on the mean curve behavior, has been excluded from the bootstrapping procedure
and kept fixed at its estimated value ̂𝜈. Diagnostic check on the model has been performed through the Pearson residuals
and the Deviance residuals. Computation of the former is trivial, where we recall their definition as: ̂𝜌t = yt −̂yt
̂
Var[Yt]
,
t = 1, … , T. ALAIMO DI LORO et al. 12 and Negative Binomial assumptions we have: Under the Poisson and Negative Binomial assumptions we have: Under the Poisson and Negative Binomial assumptions we have: ̂
VarPoi[Yt] = 𝜇̂𝜽(t),
̂
VarNB[Yt] = 𝜇̂𝜽(t) + 𝜇̂𝜽(t)2
̂𝜈
,
(5) (5) (5) respectively. The Deviance Residuals are instead defined as the individual contributions of each observation to the Deviance
of the model, that is, the discrepancy between the proposed model and the full model (perfect fit) fits in terms of
log-likelihood: ̂dt = 2 ⋅[log(f(yt|̂𝜽s) −log(f(yt|̂𝜽)], where f(⋅|⋅) is the chosen distribution function and ̂𝜽s is the parameter vector of the saturated model. For the Poisson and
Negative Binomial this can be computed as: where f(⋅|⋅) is the chosen distribution function and ̂𝜽s is the parameter vector of the saturated model. ̂V
R
𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), For the Poisson and
Negative Binomial this can be computed as: ̂d
Poi
t
= sgn(yt −𝜇̂𝜽(t)) ⋅
√
2yt log
( yt
𝜇̂𝜽
)
−(yt −𝜇̂𝜽(t)),
̂d
NB
t
= sgn(yt −𝜇̂𝜽(t)) ⋅
√
2
[
yt log
( yt
𝜇̂𝜽(t)
)
−(yt + 𝜈) ⋅log
( yt + 𝜈
𝜇̂𝜽(t) + 𝜈
)]
, respectively.50 If the model correctly describes the variability in the data, then both the Pearson residuals and the Deviance
residuals are expected to be Normally distributed and independent, with the latter being generally more robust to outliers. 3.5
Validation Fitting performances are further evaluated through numerical metrics such as the pseudo-R2 and coverage of the 95%
prediction intervals: R2 = 1 −MSE
𝜎2
y
= 1 −
∑T
t=1 (yt −̂yt)2
∑T
t=1 (yt −y)2 ,
Cov95% = 1
T ⋅
T
∑
t=1
I(̂yl
t;̂yu
t )(yt), where MSE is the Mean Squared Error, y = 1
T
∑T
t=1 yt and I(⋅) denotes the indicator function over the set . where MSE is the Mean Squared Error, y = 1
T
∑T
t=1 yt and I(⋅) denotes the indicator function over the set . 4
NOWCASTING THE ITALIAN OUTBREAK OF COVID-19 For the sake of brevity, here we present results referred to the proposed Richards’ growth model only for daily positives
aggregated at the national level. Further results of the model performances for daily deceased are included in the supple-
mentary material. We only present results obtained adopting the Negative Binomial distribution because of the substantial
overdispersion present at all levels for these indicators (spatially and temporally heterogeneous data collection process,
varying containment measures, and so on). We first show the fitted curve for each indicator, and compare its shape with the observed time series. We also calculate
the residuals and check if model assumptions under the proposed framework hold. According to the results drawn from
the residual analysis, we modify the empirical setting, keeping the theoretical one fixed, to better capture specific data
features. Later on, we show the performance for two fundamental issues: (i) predicting the epidemic trend in advance and (ii)
predicting the date of the peak of the epidemic. 3.6
Step-ahead predictions We test our model’s ability to predict the evolution of the epidemic (at least its first wave) from the short to the medium
term. Indeed, while the choice of a rigid parametric form for the mean function is penalizing in terms of flexibility and
fitting ability, it allows for extrapolation outside the observed domain and is supposed to provide robust forecasts (at
least in the short/medium term). Therefore, using the best model for the two indicators (ie, baseline + week-day additive
effect), we calculated the out-of-sample root mean squared prediction error (RMSPE) for: • different fitting windows t = 1, … , ̃t; • different forecast horizons, say K ∈{1, 5, 10, 15}. We recall that, given the fitting window set 1, … , ̃t: RMSPẼt,K =
√
√
√
√1
K
K
∑
j=1
(ỹt+j −̂ỹt+j)2. 13 ALAIMO DI LORO et al. 13
Index
Model without
baseline
Model with
baseline
log-likelihood
−1081.4
−982.8
AIC
2152.7
1953.6
BIC
2162.3
1965
AICc
2137.8
1935.7 13 TA B L E 1
Log-likelihood, AIC, BIC, and AICc for the model without
baseline and the model with baseline, on daily positives TA B L E 2
Parameters’ points estimates and 95%
confidence intervals for the model with baseline on daily
positives TA B L E 2
Parameters’ points estimates and 95%
confidence intervals for the model with baseline on daily
positives Parameter
Point estimate
95% Interval
𝛼
173.17
(103.2, 290.54)
r
222.95 × 103
(220.56 × 103, 225.36 × 103)
h
0.0288
(0.0285, 0.0291)
p
−31.18
(−32.75, −29.62)
s
72.54
(48.29, 96.79)
𝜈
18.73
(17.77, 19.73) 4.1
Model on daily positives 14 (B) Cumulative
0K
50K
100K
150K
200K
250K
01−Mar
01−Apr
01−May
01−Jun
01−Jul
01−Aug
µt F I G U R E 5
Bootstrapped trajectories corresponding to the Huber Sandwich covariance matrix in the point of maximum for the model
with baseline on daily positives viceversa). Finally, 𝜈is an overdispersion parameter and does not present any evident communicable interpretation. The
larger it is and the lower the overdispersion, according to the formula in Equation (5). viceversa). Finally, 𝜈is an overdispersion parameter and does not present any evident communicable interpretation. The
larger it is and the lower the overdispersion, according to the formula in Equation (5). We here want to stress the fact that the uncertainty characterizing some of the parameters (like s) is not alarming. In
particular, variations of s at values distant from 1 have very little effect on the curve shape. Furthermore, the parameter
vector presents a covariance structure that highlights how different combination of parameters can yield similar curves. Indeed, simulating M = 5000 set of parameters from the Normal distribution with variance corresponding to the covari-
ance underlying the Huber Sandwich covariance matrix, we get the set of difference and cumulative curves represented
in Figure 5. g
We can also directly obtain point predictions {̂yt}T
t=1 as: point predictions {̂yt}T
t=1 as: We can also directly obtain point predictions {̂yt}T
t=1 as: (6) ̂yt = 𝜇̂𝜽(t),
t = 1, … , T,
(6) and prediction intervals {(̂yl
t; ̂yu
t )}T
t=1 through the same set of bootstrapped trajectories, whose statistical validity relies on
the asymptotic properties introduced in Section 3.4. Figure 6 shows the model fit on the whole available time series of counts: the former on the daily series, the latter on
the cumulative one. We can see how the estimated curve does catch the observed general behavior, providing a smooth
approximation only marginally influenced by extreme values. Our model produces an R2 = 0.941 and coverage Cov95% =
0.945, meaning that the percentage of observed daily counts falling inside the estimated bounds is perfectly coherent with
the specified confidence level. Looking at Figure 6, we notice how daily counts boundaries get smaller as time passes,
due to the implicit relationship between mean and variance that characterizes count distributions. At the same time, the
opposite happens to the bounds on the cumulative counts. 4.1
Model on daily positives To decide whether or not to include the kink effect, we fitted the model with and without the baseline 𝛼and compared
the two fits in terms of log-likelihood, AIC, BIC, and corrected AIC (AICc). The values are presented in Table 1 and pro-
vide clear evidence in favor of the model with baseline (ie, with mean 𝜇𝜽(⋅) as in Equation (2)). Parameters’ estimates of
the model ̂𝜽and the respective 95% confidence intervals are shown in Table 2, where the baseline 𝛼is estimated to be
̂𝛼= 173.17, with interval (103.2, 290.54), which confirms that the baseline is estimated to be significantly different from
0, and it should be included in the model. As explained in Section 3.1, this parameter represents the long-term endemic
incidence rate that may (possibly indefinitely) follow the end of the main outbreaks. This obviously would hold exactly
with constant social interactions, containment measures, control of cases, and so on. Hence, in the considered time hori-
zon, we expect this endemic level to be of ≈173 daily positives per day. When the baseline is included, the parameter r
does not indicate anymore the final epidemic size, but only the final outbreak size. This is the number of positive cases due
to the uncontrolled outbreak, additional to what would have been observed in the steady endemic state. This amount is
estimated to be ≈222 950, an amount that would have been reached in ≈1288 days at the endemic state level. The parame-
ters h, p, and s do not have an easily quantifiable and absolute interpretation, but are useful for comparison. As explained
in Section 3.1, the first indicates how fast the infection spreads, the second how soon it starts descending (lag-phase) and
the last asymmetries between the ascending and descending phase (s < 1 the ascending is slower than the descending and 14
ALAIMO DI LORO et al. 0K
2K
4K
01−Mar
01−Apr
01−May
01−Ju
(A) First differences
(B) Cumulative
n
01−Jul
01−Aug
µt
0K
50K
100K
150K
200K
250K
01−Mar
01−Apr
01−May
01−Jun
01−Jul
01−Aug
µt
F I G U R E 5
Bootstrapped trajectories corresponding to the Huber Sandwich covariance matrix in the point of maximum for the model
with baseline on daily positives ALAIMO DI LORO et al. 4.1
Model on daily positives The latter is not surprising: indeed, they are built marginally
on all the epidemic’s possible scenarios. Therefore, they give us a clear sight of what we could have currently observed,
keeping into account and aggregating the uncertainty at each stage of the epidemic. We performed a diagnostic check on
both the Pearson and the Deviance residuals. The plots in Figure 7 show the Deviance residuals behavior: histogram (A),
including the P-value from the Shapiro test; Normal qq-plot (B); autocorrelation plot (C); plot of the residuals vs fitted
values (D). The first two check the (approximated) Normality assumption on the residuals, while the second two control
for the correlation of the residuals (among them and with the observed values). 4.1.1
Weekly seasonality The diagnostic check on both type of residuals showed that the Normality assumption is not rejected, but the correla-
tion plot manifests undesirable patterns (see Figure 7). In particular, the autocorrelation between errors is larger at lag 7 ALAIMO DI LORO et al. 15
F I G U R E 6
Observed
(black dots) and fitted values
(gray solid lines) with 95%
confidence intervals (gray
dashed lines) for the model with
baseline on daily positives
(A)
(B)
F I G U R E 7
Deviance
residuals for the model with
baseline on daily positives
(A)
(B)
(C)
(D)
(and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur-
ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively, ALAIMO DI LORO et al. 15 (B) (A) (A)
(B)
F I G U R E 7
Deviance
residuals for the model with
baseline on daily positives
(A)
(B)
(C)
(D)
(and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur-
ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively,
the system has less capacity at the weekend, meaning it is more challenging to get a test. Undeniably, viruses work 7 days
a week. Looking at the low numbers during/after the weekend might give you a false sense of reassurance. This is because
it seems cases are down, and therefore elimination of the virus is possible. But, unlike our population, viruses do work
on weekends. This may be adjusted by simply adding a weekday effect in our model as a covariate, using the approach in
Section 3.3. Such effect may be included either in an additive or a multiplicative fashion. At first, we considered effects
for each day of the week, taking Monday as a corner point. Preliminary results showed that not all week-days present a
significant deviation from the common mean. On the other hand, the distribution of the Deviance residuals ̂dt of the stan-
dard model aggregated by week-day (see Figure 8) shows that an evident overestimation pattern (ie, negative deviations)
is taking place on Monday and Tuesday. 4.1.1
Weekly seasonality −2
0
2
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
d^
F I G U R E 8
Deviance residuals distribution
aggregated by day of the week for daily positives
Index
Additive
effect
Multiplicative
effect
log-likelihood
−971.74
−974.1
AIC
1929.48
1934.3
AICc
1942.67
1947.5
BIC
1908.60
1913.4
TA B L E 3
Log-likelihood, AIC, BIC, and AICc for the models with
baseline including additive or multiplicative week-day effect on daily positives
(A)
(B)
F I G U R E 9
Observed
(black dots) and fitted values
(gray solid lines) with 95%
confidence intervals (gray dashed
lines) for the model with baseline
and week-day additive effect,
estimated on the daily positives
may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC,
BIC, and AICc score (see Table 3). The resulting fit of the model with week seasonality on the observed data are shown in Figure 9, where, on the left, we
show the fitted curve and the 95% confidence intervals; on the right, we can observe the fit on the cumulative indicator. Estimated parameters are shown in Table 4 This model estimates the baseline to be at e ̂𝛽0 = 192 48 on Wednesday to 16
ALAIMO DI LORO et al. −2
0
2
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
d^
F I G U R E 8
Deviance residuals distribution
aggregated by day of the week for daily positives
Index
Additive
effect
Multiplicative
effect
log-likelihood
−971.74
−974.1
TA B L E 3
Log-likelihood, AIC, BIC, and AICc for the models with
baseline including additive or multiplicative week-day effect on daily positives 16
−2
0
2
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
d^ ALAIMO DI LORO et al. 4.1.1
Weekly seasonality 16 F I G U R E 8
Deviance residuals distribution
aggregated by day of the week for daily positives F I G U R E 8
Deviance residuals distribution
aggregated by day of the week for daily positives TA B L E 3
Log-likelihood, AIC, BIC, and AICc for the models with
baseline including additive or multiplicative week-day effect on daily positives Index
Additive
effect
Multiplicative
effect
log-likelihood
−971.74
−974.1
AIC
1929.48
1934.3
AICc
1942.67
1947.5
BIC
1908.60
1913.4 (A)
(B)
F I G U R E 9
Observed
(black dots) and fitted values
(gray solid lines) with 95%
confidence intervals (gray dashed
lines) for the model with baseline
and week-day additive effect,
estimated on the daily positives
may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC,
BIC, and AICc score (see Table 3). (B) F I G U R E 9
Observed
(black dots) and fitted values
(gray solid lines) with 95%
confidence intervals (gray dashed
lines) for the model with baseline
and week-day additive effect,
estimated on the daily positives (A) (A) (B) may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC,
BIC, and AICc score (see Table 3). h
l i
fi
f h
d l
i h
k
li
h
b
d d
h
i
i
h
h l f may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC,
BIC, and AICc score (see Table 3). The resulting fit of the model with week seasonality on the observed data are shown in Figure 9, where, on the left, we
show the fitted curve and the 95% confidence intervals; on the right, we can observe the fit on the cumulative indicator. ̂ Estimated parameters are shown in Table 4. This model estimates the baseline to be at e ̂𝛽0 = 192.48 on Wednesday to
Sunday and at e ̂𝛽0+ ̂𝛽wd = 121.51 on Mondays and Tuesdays. Deriving the corresponding 95% intervals, these two baselines
result significantly different from the estimate of the overall baseline ̂𝛼in the model without covariates. 4.1.1
Weekly seasonality (A) (B) F I G U R E 7
Deviance
residuals for the model with
baseline on daily positives F I G U R E 7
Deviance
residuals for the model with
baseline on daily positives (B) (A) (A) (B) (D) (C) (C) (D) (and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur-
ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively,
the system has less capacity at the weekend, meaning it is more challenging to get a test. Undeniably, viruses work 7 days
a week. Looking at the low numbers during/after the weekend might give you a false sense of reassurance. This is because
it seems cases are down, and therefore elimination of the virus is possible. But, unlike our population, viruses do work
on weekends. This may be adjusted by simply adding a weekday effect in our model as a covariate, using the approach in
Section 3.3. Such effect may be included either in an additive or a multiplicative fashion. At first, we considered effects
for each day of the week, taking Monday as a corner point. Preliminary results showed that not all week-days present a
significant deviation from the common mean. On the other hand, the distribution of the Deviance residuals ̂dt of the stan-
dard model aggregated by week-day (see Figure 8) shows that an evident overestimation pattern (ie, negative deviations)
is taking place on Monday and Tuesday. f Therefore, in the sequel, we will present only results obtained with the dichotomous variable that is equal to 1 when-
ever the week-day is Monday or Tuesday (0 vice versa). Note that lower tests effort during the weekend shows in the data on
Monday and Tuesday, since daily reports involve mostly results received the day before, with swabs therefore dating back
48 hours on the day of publication. This confirms that working with daily data require special care as the cases reporting 16
ALAIMO DI LORO et al. 4.1.1
Weekly seasonality The diagnostic check of the Pearson’s and Deviance residuals showed that adherence to
Gaussianity improved and the correlation pattern at lag 7 is still present but mitigated (see Figure 10 for the Deviance F I G U R E 10
Deviance
residuals for the model with
baseline and week-day additive
effect estimated on daily positives (A) (B) (A) (D) (C) (C) (D) covariates, denoting less overdispersion with respect to the equivariance hypothesis. This is completely reasonable since
the week-day effect is able to explain some of the previously unaccounted heterogeneity. In terms of model validation, the inclusion of this effect improves sensibly the R2 (0.956), while the average cover-
age Cov95% is constant (0.950). The diagnostic check of the Pearson’s and Deviance residuals showed that adherence to
Gaussianity improved and the correlation pattern at lag 7 is still present but mitigated (see Figure 10 for the Deviance
residuals). 4.1.1
Weekly seasonality The estimates
of the outbreak size ̂r and of the infection rate ̂h of the two models are in agreement, while the point estimates of the
asymmetry parameter ̂s are different but both large and mutually included in the corresponding 95% intervals. This is
reasonable since we would not expect the outbreak size, rate and symmetry to vary after accounting for week-day het-
erogeneity. On the other hand, the new estimate ̂p of p detects a shorter lag-phase and hence a slightly faster approach
to the descending phase. Finally, the estimate of the dispersion parameter ̂𝜈is slightly larger than in the model without ALAIMO DI LORO et al. 17 ALAIMO DI LORO et al. 17
TA B L E 4
Parameters’ point estimates and 95% confidence
intervals for the additive model on daily positives
Parameter
Point estimate
95% Interval
𝛽0
5.26
(5.18, 5.34)
𝛽wd
−0.46
(−0.53, −0.38)
r
224.57 × 103
(224.13 × 103, 225.01 × 103)
h
0.0289
(0.0287, 0.0291)
p
−23.26
(−29.64, −16.88)
s
44.42
(−35.67, 124.51)
𝜈
22.01
(21.35, 22.70)
F I G U R E 10
Deviance
residuals for the model with
baseline and week-day additive
effect estimated on daily positives
(A)
(B)
(C)
(D) TA B L E 4
Parameters’ point estimates and 95% confidence
intervals for the additive model on daily positives Parameter
Point estimate
95% Interval
𝛽0
5.26
(5.18, 5.34)
𝛽wd
−0.46
(−0.53, −0.38)
r
224.57 × 103
(224.13 × 103, 225.01 × 103)
h
0.0289
(0.0287, 0.0291)
p
−23.26
(−29.64, −16.88)
s
44.42
(−35.67, 124.51)
𝜈
22.01
(21.35, 22.70) s
44.42
(−35.67, 124.51)
𝜈
22.01
(21.35, 22.70)
F I G U R E 10
Deviance
residuals for the model with
baseline and week-day additive
effect estimated on daily positives
(A)
(B)
(C)
(D)
covariates, denoting less overdispersion with respect to the equivariance hypothesis. This is completely reasonable since
the week-day effect is able to explain some of the previously unaccounted heterogeneity. In terms of model validation, the inclusion of this effect improves sensibly the R2 (0.956), while the average cover-
age Cov95% is constant (0.950). 4.1.2
Prediction of future cases and of the peak date For the latter empirical model, the RMSPEs for each steps-ahead are presented in Figure 11. Results match the expecta-
tions as: (i) the error decreases with the length of the fitting window; (ii) the error trend is more stable on larger testing
windows (10-15 steps ahead vs 1-5 steps ahead); (iii) larger errors are made around the day of the peak. It can be seen
nevertheless that predictions are always reasonable at these time horizons. This is a good point for our theoretical frame-
work, as it can be used as a guidance tool to plan nonpharmaceutical-interventions due to its capability to predict future
scenarios with reasonable accuracy. Of course, with more detailed data and including confounding factors, the accuracy
may be further improved. Unfortunately, the aggregated available data do not contain important information which may
strongly improve the prediction, for example, stratifications of cases by age, gender, comorbidities, and so on. Finally, we evaluate the model’s ability to predict the date of the peak. The approximate dates and heights of the peak
have important epidemiological implications. This becomes possible under the assumption that sensible modifications ALAIMO DI LORO et al. 18 18
ALAIMO DI LORO et al. 4.1.2
Prediction of future cases and of the peak date kk
k
k
k
k
k
k
k
k
k
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k
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kkkkkkkkkkkkkk
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k
kkkkkkkkk
0
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1500
01−Apr
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01−Jul
RMSPE
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k
kkk
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kk
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kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
0
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RMSPE
10 step−ahead
kkk
k
k
k
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kkk
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kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
0
500
1000
1500
01−Apr
01−May
01−Jun
01−Jul
RMSPE
15 step−ahead
F I G U R E 11
Root mean
squared prediction error for daily
positives at different steps-ahead
(A)
(B)
(C)
(D)
F I G U R E 12
Estimation
of the date of the peak for daily
positives at different
steps-before
of the adopted epidemiological strategies do not emerge. However, if exogenous events, for example, efficient treatments
or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as
we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until
K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1}
as shown in Figure 12. When s = 1, the peak ̂t is directly expressed by the parameter p. 4.1.2
Prediction of future cases and of the peak date When s ≠1, after some algebra it can be seen that the
peak can still be computed analytically as: k
kkk
k
k
k
k
k
k
k
k
k
k
k
k
k
k
k
k
k
k
k
kkkkk
kkkkkkkk
kkkkk
k
kkkkkk
kkkkkkkkkkkkkkkkk
kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
0
500
1000
1500
01−Apr
01−May
01−Jun
01−Jul
RMSPE
5 step−ahead F I G U R E 11
Root mean
squared prediction error for daily
positives at different steps-ahead kk
k
k
k
k
k
k
k
k
k
kk
k
k
k
k
k
k
k
k
k
k
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kkkkkkkkkkkkkk
k
kkk
k
kkkkkkkkk
0
500
1000
1500
01−Apr
01−May
01−Jun
01−Jul
RMSPE
1 step−ahead kkk
k
k
k
k
k
k
k
k
kkk
k
k
k
k
kk
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kkk
kkkkkkkkkkkkkkk
kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
0
500
1000
1500
01−Apr
01−May
01−Jun
01−Jul
RMSPE
15 step−ahead kk
k
k
k
k
kk
k
k
k
kk
k
k
k
k
kk
kk
k
k
kkkkkkkk
kkkkkkkkkk
kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
0
500
1000
1500
01−Apr
01−May
01−Jun
01−Jul
RMSPE
10 step−ahead RMSPE RMSPE (B) (A) F I G U R E 12
Estimation
of the date of the peak for daily
positives at different
steps-before F I G U R E 12
Estimation
of the date of the peak for daily
positives at different
steps-before (A) (B) (D) (C) (C) (D) of the adopted epidemiological strategies do not emerge. However, if exogenous events, for example, efficient treatments
or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as
we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until
K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1}
as shown in Figure 12. of the adopted epidemiological strategies do not emerge. 4.1.2
Prediction of future cases and of the peak date The dashed gray
vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded
with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the
observed counts through nonparametric polynomial approximations). The observed time-series is represented through
point and lines, where the black section is referred to the training window while the gray section is referred to the testing
(out-of-sample) window. Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. The dashed gray
vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded
with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the
observed counts through nonparametric polynomial approximations). The observed time-series is represented through
point and lines, where the black section is referred to the training window while the gray section is referred to the testing
(out-of-sample) window. As expected, as we approach the real date of the peak, we predict it more accurately. Point predictions are very accu-
rate since 5 days before the actual peak. At the same time, interval bounds get tighter and tighter as the fitting interval
approached the day of the peak and, in general, the day of the peak is always included in such bounds (see Table 5 for
exact numerical evaluation). All the aforementioned results have been calculated also for the national aggregated daily deceased. Exposition and
discussion of these results, which are in fact very similar to the daily positivesones, are included in the supplementary
material. Here, we just want to highlight how the peak is accurately predicted with a shorter delay and generally smaller
uncertainty for the daily deceased than for the daily positives (see Table 5). This is probably related to the more regular
behavior of the series, due to a likely more homogeneous collection process of the records. Finally, we here want to stress the point that we are introducing a framework with the highly desirable goal to formu-
late a model which would predict an evolution curve. 4.1.2
Prediction of future cases and of the peak date To be more precise, a great variety of epidemiological models have
been proposed in the literature, but most standard versions of SIR-like models typically yield an increase before the peak
that is quite similar to the decrease after the peak. The proposed framework, based on more complex evolution dynamics,
is robust enough to be fitted successfully on the (poor quality) available data while explaining and forecasting different
increasing and decreasing behavior before and after the peak. We emphasize that such increase-decrease quantitative
behaviors appear to satisfactorily conform to reality. 4.1.2
Prediction of future cases and of the peak date However, if exogenous events, for example, efficient treatments
or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as
we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until
K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1}
as shown in Figure 12. When s = 1, the peak ̂t is directly expressed by the parameter p. When s ≠1, after some algebra it can be seen that the
peak can still be computed analytically as: ̂t ̂𝜸= ̂p + log10(̂s)
̂h
. ALAIMO DI LORO et al. 19
TA B L E 5
Delay (days) in point estimation of the peak
10
5
2
1
Days before
Delay
Width
Delay
Width
Delay
Width
Delay
Width
daily deceased
−1
37
–3
25
–4
22
–3
21
daily positives
20
106
17
69
1
37
2
37
Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. The dashed gray
vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded
with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the
observed counts through nonparametric polynomial approximations). The observed time-series is represented through
point and lines, where the black section is referred to the training window while the gray section is referred to the testing
(out-of-sample) window. As expected, as we approach the real date of the peak, we predict it more accurately. Point predictions are very accu-
rate since 5 days before the actual peak. At the same time, interval bounds get tighter and tighter as the fitting interval ALAIMO DI LORO et al. 19 TA B L E 5
Delay (days) in point estimation of the peak
10
5
2
1
Days before
Delay
Width
Delay
Width
Delay
Width
Delay
Width
daily deceased
−1
37
–3
25
–4
22
–3
21
daily positives
20
106
17
69
1
37
2
37 TA B L E 5
Delay (days) in point estimation of the peak Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. ORCID Pierfrancesco Alaimo Di Loro
https://orcid.org/0000-0002-6075-3659
Alessio Farcomeni
https://orcid.org/0000-0002-7104-5826
Giovanna Jona Lasinio
https://orcid.org/0000-0001-8912-5018
Gianfranco Lovison
https://orcid.org/0000-0003-3861-8204
Antonello Maruotti
https://orcid.org/0000-0001-8377-9950
h
//
id
/ Pierfrancesco Alaimo Di Loro
https://orcid.org/0000-0002-6075-3659
Alessio Farcomeni
https://orcid.org/0000-0002-7104-5826
Giovanna Jona Lasinio
https://orcid.org/0000-0001-8912-5018
Gianfranco Lovison
https://orcid.org/0000-0003-3861-8204
Antonello Maruotti
https://orcid.org/0000-0001-8377-9950 Marco Mingione
https://orcid.org/0000-0002-5662-3499 20 20 A limitation of our approach is that logistic growth curves are constrained so that only one wave at a time can be
successfully modeled. This implies that initial (and possibly final) dates shall be set by the user to identify a wave. This
is rather simple empirically (eg, the initial date can be the last day with zero incidence, and the final date can be the first
day with incidence above (or under) a prespecified threshold). On the other hand, multiple waves could be modeled by
modification of our nonlinear model as a weighted average of multiple Richards’ curves (one for each wave), in which
weights of the noncurrent wave are forced to decay to zero with the distance from the wave-specific peak. We leave this
as grounds for further work. A Bayesian approach will also be experimented in order to overcome possible issues with the asymptotic properties
of the maximum likelihood estimator. Notably, implementation of the no-U-turn sampler algorithm for the estimation of
nonlinear models might be a valid working solution. In addition, a Bayesian approach may also be used to include spatial
dependence into the modeling framework and also to relax the first-order Markov assumption for taking into account
more complex temporal dependence. In particular, the latter may be key in order to adapt the introduced Richards’ curve
model for the nowcasting of prevalence indicators, for example, current positives and current intensive care units occupancy. Indeed, any modeling effort shall account for the strong temporal dependence between subsequent counts stemming from
the fact that daily counts at time t potentially include units which are in stock since times 𝜏< t. Furthermore, as specified
in Section 2.1.2, prevalence indicators are nonmonotonic and their value is the result of the combination of the incidence
components building up each of those. These two last issues may be addressed by adapting the Richards’ response function
to accommodate nonmonotonicity and/or by hierarchically specifying a model for the prevalence indicators through the
combination of models for their incidence components. A successful attempt in accurately nowcasting the ICU occupancy
is given in Reference 51. SOFTWARE Software in the form of R code, together with a sample input dataset and complete documentation is available on request
from the corresponding author. DATA AVAILABILITY STATEMENT The data that support the findings of this study are openly available in “Protezione Civile Italiana GitHub Repository” at
https://github.com/pcm-dpc/COVID-19. 20 ALAIMO DI LORO et al. 5
DISCUSSION AND FURTHER WORK We presented an approach to modeling and prediction of epidemic indicators that has proven useful during the first
outbreak of COVID-19 in Italy. The model has been validated on publicly available data, and has proved flexible enough
to adapt to different indicators. It is important to underline up front that the available data are clearly biased. Incidence depends on testing and trac-
ing efforts, whose indications have varied wildly over time and space. Comparability of indicators over time and space
might in part be achieved by including the daily number of swabs as a predictor, which anyway would make predictions
cumbersome. Different definitions of COVID-19 related death make it also very hard to compare mortality across coun-
tries. This problem does not apply to our data, that refer only to Italy. However, while this definition has been constant
over time in Italy, it shall be remarked that also deaths might be underestimated, with the degree of undercount positively
associated with incidence. Correcting for this bias is not trivial, and would require corrections based on individual-level
data and/or reliable statistics about excess mortality. Summarizing the results, we would like to emphasize that the proposed Richards’ curve model describes properly the
growth in the number of COVID-19 daily positives and daily deceased, despite its simplicity. Indeed, it is able to reflect
properly the trend of the daily incidence indicators; and also allows for the straightforward inclusion of exogenous infor-
mation. Basic covariates such as the week-day effect proved to sensibly enhance model fitting and prediction accuracy. While we have illustrated results at the national level, the model can be used also at the regional/local level (perhaps
including specific local effects). The resulting fits are included in the supplementary material. The maximum likelihood
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occupancy in Italian regions. Biom J. 2020;63:503-513. 51. Farcomeni A, Maruotti A, Divino F, Jona-Lasinio G, Lovison G. An ensemble approach to short-term forecast of COVID-19 intensive care
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https://openalex.org/W4213434700 | https://eduvest.greenvest.co.id/index.php/edv/article/download/361/529 | English | null | Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) | Eduvest | 2,022 | cc-by-sa | 5,040 | ANALYSIS OF THE INFLUENCE OF THE BOARD OF
DIRECTORS, COMPANY SIZE, MANAGEMENT
OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL
PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) This type of research is associative research. In this
study, the population of rural banks located in the Bekasi area was
used. The data obtained is based on financial reports that have
been published on the website of the Financial Services Authority
(www.ojk.go.id) for the period 2018-2021. The data obtained from
the results of the study were analyzed using multiple linear
regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant
influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the
firm size variable significantly affects non-performing loans with a
negative relationship direction. The KAP audit variable was also
proven to have a significant effect on non-performing loans with a
similar direction, namely negative. Both are able to affect non-
performing loans because the p-value obtained is smaller than
0.05. Simultaneously also found the effect of the board of directors,
company size, managerial ownership, and KAP audits on the return
on assets or non-performing loans of BPRs in the Bekasi area for
the 2018-2021 period. KEYWORDS
Board of Directors, Company Size, Managerial Ownership,
KAP Audit, Return on Assets, Non Performing Loan
This work is licensed under a Creative Commons
Attribution-ShareAlike 4.0 International This study aims to analyze the effects of the board of directors, firm
size, managerial ownership, and audit of KAP (Public Accounting
Firm) audit on the financial performance of Bank Perkreditan
Rakyat (BPR). This type of research is associative research. In this
study, the population of rural banks located in the Bekasi area was
used. The data obtained is based on financial reports that have
been published on the website of the Financial Services Authority
(www.ojk.go.id) for the period 2018-2021. The data obtained from
the results of the study were analyzed using multiple linear
regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant
influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the
firm size variable significantly affects non-performing loans with a
negative relationship direction. The KAP audit variable was also
proven to have a significant effect on non-performing loans with a
similar direction, namely negative. ANALYSIS OF THE INFLUENCE OF THE BOARD OF
DIRECTORS, COMPANY SIZE, MANAGEMENT
OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL
PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) How to cite:
Riwandari Juniasti. (2022). Analysis of the Influence of the Board of
Directors, Company Size, Management Ownership, and Kap Audit on
the Financial Performance of Bank Perkreditan Rakyat (BPR). Journal
Eduvest. Vol 2(2): 397-405
E-ISSN:
2775-3727
Published by:
https://greenpublisher.id/
Riwandari Juniasti
Universitas Kristen Indonesia
Email: Riwandari.juniasti@uki.ac.id
ARTICLE INFO ABSTRACT
Received:
January, 26th
2022
Revised:
February, 17th
2022
Approved:
February, 18th
2022
This study aims to analyze the effects of the board of directors, firm
size, managerial ownership, and audit of KAP (Public Accounting
Firm) audit on the financial performance of Bank Perkreditan
Rakyat (BPR). This type of research is associative research. In this
study, the population of rural banks located in the Bekasi area was
used. The data obtained is based on financial reports that have
been published on the website of the Financial Services Authority
(www.ojk.go.id) for the period 2018-2021. The data obtained from
the results of the study were analyzed using multiple linear
regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant
influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the
firm size variable significantly affects non-performing loans with a
negative relationship direction. The KAP audit variable was also
proven to have a significant effect on non-performing loans with a
similar direction, namely negative. Both are able to affect non-
performing loans because the p-value obtained is smaller than
0.05. Simultaneously also found the effect of the board of directors,
company size, managerial ownership, and KAP audits on the return
on assets or non-performing loans of BPRs in the Bekasi area for
the 2018-2021 period. KEYWORDS
Board of Directors, Company Size, Managerial Ownership,
KAP Audit, Return on Assets, Non Performing Loan
This work is licensed under a Creative Commons
Attribution-ShareAlike 4.0 International How to cite:
Riwandari Juniasti. (2022). Analysis of the Influence of the Board of
Directors, Company Size, Management Ownership, and Kap Audit on
the Financial Performance of Bank Perkreditan Rakyat (BPR). Journal
Eduvest. Vol 2(2): 397-405
E-ISSN:
2775-3727
Published by:
https://greenpublisher.id/
Received:
January, 26th
2022
Revised:
February, 17th
2022
Approved:
February, 18th
2022
This study aims to analyze the effects of the board of directors, firm
size, managerial ownership, and audit of KAP (Public Accounting
Firm) audit on the financial performance of Bank Perkreditan
Rakyat (BPR). Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022
p- ISSN 2775-3735 e-ISSN 2775-3727 Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022
p- ISSN 2775-3735 e-ISSN 2775-3727 ANALYSIS OF THE INFLUENCE OF THE BOARD OF
DIRECTORS, COMPANY SIZE, MANAGEMENT
OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL
PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) INTRODUCTION In this era of free competition, banks must be good at reading opportunities and
taking advantage of them in order to survive. Various methods are used by banks to
increase market share and profits (Indiatsy, Mucheru, Mandere, Bichanga, & Gongera,
2014). One way that can be done to improve banking performance is through the
implementation of Good Corporate Governance (GCG) (Napitupulu, Primiana, Nidar,
Effendy, & Puspitasari, 2020). The The factor that underlies the company implementing
GCG is due to the agency theory which assumes a conflict of interest between the
executive (agent) and the shareholders (principal) and other stakeholders, where the
company's management does not act in the interests of shareholders but prioritizes the
interests of shareholders (Jahja, Mohammed, Lokman, & Mohamed, 2020). himself. In
such conditions, GCG is present. The implementation of GCG is expected to increase
supervision over management to encourage effective decision making, prevent
opportunistic actions that are not in line with the interests of the company, and reduce
information asymmetry between executives and company stakeholders. Thus, GCG is
expected to be able to create conducive conditions and a solid foundation for a good
Rural Bank (BPR) operation (Manor & Desiana, 2018). Rural Banks (BPR) are banks that
carry out conventional business activities which in their activities do not provide services
in payment traffic as referred to in the Law concerning banking (Financial Services
Authority Number 4/POJK.03/2015). y
Based on the Financial Services Authority Regulation Number 4/POJK.03/2015
concerning the Implementation of Governance for Rural Banks, it is stated that
Governance is the governance of BPRs that apply the principles of transparency,
accountability, and responsibility independence (independency), and fairness (fairness). BPRs are required to implement Good Corporate Governance in each of their business
activities at all levels or levels of the organization (Harjanto, 2019). One of them is
implementing regulations regarding the number of directors based on core capital, a BPR
with a core capital of at least 50 billion must have at least 3 (three) directors and a BPR
with a core capital of less than 50 billion must have at least 2 (two) members of the board
of directors. . Even for share ownership alone, the directors, either individually or jointly,
are prohibited from owning shares of more than 25%. ANALYSIS OF THE INFLUENCE OF THE BOARD OF
DIRECTORS, COMPANY SIZE, MANAGEMENT
OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL
PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) Both are able to affect non-
performing loans because the p-value obtained is smaller than
0.05. Simultaneously also found the effect of the board of directors,
company size, managerial ownership, and KAP audits on the return
on assets or non-performing loans of BPRs in the Bekasi area for
the 2018-2021 period. Analysis of the Influence of the Board of Directors, Company Size, Management
Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat
(BPR)
398 Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022 companies. On the other hand, board size in non-family firms has no systematic
relationship with firm performance (Saidat, Silva, & Seaman, 2019). companies. On the other hand, board size in non-family firms has no systematic
relationship with firm performance (Saidat, Silva, & Seaman, 2019). The financial report is an information product produced by the company, and is a
very important instrument related to the condition of the company (Lev, 2018). Therefore,
every policy and decision taken in the process of preparing financial statements will
greatly influence the assessment of the company's performance (Lev, 2018). According to
POJK No. 4/POJK.03/2015 concerning Implementation of BPR Governance Article 76,
RBs are required to send reports on the implementation of governance to the Financial
Services Authority, the BPR Association in this case Perbarindo, and to 1 (one) media
office or economic and financial magazine. Based on the data from Perbarindo, the names
of 32 BPRs in the Bekasi area were taken which sent reports on their governance
implementation as well as the published financial reports of BPRs for the first quarter of
2019 - until the second quarter of 2021 in the Bekasi area from the website of the
Financial Services Authority. By nature, banks are no different from other commodity companies or service
companies. In this case, the bank produces output in the form of credit and input in the
form of public savings funds (Bvirindi, 2021). Thus, banks can bridge the interests of the
owners of funds with those who need funds or are called carrying out the intermediation
function (Disemadi, 2019). The banking industry has a very important role in economic
development. The history of the Indonesian economy shows that the Indonesian economy
moves in tandem with the banking industry (Rizvi, Narayan, Sakti, & Syarifuddin, 2020). The Indonesian economy is a bank-based economy, an economy that depends on the
existence of banks as a source of financing. Therefore, efforts to strengthen a healthy,
efficient and beneficial banking system for the economy are the key to success in
maintaining the sustainability of national economic development (Zhang, Shi, Zhang, &
Xiao, 2019). Examines the relationship between the GCG index and five financial
performance measures (Suhadak, Rahayu, & Handayani, 2019). Partially, no statistically
significant relationship was found. Simultaneously, however, statistically significant
relationships emerged in both directions for most financial performance measures. Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022 Then
Mahrani & Soewarno (2018) tested the effect of Good Corporate Governance and
Corporate Social Responsibility on the company's financial performance, from the results
of testing and analysis of the GCG and CSR mechanisms that had a positive effect on
financial performance and earnings management. Based on the study of thought above, the researcher is interested in raising the
title "Analysis of the Influence of the Board of Directors, Company Size, Managerial
Ownership, KAP Audit on the Financial Performance of BPRs in the Bekasi Region for
the 2018-2021 period”. INTRODUCTION OJK also regulates the
implementation of an external audit function, in this case BPRs are required to appoint a
Public Accountant and a Public Accounting Firm to conduct an annual audit. BPRs are
required to implement Good Corporate Governance in each of their business activities at
all levels or levels of the organization (Endah, Tarjo, & Musyarofah, 2020). The
implementation of Good Corporate Governance in financial institutions is important to do
in order to further foster trust in the community and improve banking performance and
progress (Olannye & Anuku, 2014). The problem of Good Corporate Governance and
corporate ownership structure is not new, especially public companies which are usually
owned by many shareholders (Jiang & Kim, 2020). Several studies have tested the effect
of GCG on the company's financial performance. Sa'diyah (2020) examines the Effect of
Good Corporate Governance on the Financial Performance of Islamic Commercial Banks
in Indonesia, finding that corporate governance proxied by the Board of Commissioners,
Independent Board of Commissioners, Board of Directors and Sharia Supervisory Board
has no effect on financial performance. Saidat et al. (2018) also in his research examining
the relationship between GCG and the financial performance of companies in Jordan,
found that board size has a negative relationship with the performance of family (BPR) 398 Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022 RESEARCH METHOD This research is an associative type, where the research uses four
independent variables, namely (board of directors, company size, managerial
ownership, and KAP audit) and two dependent variables (return on assets and
non-performing loans). This type of data collection uses secondary data obtained
from quarterly BPR financial reports published by the Financial Services
Authority (www.ojk.go.id) for the period March 2018 - June 2021 from a BPR in
the Bekasi area who sends a report on the implementation of its governance to the http://eduvest.greenvest.co.id 399 Riwandari Juniasti BPR Association, in this case Perbarindo. The data analysis method used in this
study is simple regression analysis with assistance program Eviews 10. The
following will explain the operational definition of each variable. Table 1 Operationalization of Research Variables
Kind of
Variable
Variable
Name
Parameter
Scala
Independent
Board of
Directors
Variable Name
Dummy = complete 1, incomplete
0
Company
Size
Board of
Directors
Ln (Total Assets)
Managerial
ownership
Company Size
Dummy = There is 1, there is not 0
KAP
Audit
managerial
ownership
Dummy = KAP audit 1, no KAP
audit 0
Dependent
Financial performance
Return on
Asset (ROA)
Non
Performing
Loan (NPL)
Source: Research Results (2021) Classic assumption test One of the classic assumptions used in this research is the normality test. Where
in this study there are two dependent variables, so that the results of the normality test are
presented as follows: Table 2 Normality Test Model 1
Variabel Dependen
Jarque-Bera
Probability
Return on Asset
66570.87
0.000000
ource: Data Processing Results with Eviews version 10 (2021) The results of the normality test of model 1 obtained a Jarque-Bera value of
66570.87 with a probability value of 0.000000 which is smaller than a significant level of
0.05, so it is stated that the data in this study is not normally distributed. Because the
results of the normality test in model 1 are not normally distributed, the data is regressed
using the eviews application and using the Newey-West HAC test. Where this method is
one way of dealing with data that are not normally distributed or data variants are not
homogeneous. For the results of the second model normality test as follows: Table 3 Normality Test Model 2
Variabel Dependen
Jarque-Bera
Probability
Non Performing Loan
331.9191
0.000000
Source: Data Processing Results with Eviews version 10 (2021) Furthermore, the results of the normality test of model 2 show that the Jarque-
Bera value is 331.9191 with a probability value of 0.000000 which is smaller than the
0.05 significant level, so it can be concluded that the data in this study is not normally Analysis of the Influence of the Board of Directors, Company Size, Management
Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat
(BPR)
400 Analysis of the Influence of the Board of Directors, Company Size, Management
Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat
(BPR)
400 400 Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022 distributed. Because the results of the normality test in model 2 are not normally
distributed either, the data is regressed using the eviews application and the Newey-West
HAC test. Multiple Linear Regression Test Because the data in model 1 and model 2 are not normally distributed, the data
analysis in this study used multiple linear regression analysis with the Newey-West HAC
test. The results of the Newey-West HAC test with multiple linear regression are
presented in table 4 below. Table 4 Newey-West Model 1 . HAC Test Results
Variable
Coefficient
Std. Error
t-Statistic
Prob. C
10.95765
2.558122
4.283475
0.0000
BOARD OF
DIRECTORS
-1.050886
1.902787
-0.552288
0.5810
SIZE
5.93E-09
3.49E-09
1.700895
0.0897
KEPMAN
-0.795014
0.952309
-0.834827
0.4043
AUDIT
-6.910605
2.472688
-2.794774
0.0054
Source: Data Processing Results with Eviews version 10 (2021) Table 4 Newey-West Model 1 . HAC Test Results Based on the results of the regression model 1 output that has been carried out in
this study, a regression equation model can be made as follows: ROA_Y1 = 10.95765 – 1.050886DIREKSI + 5.93 SIZE – 0.795014KEPMAN –
6.910605 + ε Table 5 Newey-West Model 2 . HAC Test Results
Variable
Coefficient
Std. Error
t-Statistic
Prob. C
21.54757
3.052198
7.059691
0.0000
BOARD OF
DIRECTORS
-3.417810
1.823933
-1.873868
0.0616
SIZE
-2.17E-08
4.73E-09
-4.301113
0.0000
KEPMAN
-1.108887
1.480745
-0.748871
0.4543
AUDIT
-7.087053
2.627483
-2.697278
0.0073
Source: Data Processing Results with Eviews version 10 (2021) Based on the results of the regression model 2 output that has been carried out in
this study, a regression equation model can be made as follows: Based on the results of the regression model 2 output that has been carried out in
this study, a regression equation model can be made as follows:
NPL_Y2 = 21.54757– 3.417810DIREKSI - 2.17SIZE – 1.108887KEPMAN –
7.087053AUDIT + ε
Hypothesis testing y,
g
q
NPL_Y2 = 21.54757– 3.417810DIREKSI - 2.17SIZE – 1.108887KEPMAN –
7.087053AUDIT + ε
Hypothesis testing Hypothesis testing is a testing procedure that will result in a decision, namely the
decision to accept or reject the hypothesis in a study. Hypothesis testing in this study uses
partial hypothesis testing (t test), coefficient of determination test (R2), and F test. t test (Partial Hypothesis Testing) Statistical t test is used to determine the effect of an independent variable individually in
explaining the variation of the dependent variable (Ghozali, 2013). Criteria for acceptance
and rejection of the hypothesis are based on the significance value of p-value. If the p-value (significance) > 0.05, the research hypothesis is rejected. http://eduvest.greenvest.co.id 401 Riwandari Juniasti If the p-value (significance) <0.05, the research hypothesis is accepted. Based on the results of testing the partial hypothesis (t test) in the previous table,
it can be concluded: Based on the results of testing the partial hypothesis (t test) in the previous tabl
it can be concluded: 1. Influence of the Board of Directors on Financial Performance Return on Assets Based on the table, the beta coefficient value for the model 1 board of directors variable is
-1.050886 with a negative relationship direction, the p-value of model 1 is 0.5810 > 0.05. Thus it can be concluded that the board of directors has no effect on the return on assets
of the BPR. Based on the table, the beta coefficient value for the model 1 board of directors variable is
-1.050886 with a negative relationship direction, the p-value of model 1 is 0.5810 > 0.05. Thus it can be concluded that the board of directors has no effect on the return on assets
of the BPR. 2. The Effect of Firm Size on Financial Performance Return on Assets Based on the table, the beta coefficient value of the model 1 firm size variable is 5.93 and
the p-value of model 1 is 0.0897 > 0.05. Thus it can be concluded that the size of the
company has no effect on the return on assets at BPR. Based on the table, the beta coefficient value of the model 1 firm size variable is 5.93 and
the p-value of model 1 is 0.0897 > 0.05. Thus it can be concluded that the size of the
company has no effect on the return on assets at BPR. 3. The Effect of Managerial Ownership on Financial Performance Return on Assets Based on the table, the beta coefficient value of the managerial ownership variable model
1 is -0.795014 with a negative relationship direction, the p-value of model 1 is 0.4043 >
0.05, in this model the p-value is greater than 0.05 so that concluded that managerial
ownership has no effect on return on assets at BPR. Based on the table, the beta coefficient value of the managerial ownership variable model
1 is -0.795014 with a negative relationship direction, the p-value of model 1 is 0.4043 >
0.05, in this model the p-value is greater than 0.05 so that concluded that managerial
ownership has no effect on return on assets at BPR. 4. Coefficient of Determination Test Coefficient of Determination Test The coefficient of determination (R2) test explains the percentage of total
variation in the dependent variable which is explained together. R2 describes the measure
of conformity (goodness of fit), namely the extent to which the sample regression line
matches the existing data. The criterion is that the higher the value of R2 (R2 is close to
1), the better the regression line of the sample. The results of the coefficient of
determination in this study are as follows: Table 6. Coefficient of Determination Test Results (R2)
R-Squared
Model 1
0.031170 (3,11%)
Model 2
0.133453 (13,34%)
Source: Data Processing Results with Eviews version 10 (2021) Table 6. Coefficient of Determination Test Results (R2) Based on Table 6 above, it is known that the results of the coefficient of
determination test of the two models in this study will be explained below. 1. The R-square value in model 1 is 0.031170, this indicates that 3.11% of the variables
of the board of directors, firm size, managerial ownership, and audit firm are influenced
by the return on assets variable, while the remaining 96.89% is influenced by other
variables. outside of the research. 2. The R-square value in model 2 is 0.133453 this shows that 13.34% of the board of
directors variables, company size, managerial ownership, and KAP audit are influenced
by non-performing loans, while the remaining 86.66% is influenced by other variables. outside of the research. F test (simultaneous hypothesis testing) Riwandari Juniasti The Effect of KAP Audit on Financial Performance Return on Assets 4. The Effect of KAP Audit on Financial Performance Return on Assets Based on the table, the beta coefficient value of the audit variable KAP model 1 is -
6.910605 with a negative relationship direction, the p-value of model 1 is 0.0054 <0.05. The KAP audit variable model 1 has a p-value that is smaller than 0.05, which means that
the fourth hypothesis is accepted. 5. Influence of the Board of Directors on the Financial Performance of Non-Performing
Loans Based on the table, the beta coefficient value for the board of directors variable model 2 is
-3.417810 with a negative relationship direction, the p-value of model 2 is 0.0616 > 0.05. Thus it can be concluded that the board of directors has no effect on non-performing
loans at BPR. 6. The Effect of Firm Size on the Financial Performance of Non-Performing Loans 6. The Effect of Firm Size on the Financial Performance of Non-Performing Loans
Based on the table, the beta coefficient value of the model 2 firm size variable is -2.17
with a negative relationship direction, the p-value of model 2 is 0.0000 <0.05. Thus, it
can be concluded that company size has effect on non-performing loans at BPR. 7. The Effect of Managerial Ownership on the Financial Performance of Non-Performing
Loans Based on the table, the beta coefficient value of the managerial ownership variable model
2 is -1.108887 with a negative relationship direction, the p-value of model 2 is 0.4543 >
0.05. Thus, it can be concluded that managerial ownership has no effect on non-
performing loans at BPR. 8. The Effect of KAP Audits on the Financial Performance of Non-Performing Loans
Based on the table, the beta coefficient value of the audit variable KAP model 2 is -
7.087053 with a negative relationship direction, the p-value of model 2 is 0.0073 <0.05. The p-value obtained is smaller than 0.05, so it can be concluded that the KAP audit has
effect on non-performing loans at BPR. 402 Eduvest – Journal of Universal Studies
Volume 2 Number 2, February 2022 CONCLUSION This study aims to determine the effect of the board of directors, firm size,
managerial ownership, and KAP audit on return on assets and non-performing loans at
BPR. Based on the explanation above, it is concluded that it is proven that in model 1
only KAP audits have a significant influence on return on assets. Meanwhile, for model 2,
firm size and KAP variables have a significant negative effect on non-performing loans. Simultaneously the board of directors, company size, managerial ownership, and KAP
audits are able to have an influence on both the return on assets and non-performing loans
of BPR Bekasi area for the 2018-2021 period. F test (simultaneous hypothesis testing) F test (simultaneous hypothesis testing) The F test (simultaneous test) is used to test whether together all independent
variables have a significant effect on the dependent variable. The results of the F test are
presented in the following table: Table 7 F-test
F-statistic
Prob (F-statistic)
Model 1
3.5551/12
0.007206
Model 2
17.01758
0.000000
Source: Data Processing Results with Eviews version 10 (2021) Referring to the table above, the significant value of p-value for model 1 is 0.007
< 0.05, with a statistical F value of 3.555 > 2.625. This means that the variables of the
board of directors, company size, managerial ownership, and KAP audit together have a
significant influence on the return on assets of BPR. Then the p-value of model 2 is 0.000 <0.05, with a statistical F value of 17.017 >
2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and
KAP audit together have a significant influence on non-performing loans in rural banks. Then the p-value of model 2 is 0.000 <0.05, with a statistical F value of 17.017 >
2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and
KAP
di
h
h
i
ifi
i fl
f
i
l
i
l b
k 2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and
KAP audit together have a significant influence on non-performing loans in rural banks. 403 http://eduvest.greenvest.co.id REFERENCES Bvirindi, Tinashe C. (2021). Banking. In A Practical Guide to Financial Services (pp. 39–64). Routledge. Disemadi, Hari Sutra. (2019). Risk Management In The Provision Of People’s Business
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Corporate Governance And Efforts To Prevent Fraud In Banking Companies. Jurnal Reviu Akuntansi Dan Keuangan, 10(1), 136–149. Harjanto, Nung. (2019). Developing Stronger Indonesian Rural Banks. Review of
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510–517. Jiang, Fuxiu, & Kim, Kenneth A. (2020). Corporate governance in China: A survey. Review of Finance, 24(4), 733–772. Lev, Baruch. (2018). The deteriorating usefulness of financial report information and how
to reverse it. Accounting and Business Research, 48(5), 465–493. Manor, Usman, & Desiana, Putri Mega. (2018). Work-Life Balance, Motivation and
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https://openalex.org/W2983433198 | http://revistademorfologiaurbana.org/index.php/rmu/article/download/51/44 | Portuguese | null | Intervenções temporárias no espaço público da cidade de Natal - RN | Revista de morfologia urbana | 2,019 | cc-by | 8,416 | Intervenções temporárias no espaço público da cidade de
Natal - RN: O caso do movimento Eco Praça Manuela Carvalhoa e Ruth Ataídeb
a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa d
Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail:
contatomcarquiteta@gmail.com Manuela Carvalhoa e Ruth Ataídeb
a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa de
Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail:
contatomcarquiteta@gmail.com Manuela Carvalhoa e Ruth Ataídeb
a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa de
Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail:
contatomcarquiteta@gmail.com b Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo (DARQ),
Programa de Pós-Graduação em Arquitetura e Urbanismo (PPGAU), Natal, Rio Grande do Norte, Brasil. E-mail: rataide_58@hotmail.com Submetido em 20 de março de 2019. Aceito em 30 de julho de 2019. Resumo. A atual conformação das cidades e o marcante distanciamento das
pessoas do espaço público têm proporcionado o aparecimento de
movimentos sociais de naturezas diversas que reivindicam novas formas de
uso e apropriação do espaço. Nesse contexto, o movimento Eco Praça surge
em Natal-RN como um projeto de intervenções temporárias que se
fundamenta na mobilização social, estimulando o uso de praças
subutilizadas, promovendo a transformação no seu uso e apropriação pelos
moradores da cidade. Este artigo, que resulta de uma pesquisa exploratória,
analisa esses processos e a significância deste movimento enquanto uma
ação de resistência no âmbito local com ênfase na morfologia das praças e
na percepção dos agentes envolvidos direta e indiretamente. Palavras-chave. apropriação do espaço público, territórios alternativos,
resistência, lugar, Eco Praça. Revista de MorfologiaUrbana (2019) 7(1): e00051 Introdução Ainda, analisou-se a natureza do movimento
enquanto ação transformadora desses espaços
e a rua em relação com a percepção das
pessoas envolvidas. O resultado desse processo é um
espaço fragmentado, individualista e
sem identidade, marcado pela
privatização dos espaços públicos,
pela ausência de corpos na cidade e
por uma cultura do espetáculo, que
padroniza pensamentos,
comportamentos e ações das pessoas,
gerando uma nova lógica da dinâmica
urbana (Olivi, 2012, p. 04). O ato de ocupar, ressignificar, recriar novos
lugares na cidade, passa a emergir como
resistência e reinventa, através de diversas
práticas efêmeras, os espaços da cidade. No
caso do presente estudo são destacadas as
intervenções temporárias expressas no
Movimento “Eco Praça” como formas de
apropriação que surgem de maneira
despretensiosa, muitas vezes pouco
organizadas, mas que tentam transformar a
vida pública por meio de práticas simples, as
quais visam dar uma maior dimensão à
necessidade de viver e reposicionar as
práticas coletivas na cidade. Introdução privados, maquiados e vendidos pelo
consumo, entre tantas outras ações que
modificam o espaço na contemporaneidade. O espaço urbano é um laboratório de
experiências e de construção de identidades. Apropriar-se dele é reaproximar os corpos da
rua, buscar novas formas de manifestação, ao
mesmo tempo que pensa em como
transformar e criar/recriar lugares
coletivamente. No contexto atual, o uso
lúdico dos espaços pelos movimentos
temporários de resistência, assim como a
ocupação de áreas subutilizadas com o
estímulo ao retorno das pessoas às ruas,
constituem ações que interferem e alteram o
tratamento dos nossos espaços públicos, na
medida em que evidenciam alguns problemas
enfrentados pela sociedade contemporânea. Assim, a ocupação de espaços públicos
abandonados, de praças, parques e canteiros,
ou mesmo de resíduos do espaço privado da
cidade formal, torna-se significante ao
promoverem alterações na sua dinâmica
espacial e formas de utilização, assim como
de outras alternativas para se viver a cidade. Nesse sentido, o movimento “Eco Praça” –
objeto de estudo deste trabalho e
caracterizado aqui como um tipo de
intervenção temporária – merece destaque
por se tratar de uma ação requalificadora e
transformadora na cidade de Natal-RN, que
ao ocupar diversas praças subutilizadas,
promoveu, ainda que temporariamente, a
apropriação e a ressignificação desses
espaços pela população. Tais problemas se materializam nas cidades
por meio das ações que privilegiam os
interesses individuais em detrimento dos
coletivos, por exemplo, na produção de
grandes escalas de planejamento, na
priorização do transporte motorizado, na
transformação do público em espaços O propósito do estudo foi compreender essas
ações temporárias como geradoras de novas Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 2 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN práticas coletivas e a sua relação com o
restabelecimento das condições de vitalidade
e urbanidade nos espaços ocupados e em seus
respectivos entornos. Com isso, buscou-se
analisar não apenas o espaço físico contido
nos limites das praças, mas também o
processo de apropriação dessas pelas pessoas
e a significância do movimento enquanto
ação de resistência no contexto da cidade de
Natal. As considerações da pesquisa tiveram
como enfoque principal a forma como essas
praças eram utilizadas – durante e depois das
intervenções –, assim como a relação do
existente (espaço físico e inserção dele nos
repectivos entornos com as ocupações). Morfologia, intervenções temporárias e a
criação de novos lugares na cidade O espaço público surge como palco principal
das representações socias, culturais e
políticas, respondendo assim aos discursos
dos agentes públicos e da sociedade em geral. As configurações morfológicas dele refletem
e influenciam o modo como os indivíduos e
grupos sociais usam a cidade, as suas
relações com o cotidiano, a cultura e os
costumes. Essa cidade, lida através do corpo
e dos seus usos manifestos nos lugares,
adquire significado e torna-se o principal
palco de estudo dessas experiências. Tais intervenções são definidas como
temporárias por não promoverem
necessariamente ações de longo prazo ou
tampouco se organizarem em torno de um
cronograma rígido. Movidas por novos
conceitos, como o urbanismo tático1 e o
placemaking2, essas ações buscam, por meio
de iniciativas simples de ocupação do espaço
público, promover transformações no
cotidiano das pessoas que observam e
também interagem com elas. Em geral, essas
práticas permitem que se possa apreciar e
compreender a cidade de forma lúdica,
entendida pela corpografia3 e significada
pelo uso e pela criação de lugares. A partir dessa compreensão, notam-se as
diferentes formas de transformação dos
espaços das cidades, muitos desprovidos de
vitalidade e complexidades sociais, seja pelas
relações mais fluidas e individualistas,
resultantes de um modelo funcionalista de
planejamento urbano, ou por transformações
inevitáveis, que surgem devido às estruturas
sociais/políticas emergentes. Nesse sentido,
os espaços públicos são os mais afetados,
tranparecendo na subutilização dele e no seu
distanciamento, a necessidade de constante
apropriação e ocupação por parte das
pessoas. Para Adriana Sansão Fontes (2013, p. 36), as
intervenções temporárias são basicamente
ações intencionais que buscam transformar o
espaço de forma efêmera, sem
necessariamente manter uma temporalidade. São em sua maioria pequenas, particulares
em relação aos locais utilizados, subversivas,
pois não seguem um padrão único, e
interativas por estimularem a socialização. A
autora classifica essas ações na forma de
apropriações espontâneas, intervenções de
arte pública e festas locais, mas, Para Adriana Sansão Fontes (2013, p. 36), as
intervenções temporárias são basicamente
ações intencionais que buscam transformar o
espaço de forma efêmera, sem
necessariamente manter uma temporalidade. São em sua maioria pequenas, particulares
em relação aos locais utilizados, subversivas,
pois não seguem um padrão único, e
interativas por estimularem a socialização. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Morfologia, intervenções temporárias e a
criação de novos lugares na cidade A
autora classifica essas ações na forma de
apropriações espontâneas, intervenções de
arte pública e festas locais, mas,
principalmente, as caracteriza com a marca
principal da intencionalidade transformadora,
na medida em que rompem com o cotidiano,
transitando sempre entre os usos comuns da
cidade e os grandes eventos. Alessandra Olivi (2012, p. 4) considera que o
atual modelo de produção do espaço urbano
sob os moldes capitalistas se apropria dos
lugares da vida e dos seus significados, e
ameaça a capacidade de identificação pessoal
e cultural. Isso prejudicará drasticamente a
vida urbana e a reprodução das múltiplas
identidades que a compõem. Para a autora: principalmente, as caracteriza com a marca
principal da intencionalidade transformadora,
na medida em que rompem com o cotidiano,
transitando sempre entre os usos comuns da
cidade e os grandes eventos. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 3 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Essas ações fortificam as relações já
propostas nos espaços e fomentam, por meio
das ações lúdicas e corpóreas, a criação de
novos lugares. Para Vicente Del Rio (1990),
o lugar corresponde ao conjunto de
elementos que conformam o nosso ambiente
mais imediato: “São muito fortes, e
empiricamente verificáveis, as sensações de
pertencer, de proteção, de territorialidade, de
domínio” (Del Rio, 1990, p. 88). permanece geralmente subentendida,
ainda que sempre recebendo um forte
e explícito viés de funcionalidade:
lugares seriam aqueles espaços
urbanos cuidadosamente localizados,
quantificados e definidos, destinados
basicamente ao desempenho de
funções de cunho social. Ou seja:
espaços nos quais as pessoas iriam se
encontrar e realizar seus contatos
sociais, esperando-se que, nesse
exercício, fossem sociabilizar
comunitariamente em seus
relacionamentos interpessoais. Lugares, numa visão como essa, não
seriam mais do que áreas funcionais
destinadas ao exercício da
sociabilização, isto é, áreas destinadas
a funcionar como espaços de convívio
(Castello, 2006, p. 80). Segundo esse autor, a psicologia ambiental
permite compreender o lugar a partir da
comparação dele com o espaço e esse tem em
suas dimensões uma espacialidade física;
enquanto o lugar está mais presente como
uma dimensão psicológica, o espaço “é
mensurável, o lugar é holístico” (Del Rio,
2003, p. 14). Morfologia, intervenções temporárias e a
criação de novos lugares na cidade alimentação, locais de entretenimento,
complexos esportivos, complexos híbridos,
cinemas multiplex, museus, bibliotecas”
(Castello, 2006, p. 78). alimentação, locais de entretenimento,
complexos esportivos, complexos híbridos,
cinemas multiplex, museus, bibliotecas”
(Castello, 2006, p. 78). que se exprimem no uso, no acidental: “É o
espaço passível de ser sentido, pensado,
apropriado e vivido através do corpo”
(Carlos, 2007, p. 17). Assim, afirma a autora: Anteriormente, Marc Augé (1994) definiu
esses espaços como “não-lugares”. Caracterizados como espaços criados
como/pela mercadoria, eles unificam e
simplificam a vida, a arquitetura, os desejos e
as relações dentro de si. Para esse autor,
aeroportos, shoppings centers, grandes obras
viárias, conveniências e fast foods, passam a
reproduzir em suas estruturas características
que os padronizam mesmo que em locais
diferentes do globo; a cultura de massas
passa a ser disseminada de acordo com
moldes estéticos e consumistas, que buscam,
acima de tudo, alienar as relações e
disseminar novas necessidades às pessoas. Nesse mesmo ritmo, as cidades se
modificam, na indústria, na publicidade,
comércio, turismo, tornando-se uma alegoria
de signos (Augé, 1994, p. 73). O lugar é produto das relações
humanas, entre homem e natureza,
tecido por relações sociais que se
realizam no plano do vivido, o que
garante a construção de uma rede de
significados e sentidos que são tecidos
pela história e cultura civilizadora
produzindo a identidade, posto que é
aí que o homem se reconhece porque é
o lugar da vida. Cada sujeito se situa
num espaço concreto e real onde se
reconhece ou se perde, usufrui e
modifica, posto que o lugar tem usos e
sentidos em si (Carlos, 1996, p. 29). Para Carlos (2007), o lugar não nos propõe o
entendimento enquanto parte associada do
espaço, mas como parte do processo de
reprodução da vida. Assim, o lugar abre a
perspectiva para se pensar o viver e o habitar,
o uso e o consumo, os processos de
apropriação do espaço (Carlos, 2007, p. 14). O autor destaca que os não-lugares se
apresentam na multiplicação de referências
imaginárias, nas acelerações dos meios de
transporte e nas mudanças de escala, e são
produtos da supermodernidade. Nessa
perspectiva, eles seriam essas instalações
necessárias ao trânsito rápido – viadutos,
pontes, túneis; os grandes centros comerciais;
e até mesmo áreas criadas para abrigar
pessoas, instalações efêmeras que podem ser
replicadas em qualquer lugar. Morfologia, intervenções temporárias e a
criação de novos lugares na cidade Del Rio destaca ainda que a partir dos
estudos do psicólogo ambiental David
Canter, o lugar pode ser definido por três
dimensões: as atividades que ocorrem nele,
as concepções desse ambiente construído e
seus atributos físicos, como mostra o
diagrama: Já durante o pós-modernismo, segundo
Castello (2006), o tema do lugar passa a
enquandrar-se em um enfoque mais
fenomenológico, conceituando “lugar de
modo a considerá-lo como algo mais do que
uma mera localização espacial” (Castello,
2006, p. 82). Com isso: Figura 1. Diagrama de Venn indica o conceito de
lugar pelas suas intersecções (fonte: produzido
pelas autoras a partir de Del Rio, 2003). O peso fenomenológico que o conceito
encerra vê-se consideravelmente
aumentado: lugar é consagrado como
conceito urbano de natureza
fenomenológica. A cidade, percebida
por suas características de produção
de bens e serviços é, também,
percebida por suas características de
produção de experiências humanas. Experiências que se processam em
uma rede de lugares: lugares que se
preocupam com humanismo e com a
concretização do espaço existencial
[...] A compreensão de lugar como
fenômeno passa vigorosamente a
pressionar com cada vez maior
intensidade as ponderações da
intelectualidade arquitetônico-
urbanística da época (Castello, 2006,
p. 83). Figura 1. Diagrama de Venn indica o conceito de
lugar pelas suas intersecções (fonte: produzido
pelas autoras a partir de Del Rio, 2003). Na mesma concepção urbanística de Del Rio
(1990), Lineu Castello (2006) destaca dois
momentos em que a noção de lugar ganha
destaque no século XX: no modernismo e nas
teorias arquitetônicas-urbanísticas pós-
modernas. Para o autor, durante o
modernismo, o conceito de lugar foi visto
com certo desinteresse: Ao tratar do lugar como parte da experiência
humana em um campo de estudo mais ligado
à geografia urbana, Ana Fani Alessandri
Carlos (2007) admite o lugar como a base da
reprodução da vida, que pode ser identificado
pelo conjunto – habitante, identidade e lugar. Esse lugar surge pelas relações que os
indivíduos mantêm com os espaços habitados O conceito de lugar não chega a ser
expresso de maneira clara no
Modernismo. A expressão lugar Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 4 / 13 alimentação, locais de entretenimento,
complexos esportivos, complexos híbridos,
cinemas multiplex, museus, bibliotecas”
(Castello, 2006, p. 78). Morfologia, intervenções temporárias e a
criação de novos lugares na cidade Ou ainda, o não-lugar
pode vir a se tornar um lugar à medida que é
apropriado, que ganha significado: “O lugar e
o não-lugar são, antes, polaridades fugidias: o
primeiro nunca é completamente apagado e o
segundo nunca se realiza totalmente” (Augé,
1994, p. 74). Pensando nisso, o uso de um espaço em
determinado intervalo de tempo – mesmo que
curto e pontual – por ações dotadas de
significado e identidade, transmitem e criam
lugares, sendo eles efêmeros ou não. Essa
improvisação colide diretamente com a
lógica racional de produção e utilização do
espaço, reproduzindo um cotidiano marcado
pela presença nas ruas, convívios reais e
trocas simultâneas de experiências. A importância de se discutir os conceitos de
lugar e não-lugar dentro do contexto da
cidade contemporânea está na compreensão
da atividade temporária como resistência e
marco na criação de novos lugares, ou,
simplesmente, da modificação dos não-
lugares, garantindo a esses uma nova
identidade específica. Para isso, cabe
relacionar essas ações à novas formas de
reinventar o “lugar” e de ressignificar a
memória coletiva da cidade. Entende-se, à vista disso, que as intervenções
temporárias recriam e reestabelecem as
condições necessárias à geração de novos
lugares da cidade, proporcionando aos
espaços subutilizados um novo caráter
identitário – mesmo que temporariamente – e
dotando-os de um significado comum às
pessoas que dele partilham. O uso efêmero
garante um ecoar de possibilidades cotidianas
que podem ser usadas coletivamente,
recorrendo às soluções simples como a
utilização alternativa de mobiliários, o uso
artístico das calçadas ou simplesmente o
encontro grupal em um determinado local da
cidade. É nessa criação de novos lugares na cidade
que as intervenções temporárias ganham
corpo e podem ser tratadas como efetivadoras
e promotoras do direito à cidade, aos espaços
públicos e à vida coletiva. O lugar passa a
ser resistente a um modelo de cidade
fragmentada, hierarquizada e excludente, que
nega as experiências da vida cotidiana e as
vende a partir das necessidades do capital. Portanto, as intervenções temporárias
aparecem aqui como formas apropriadas de
ocupação de espaços residuais na cidade,
assim como de não-lugares, que, realçando o
valor da arte, da cultura, da música, ou dos
simples encontros e derivas casuais, são
capazes de agitar e recriar lugares, fomentar
novas relações e promover diversas práticas
colaborativas, contribuindo para o espaço da
cidade. Morfologia, intervenções temporárias e a
criação de novos lugares na cidade Segundo o
autor: Nesse mesmo sentido, Eugenio Queiroga
(2012) traz o lugar enquanto “lugar público”,
como aquele espaço que se situa como o
local que é apropriado pelo coletivo, mesmo
não se trata de um espaço público
propriamente dito; podendo, portanto,
combinar espaços públicos e privados. Para o
autor, o lugar público nos permite
compreender as relações entre a vida pública
e os espaços da cidade, e ainda pode se
prestar à esfera pública ou privada, tendo
assim um caráter dual em sua atuação. Para
ele: “Todo lugar público é, ainda que
esporadicamente, um subespaço da esfera
pública, mas nem todas as ações da esfera
pública se manifestam nos espaços públicos”
(Queiroga, 2012, p. 216). Se um lugar pode se definir como
identitário, relacional e histórico, um
espaço que não pode se definir nem
como identitário, nem como
relacional, nem como histórico
definirá um não-lugar. A hipótese aqui
defendida é a de que a
supermodernidade é produtora de
não-lugares, isto é, de espaços que
não são em si lugares antropológicos e
que, contrariamente à modernidade
baudelairiana, não integram os
lugares antigos: estes, repertoriados,
classificados e promovidos a ‘lugares
de memória’, ocupam aí um lugar
circunscrito e específico (Augé, 1994,
p. 73). Para tanto, cabe aqui mencionar que na
cidade contemporânea tem surgido diversos
novos lugares – sejam públicos ou privados –
que se concretizam perante às necessidades
das novas informações, dos fluxos e,
principalmente, do capital. A partir disso,
Castello (2006, p. 78) denota esses novos
espaços como “lugares geneticamente
modificados”. Esses novos lugares se apresentam sobre
diversas conformações: “nos shopping malls,
cenários históricos revitalizados, praças de O não-lugar não possui relações/trocas
sociais, identidade e não transmite, portanto,
a história de um grupo, de uma sociedade. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 5 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN medianeiras abandonadas. A sua
flexibilidade, diversidade – de público, de
organização, de efeitos – e a fluidez com que
acontecem, potencializam tais realizações e
transgridem a formalidade estrutural do
espaço público, ao lidar diretamente com as
regras impostas pela cidade. Logo, o não-lugar se relaciona com o lugar,
na medida que sempre existe uma relação
entre os dois: um só existe sobre a forma do
outro; o não-lugar existe sob a perspectiva da
ausência do lugar. Morfologia, intervenções temporárias e a
criação de novos lugares na cidade Essas ações traduzem então uma
forma de apropriação dos espaços públicos,
que remodelam a vida urbana a partir das
necessidades de diferentes pessoas e grupos
diversos. Aproximação: O Movimento “Eco Praça”
na cidade de Natal - RN Aproximação: O Movimento “Eco Praça”
na cidade de Natal - RN Como discutido, os Movimentos temporários
diversos têm surgido nas grandes cidades
como forma de resistência, para confrontar os
padrões individualistas de vivência do
espaço, as pressões do capital na
mercantilização da cidade e um modelo de
planejamento que segrega e exclui a vida
pública. Nesse contexto, tem surgido nos
últimos anos na cidade de Natal - RN,
movimentos temporários diversos,
representados por ocupações efêmeras
materializadas na arte, na cultura e nas
práticas de lazer, que retomam os espaços
públicos tidos como subutilizados. Assim, essas intervenções resultam de várias
motivações, desde a resistência a uma ideia
de cidade que segrega a vida pública a um
combate a essa nova individualidade presente
em nossa sociedade. Por motivos diversos,
uns mais pessoais, outros mais coletivos, tais
apropriações resultam em feiras livres,
projetos de arte em comunidades, ocupação
de praças de bairros, vendas ambulantes,
festas ao ar livre ou simples grafites em Tais ações, convertem o espaço público em
palcos de eventos com expressões artísticas,
como a dança e a música, com bazares
culturais e outras oportunidades de trocas
comerciais; e o mais importante, criam
lugares afetivos e ativos que proporcionam Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 6 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN atividades no interior do estado do Rio
Grande do Norte, nos municípios de Pedro
Avelino e Lajes. Para este artigo, foram
destacadas apenas as dez praças, excluindo as
demais ocupações (Quadro 1 e Figura 02). atividades no interior do estado do Rio
Grande do Norte, nos municípios de Pedro
Avelino e Lajes. Para este artigo, foram
destacadas apenas as dez praças, excluindo as
demais ocupações (Quadro 1 e Figura 02). atividades no interior do estado do Rio
Grande do Norte, nos municípios de Pedro
Avelino e Lajes. Para este artigo, foram
destacadas apenas as dez praças, excluindo as
demais ocupações (Quadro 1 e Figura 02). conversas e trocas de experiências. Segundo
Alessandra Olivi (2012), esse controle do
espaço pelos movimentos sociais adquire
relevância particular em um contexto onde a
privatização, a homogeneização, a
mercantilização e a vigilância do espaço
passam a alterar os valores públicos, sociais e
políticos. Figura 2. Localização por bairros das praças
ocupadas pelo movimento entre 2013 e 2016
(fonte: produzido pelas autoras a partir de
Carvalho, 2017). Aproximação: O Movimento “Eco Praça”
na cidade de Natal - RN Nesse sentido, o movimento “Eco Praça” em
Natal - RN se apresenta como um movimento
efêmero de apropriações de praças
subutilizadas, que conseguiu alterar, ainda
que temporariamente, as suas funções e
formas de apropriação de lugar de passagem
para espaços de integração e convivência no
cotidiano das comunidades onde se inserem. Iniciado em 2013 na Praça dos Eucaliptos,
localizada no bairro de Candelária, suas
ações tiveram prosseguimento e destaque até
o ano de 2016, promovendo a ocupação de
dez praças em nove bairros – Candelária,
Capim Macio, Potengi, Cidade Alta, Mãe
Luiza, Ponta Negra, Neópolis e Petrópolis –
do município; um espaço semi-público – a
Cidade da Criança; e um espaço privado – a
fundação Hélio Galvão, ambos em Natal. Ainda, em outros momentos, realizou Figura 2. Localização por bairros das praças
ocupadas pelo movimento entre 2013 e 2016
(fonte: produzido pelas autoras a partir de
Carvalho, 2017). Quadro 1. Localização das praças por bairros (fonte: produzido pelas autoras em 2018 a partir de
Carvalho, 2017). Bairros x Regiões Administrativas de Natal
Praças
Bairro
Região
Praça do Ralf
Lagoa Azul
Norte
Área de Lazer Panatis
Potengi
Norte
Praça André de Albuquerque
Cidade Alta
Leste
Praça 7 de Setembro
Cidade Alta
Leste
Praça Cívica
Petrópolis
Leste
Praça Edgar Borges
Mãe Luiza
Leste
Praça dos Eucaliptos
Candelária
Sul
Parque de Capim Macio
Capim Macio
Sul
Praça Central de Neópolis
Neópolis
Sul
Praça Omar O’Graddy
Ponta Negra
Sul Praças
Praça do Ralf
Área de Lazer Panatis
Praça André de Albuquerque
Praça 7 de Setembro
Praça Cívica
Praça Edgar Borges
Praça dos Eucaliptos
Parque de Capim Macio
Praça Central de Neópolis
Praça Omar O’Graddy nos quais elas se inserem. De acordo com o
Anuário Estatístico do município de 2018,
publicado pela SEMURB4, Natal se divide
em quatro regiões administrativas (Norte,
Sul, Leste e Oeste), sendo a Região Norte a
maior delas em superfície e em população,
envolvendo sete bairros. Neste trabalho, Da configuração morfológica dos espaços:
As praças e seus respectivos entornos Ao tratar das dez praças discutidas neste
artigo, cabe apresentar algumas notas sobre a
configuração espacial e a divisão
administrativa do município, assim como
uma abordagem geral de alguns dos bairros Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Intervenções temporárias no espaço público da cidade de Natal - RN 7 / 13 redes sociais. Tais realizações ocorriam de
forma despretensiosa e se manifestavam em
cangas estendidas, pequenas vendas, rodas de
conversas e apresentações musicais pontuais. Para Adriana Sansão Fontes (2013), essas
ações eventuais de poetização e reconquista
da cidade se intensificaram nos últimos anos,
muitas vezes motivadas pelas redes sociais,
movidas por uma causa comum de usar a
cidade, e buscam nas estratégias de
intervenções temporárias reestabelecer um
elo com o cotidiano e com a vida coletiva. devido ao recorte da ocorrência das
ocupações, foram analisadas dez praças
localizadas nas regiões Norte, Sul e Leste,
em nove bairros da cidade. Para entender a inserção do movimento
nessas regiões, cabe evidenciar alguns
aspectos urbanísticos, especialmente os
referentes à oferta de serviços e
equipamentos coletivos. A Região Norte
possui 55 equipamentos desportivos
(quadras, estádios, campos de futebol) e 62
praças; a Região Sul possui 34 equipamentos
e 87 praças; a Região Leste 16 equipamentos
e 74 praças; e a Região Oeste, 18
equipamentos e 31 praças. Com isso, nota-se
que a Região Oeste – única a não possuir
intervenção em suas praças – é a mais carente
de equipamentos de lazer públicos
(SEMURB, 2018, p. 152). Com o avanço das experiências, as
ocupações foram se ampliando e agregando
novos participantes de diferentes tribos e
idades, estimulando o surgimento de novas
demandas e evidenciando a necessidade de
estruturação do movimento, como o apoio do
poder público e o patrocínio de empresas
privadas. As ações se converteram em
grandes encontros marcados por práticas
esportivas, apresentações culturais e
musicais, hortas urbanas, conversas e
discussões sobre temas atuais, barracas
gastronômicas e bazares de diferentes estilos;
tendo como principais atores: os
organizadores do movimento, expositores e
apoios, moradores do entorno das praças
analisadas e os participantes. Da configuração morfológica dos espaços:
As praças e seus respectivos entornos Ainda com relação às atividades instaladas e
à infraestrutura, os bairros de Candelária,
Capim Macio e Ponta Negra (Região Sul) são
predominantemente residenciais, com uma
grande diversidade de serviços e comércios
localizadas nas avenidas principais, e seus
moradores, em sua maioria, se inserem nos
extratos de média e alta renda, residindo em
casas e apartamentos de médio e alto padrão. Enquanto os bairros de Mãe Luiza (região
Leste), Potengi e Lagoa Azul (Lagoa Azul)
concentram uma população de pouca renda
(até três salários mínimos) e que vivem, em
sua maioria, em condições de precariedade
urbanística e de moradia (Semurb, 2018). Mesmo estruturado em ações pontuais, o
movimento “Eco Praça” reafirma a
necessidade de reocupar a cidade através do
corpo, do uso do espaço público e da
coletividade transcrita nessas apropriações. Mesmo estruturado em ações pontuais, o
movimento “Eco Praça” reafirma a
necessidade de reocupar a cidade através do
corpo, do uso do espaço público e da
coletividade transcrita nessas apropriações. Essas intervenções, tornam-se
revolucionárias por criarem uma nova
consciência sobre como ocupar os largos,
parques, praças, de maneira simples e
despretensiosa; proporcionando através de
diversos atrativos um novo sentido de lugar a
esses espaços. Nesse sentido, também se
encontra o olhar de David Harvey (2012),
quando afirma que Essas intervenções, tornam-se
revolucionárias por criarem uma nova
consciência sobre como ocupar os largos,
parques, praças, de maneira simples e
despretensiosa; proporcionando através de
diversos atrativos um novo sentido de lugar a
esses espaços. Nesse sentido, também se
encontra o olhar de David Harvey (2012),
quando afirma que Com relação às praças escolhidas pelo
movimento “Eco Praça”, cabe destacar:
44,44% das praças utilizadas estão
localizadas em conjuntos habitacionais que
deram origem ou impulsionaram a ocupação
do solo dos respectivos bairros (Candelária,
Lagoa Azul, Potengi, Ponta Negra e
Neópolis), e muitas delas são espaços
centrais em seus bairros, lugares mais
legíveis e de maior movimentação de
pessoas, moradores ou passantes. Constatado
esse cenário, foi possível analisar a forma
como o movimento enxerga a escolha e a
ocupação dos espaços para a realização das
suas atividades e a importância dessas
escolhas para o sucesso das suas
intervenções. [...] as táticas das ocupações
consistem em tomar um espaço público
central […] e convertê-lo em um
espaço político de iguais, um lugar de
discussão aberta e debate sobre o que
esse poder está fazendo e as melhores
formas de se opor ao seu alcance. Da configuração morfológica dos espaços:
As praças e seus respectivos entornos Essa tática […] mostra como o poder
coletivo de corpos no espaço público
continua sendo o instrumento mais
efetivo de oposição quando o acesso a Como referido, as intervenções do
movimento “Eco Praça” se caracterizavam
inicialmente como ocupações simples,
organizadas por poucas pessoas por meio das Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 8 / 13 todos os outros meios está bloqueado
(Harvey, 2012, p.64). quais se agruparam em três níveis para uma
melhor caracterização dos espaços ocupados: 1. configuracionais, onde se analisa o
entorno imediato e os elementos
constituintes das praças a partir de uma
classificação tipológica; Nesses novos movimentos, o ato de reocupar
passa a ser uma luta constante por espaços
mais dignos e uma melhor qualidade da vida
urbana, seja ela proporcionada por uma
infraestrutura mais eficiente, por maiores
atrativos – música, arte, feiras ao ar livre –,
assim como novas possibilidades de
encontros, marcados por uma maior
corporeidade na cidade, tudo isso
acontecendo de maneira simples. Diante
disso, torna-se relevante compreender as
ações realizadas pelo movimento “Eco
Praça” na busca da relação dessas práticas
com o restabelecimento das condições de
vitalidade – mesmo que temporárias – nos
locais ocupados, como também o seu real
significado para a população natalense e seus
visitantes. ç
p
g
2. perceptivos, destacando o significado e a
legibilidade; 3. físicos e paisagísticos, com atenção
especial para os equipamentos urbanos,
o plano de suporte, a segurança e a
arborização. Ao tomar como referência a estrutura
metodológica proposta por Panerai (2006), a
análise configuracional foi estruturada para
enfatizar a relação com a cidade e os padrões
de ocupação do entorno imediato (levando
em consideração as quadras mais próximas à
praça) com destaque para os usos e
atividades e a intensidade construtiva dada
pelo gabarito. Essa análise dos padrões de
ocupação também procura realçar as relações
entre a arquitetura do entorno e a rua,
destacando os graus de acessibilidade e
integração (aberturas, fechamentos) nos
termos definidos por Ferdinando Rodrigues
(2005). A classificação das tipologias das
praças teve como referência Robba e Macedo
(2002), levando em consideração uma análise
mais paisagística, e Rodrigues (2005) ao
analisar de forma mais geométrica. Percursos
metodológicos
e
resultados
prévios Métodos e técnicas aplicados à pesquisa Buscou-se com este artigo demonstrar como
as intervenções temporárias realizadas pelo
Movimento “Eco Praça”, na cidade de Natal,
durante o período de 2014 à 2016, tiveram
um impacto significativo no uso e na
apropriação das praças utilizadas pelas ações,
assim como nos seus entornos, recorrendo-se
a uma análise morfológica e perceptiva. Quanto à percepção, utilizou-se os conceitos
de visibilidade e legibilidade propostos por
Lynch (1990), buscando compreender a
imagem dos usuários sobre as praças no
contexto da cidade, seja pela sua tipologia,
pelo do reconhecimento visual e dos
elementos simbólicos no seu entorno. Cabe mencionar que a pesquisa foi
estruturada em dois momentos: no primeiro
foi realizada uma análise morfológica das
praças e seus entornos a partir da observação
e da catalogação de atributos físicos; no
segundo, foram realizadas entrevistas
semiestruturadas com os principais agentes
envolvidos. Neste artigo, recortamos apenas
a análise morfológica, e para tanto, recorreu-
se às contribuições dos seguintes autores:
Philippe Panerai (2006), Ferdinando de
Moura Rodrigues (2005), Roberto Lobato
Corrêa (2004), Robba e Macedo (2002),
Kevin Lynch (1990), Jan Gehl (2015) e Jane
Jacobs (2014). No estudo dos elementos físicos, considerou-
se fatores como: grau de conservação,
quantidade e distribuição dos equipamentos
urbanos; os desníveis, rampas e acessos;
segurança – presença de policiamento e
sinais de vandalismo para caracterizar o
plano suporte; quantidade de árvores,
vegetação predominante, porte predominante,
e relevância do sombreamento, sem levar em
consideração análises quantitativas mais
aprofundadas através dos conceitos de Robba
e Macedo (2002). A primeira etapa da análise consistiu na
escolha das intervenções a serem analisadas,
baseando-se no recorte temporal e nos atores
a serem entrevistados. Alguns resultados da análise morfológica A partir desse estudo, tem-se que as praças
localizadas na Região Norte (Praça do Ralf e
Área de Lazer Panatis) possuem em comum A partir do recorte, demonstrado no quadro A partir do recorte, demonstrado no quadro
1, foram analisados os atributos físicos, aos p
,
q
1, foram analisados os atributos físicos, aos Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 9 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Norte e o Tribunal de Justiça do Estado. Norte e o Tribunal de Justiça do Estado. Ainda, trata-se de locais bastante permeáveis,
sem cercamentos, desníveis ou barreiras
físicas, fato que contribuiu também para
esses usos. o fato de estarem em áreas mais degradadas e
descuidadas do olhar do poder público. Os
dois espaços têm seus equipamentos bastante
depredados e necessitados de manutenção,
apesar de constatarmos a intensidade do uso
e da apropriação do lugar pela população
residente no entorno e nos bairros onde se
inserem. Figura 3. “Eco Praça” na Área de Lazer Panatis,
Região Norte, Natal (fonte: Carvalho, 2017). A Praça do Ralf está localizada no Bairro de
Lagoa Azul, mais precisamente no Conjunto
Gramoré, entre as Avenidas Guaíra e
Tocantina, em uma área predominantemente
residencial, de baixo gabarito e de fácil
conexão com a cidade, além de estar
adequadamente ajustada às necessidades do
pedestre e ser totalmente permeável e
acessível, física e visualmente. Diferente
disso, observou-se que a Área de Lazer
Panatis5 (figura 3) tem seu único acesso
público em uma importante avenida coletora
da cidade – Av. João Medeiros Filho6 –, fato
que dificulta o acesso livre dos pedestres que
circulam na sua outra margem, além de
possuir um cercamento e ter seu horário de
funcionamento limitado. Essas reflexões
inferem em como o movimento tratou essas
intervenções e as relações estabelecidas entre
os ocupantes dessas áreas, as ações
temporárias e os novos participantes, levados
por essas realizações a participarem da
ocupação. As Praças André de Albuquerque, 7 de
Setembro e Cívica ou Pedro Velho,
localizadas na Região Leste, destacam-se
pelo valor simbólico e patrimonial,
principalmente por serem berço e palco das
principais manifestações políticas e sociais
ocorridas na cidade desde a sua fundação. Alguns resultados da análise morfológica Além disso, evidenciam-se nos seus entornos
a presença marcante de edificações de valor
patrimonial, grandes instituições
governamentais, e a abundância de atividades
de comércio e serviços, o que contribuiu para
um fácil acesso dos participantes, resultando
em ocupações de grande impacto organizadas
pelo movimento. Figura 3. “Eco Praça” na Área de Lazer Panatis,
Região Norte, Natal (fonte: Carvalho, 2017). Igualmente localizada na Região Leste, a
Praça Edgar Borges traz características
diferentes das mencionadas anteriormente,
por se tratar de uma área mais periférica e de
menos visibilidade dentro da cidade, ao se
encontrar em um bairro residencial
socialmente vulnerável
socioeconomicamente (Mãe Luiza), e
localizado em uma área de acesso mais
restrito (sobre um morro). Apesar disso, em
uma visão micro, o seu espaço físico é
bastante permeável, de fácil reconhecimento
no bairro por estar situada em sua área
central, próxima à Igreja Católica Nossa
Senhora da Conceição e ao Centro Sócio
Pastoral local. Igualmente localizada na Região Leste, a
Praça Edgar Borges traz características
diferentes das mencionadas anteriormente,
por se tratar de uma área mais periférica e de
menos visibilidade dentro da cidade, ao se
encontrar em um bairro residencial
socialmente vulnerável Igualmente localizada na Região Leste, a
Praça Edgar Borges traz características
diferentes das mencionadas anteriormente,
por se tratar de uma área mais periférica e de
menos visibilidade dentro da cidade, ao se
encontrar em um bairro residencial
socialmente vulnerável
socioeconomicamente (Mãe Luiza), e
localizado em uma área de acesso mais
restrito (sobre um morro). Apesar disso, em
uma visão micro, o seu espaço físico é
bastante permeável, de fácil reconhecimento
no bairro por estar situada em sua área
central, próxima à Igreja Católica Nossa
Senhora da Conceição e ao Centro Sócio
Pastoral local. socioeconomicamente (Mãe Luiza), e
localizado em uma área de acesso mais
restrito (sobre um morro). Apesar disso, em
uma visão micro, o seu espaço físico é
bastante permeável, de fácil reconhecimento
no bairro por estar situada em sua área
central, próxima à Igreja Católica Nossa
Senhora da Conceição e ao Centro Sócio
Pastoral local. Alguns resultados da análise morfológica A visibilidade e o reconhecimento desses
espaços dentro da cidade favoreceram
ocupações mais bem-sucedidas,
principalmente devido à facilidade de acesso
a esses – seja por meio do transporte coletivo
ou mesmo individual – e por estarem
localizadas em áreas centrais, com muito
movimento e próximos de diversas atividades
institucionais, como a prefeitura de Natal, a
Assembleia Legislativa do Rio Grande do A visibilidade e o reconhecimento desses
espaços dentro da cidade favoreceram
ocupações mais bem-sucedidas, principalmente devido à facilidade de acesso
a esses – seja por meio do transporte coletivo
ou mesmo individual – e por estarem
localizadas em áreas centrais, com muito
movimento e próximos de diversas atividades
institucionais, como a prefeitura de Natal, a
Assembleia Legislativa do Rio Grande do No seu entorno, nota-se a predominância de
edificações de uso comercial, de um
pavimento e com fachadas de grande Rede Lusófona de Morfologia Urbana ISSN 2182-7214 a de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Intervenções temporárias no espaço público da cidade de Natal - RN 10 / 13 O Parque de Capim Macio foi o segundo
espaço mais utilizado pelo movimento “Eco
Praça”, tendo um total de seis ocupações
realizadas entre os anos de 2014 à 2016. Todas as ocupações tiveram uma temática de
apropriação: primavera, permanência e
sustentabilidade criativa. Acredita-se que
essa popularidade na escolha do Parque como
palco ao movimento se deu, principalmente,
devido a sua localização privilegiada e a
existência de outros grupos ativos que já
realizavam ações na praça. permeabilidade em relação ao espaço
público. A praça não possui policiamento e
apresenta sinais de vandalismo, assim como
equipamentos depredados, mas, apesar disso,
os moradores entrevistados afirmam que a
área é tranquila e bastante frequentada em
todos os horários. Contudo, durante a
ocupação pelo Movimento “Eco Praça”, foi
observada a pouca presença de participantes
externos – de outros lugares da cidade, em
comparação a uma participação destacada
dos moradores do bairro. Na Região Sul, a Praça dos Eucaliptos,
localizada no bairro de Candelária, foi o
espaço mais utilizado pelo movimento para
suas intervenções, tendo sido ocupada sete
vezes em três anos. Ao longo das análises e
conversas com participantes e com a própria
organização, notou-se que o fato se deu
principalmente pela localização e a
proximidade de moradia do organizador, mas
também pelas características físicas e
ambientais da praça. Alguns resultados da análise morfológica A Praça dos Eucaliptos
(figura 4) se destaca pela sua centralidade,
pela proximidade com vias estruturantes e
instituições de destaque (Avenidas Salgado
Filho e Prudente de Morais e Universidade
Federal), pela grande área sombreada
proporcionada pelos eucaliptos durante quase
todo o dia, além do fácil acesso no interior do
bairro e entre esse e a cidade. Figura 4. “Eco Praça” na Praça dos Eucaliptos,
Candelária, Natal (fonte: Carvalho, 2017). A escolha dessa praça para diversos eventos
do movimento reafirma a importância
geográfica, física e simbólica adotada na
escolha do espaço a ser ocupado, o que
demonstra certa exclusão de áreas mais
periféricas e de difícil acesso. Apesar disso, é
de suma importância apresentar a ocupação
dessas praças como momentos de
reapropriação, os quais, mesmo temporários,
fomentaram discussões, encontros e outras
ações, desencadeadas pelo movimento inicial
da “Eco Praça”. Figura 4. “Eco Praça” na Praça dos Eucaliptos,
Candelária, Natal (fonte: Carvalho, 2017). Considerações finais Ainda na Região Sul, o Parque de Capim
Macio, a Praça de Neópolis e a Praça Anjo
Azul, estão situados em bairros de classe
média e de localização geográfica favorável
no contexto da cidade. Os bairros de Capim
Macio, Neópolis e Ponta Negra, destacam-se
pela proximidade com avenidas principais da
cidade – Avenida Roberto Freire, Salgado
Filho e Ayrton Senna – e se constituem como
importantes áreas residenciais, de serviço e
comércio variados. Com as análises físicas, o contato com
moradores dos entornos das praças e
entrevistas realizadas com a organização,
concluiu-se que em algumas situações, como
o Parque de Capim Macio e a Praça Edgar
Borges, a escolha do local pelo movimento
foi motivada a pedidos de outros grupos
atuantes nesses espaços. No Parque, o Grupo
Amigos de Capim Macio, que já atuava com
ações recorrentes no bairro, convidou a
organização do “Eco Praça” a se mobilizarem Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-72 Intervenções temporárias no espaço público da cidade de Natal - RN 11 / 13 11 / 13 para as suas realizações. Pode-se afirmar que
cada praça e seu entorno reagiu de maneira
diferente às ações da “Eco Praça”. juntos; enquanto na Praça Edgar Borges, a
ocupação foi realizada a pedidos da própria
comunidade de Mãe Luiza por meio do seu
Centro Sócio Pastoral. A partir disso,
entende-se como necessária a importância de
uma articulação constante entre os diversos
movimentos sociais atuantes na cidade, seja
por meio de parcerias, apoio ou
reconhecimento. Conclui-se ainda a constante necessidade de
apropriação do espaço público, de forma
efêmera ou não, de modo a reestabelecer as
condições necessárias à democratização da
cidade. Isso promoverá novos padrões de
urbanidade e vitalidade e reconhecerá as
conformidades existentes nesses espaços. A Praça Central de Neópolis e a Praça Omar
O’Graddy (Praça Anjo Azul) em Ponta
Negra, diferentes do Parque de Capim Macio,
não se localizam em áreas com fluxo intenso
de carros e pessoas, mesmo estando em áreas
de centralidade nos seus bairros. As praças
são bastante permeáveis visualmente e de
fácil reconhecimento para quem não conhece
os bairros; em Neópolis, seu maior uso
ocorre pela manhã e final da tarde,
principalmente por moradores do entorno; a
praça Anjo Azul possui um uso menos
frequente e se encontra mais depredada. Considerações finais Portanto, entende-se que apesar do
Movimento “Eco Praça” não ter obtido
grandes transformações físicas nos espaços
ao longo das suas ações, a sua significância
se rebate no legado que é transmitido através
da reinvenção de novos lugares na cidade. Assim como na criação de novos potenciais
para o estabelecimento de novas relações de
ação pessoa-ambiente e da promoção de uma
memória coletiva movida por essas novas
formas de resistir. A Praça Central de Neópolis reúne
significativa quantidade de equipamentos de
esporte e lazer (quadras, academia, bancos),
em sua maioria com problemas de
manutenção. Tal situação, associada à
iluminação precária, contribui para a sua
subutilização, principalmente à noite. No
caso da praça Anjo Azul, verifica-se a
inexistência de equipamentos e a total
ausência de manutenção, visto que o espaço
se encontrava coberto de vegetação e lixo, o
que contribui também para o seu pouco uso. Notas João Medeiros Filho, Paulistana e Acaraú, no
bairro Potengi, na Região Norte de Natal. Possui
uma área de 29.222 m² distribuída em pista de
cooper, quadras, parques, pista de skate e áreas
verdes. Fonte: Carvalho, 2017. experimenta, mesmo que involuntariamente
(Carvalho, 2017, p. 28). 4 O Anuário Natal 2017-2018 publicado pela
Secretaria de Meio Ambiente e Urbanismo de
Natal (SEMURB) apresenta informações gerais e
específicas do Município referente aos aspectos
sociais, demográficos, territoriais, econômicos, de
infraestrutura, de serviços públicos e culturais. Disponível em: < 6 A Avenida Doutor João Medeiros Filho é a
maior e mais importante via da Região Norte de
Natal, tendo seu início no bairro da Redinha e fim
no bairro de Igapó. https://www.natal.rn.gov.br/bvn/publicacoes/anua
rio_2016.pdf >. Acesso em: jun. 2018. Jacobs, J. (2014) Morte e vida de grandes
cidades. São Paulo: Martins Fontes. 3ª ed. Jacobs, J. (2014) Morte e vida de grandes
cidades. São Paulo: Martins Fontes. 3ª ed. Notas 1 De acordo com o Tactical Urbanism Guide, o
urbanismo tático se refere a uma abordagem
urbana, organizacional e/ou liderada pelo cidadão
para construção do sentimento de vizinhança
usando intervenções de curto prazo, de baixo
custo e escaláveis. Essas ações podem vir através
de um parklet, uma pequena praça, pinturas no
chão, grafitagem; e são catalisadores temporárias
que buscam interferir no espaço urbano para
demonstrar, através de soluções simples, como ele
poderia ser utilizado de uma forma melhor. Disponível em: É importante destacar que a pouca
iluminação no turno da noite, a degradação
dos equipamentos das praças, assim como
sinais de vandalismo, foram os indícios mais
apontados pelos entrevistados como fatos
agravantes da subutilização desses espaços. Nota-se o descaso do município enquanto
gestor e mantenedor do espaço público, fato
que tem contribuído para a estigmatização,
estranhamento e medo em relação ao uso da
cidade. <http://tacticalurbanismguide.com/about/>. Acesso em: 15 Jun. 2018. 2 Placemaking é um processo de planejamento,
criação e gestão de espaços públicos totalmente
voltado para as pessoas, visando transformar
‘espaços’ e pontos de encontro em uma
comunidade – ruas, calçadas, parques, edifícios e
outros espaços públicos – em ‘lugares’, que eles
estimulem maiores interações entre as pessoas e
promovam comunidades mais saudáveis e felizes. Disponível em: http://www.placemaking.org.br/home/o-que-e-
placemaking/. Acesso em: 15 Jun. 2018. Por fim, conclui-se como a forma urbana das
praças, assim como a relação com seus
respectivos entornos, admitindo sua
visibilidade e localização dentro da cidade,
influenciaram a forma como as intervenções
ocorreram – bem-sucedidas ou não. Admite-
se que a diferença principal entre as ações –
desde a quantidade de pessoas envolvidas, o
número de atividades, a duração das ações –
está intimamente ligada ao espaço escolhido 3 Segundo Fabiana Dultra Britto e Paola
Berenstein Jacques (2008), a corpografia seria a
memória urbana no corpo, onde esse surge como
um conjunto de condições interativas que
expressa assim a sua corporalidade na forma da
corpografia urbana. Essa corpografia é uma
cartografia corporal, onde a experiência urbana se
inscreve no próprio corpo daquele que a Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 12 / 13 12 / 13 5 A Área de Lazer do Panatis é um complexo de
cultura e lazer localizado entre as avenidas Dr. Referências Augé, M. (1994) Não-lugares. Introdução a uma
antropologia da supermodernidade. 5 ed. São
Paulo: Papirus. 111p. Lynch, K. (1990) A imagem da cidade. São
Paulo: Martins Fontes. 280 p. Olivi, A. (2012) La política de los lugares:
prácticas
de
resistência
en
la
ciudad
contemporânea. In: Jornada Sobre capital y
território
III,
Sevilla. Disponível
em:
http://ayp.unia.es/dmdocuments/scyt3_com09.pdf
. Acesso em: 15 jun. 2017. Carlos, A. F. A. (2007) O lugar no/do mundo. São
Paulo: FFLCH. 85p. Carvalho, M. C. R. (2017) Práticas de resistência
através de intervenções temporárias na cidade de
Natal: o caso da Eco Praça. Trabalho de
Conclusão de Curso (Arquitetura e Urbanismo) –
Departamento de Arquitetura e Urbanismo,
UFRN, Natal – RN. Panerai, P. (2006). Análise Urbana. Brasília:
Editora Universidade de Brasília. 198 pg. Castello, L. (2006) O lugar geneticamente
modificado. Arqtexto (UFRGS), v. 9, p. 76-91,
2006. Queiroga, E. (2012) Dimensões públicas do
espaço
contemporâneo:
resistências
e
transformações
de
territórios,
paisagens
e
lugares urbanos brasileiros. 284 p. Tese (Livre
docência em Arquitetura e Urbanismo) –
Faculdade
de
Arquitetura
e
Urbanismo,
Universidade de São Paulo, São Paulo, 2012. Del Rio, V. (2003) Construindo o nosso lugar:
Intersecções entre o mundo interior e o ambiente. Cadernos do Proarq. 7(7), 03-19. Disponível em:
http://cadernos.proarq.fau.ufrj.br/public/docs/cade
rnosproarq07.pdf. Acesso em 07 de julho de
2019. Robba, F. e Macedo, S.S. (2002) Praças
brasileiras. São Paulo: Edusp/ Imprensa Oficial
do Estado [Coleção Quapá]. Del Rio, V. (1990) Introdução ao desenho urbano
no processo de planejamento. São Paulo: Pini. Rodrigues, F. M. (2005) Forma, imagem e
significado em estruturas urbanas centrais. Centro da cidade de Niterói. Projeto de
Reestruturação
Urbana. Niterói:
EdUFF
/
ProEditores. Fontes, A. S. (2013) Intervenções temporárias,
marcas permanentes. Apropriações, arte e festa
na cidade contemporânea. 1. ed. Rio de Janeiro:
Casa da Palavra. v. 1. 398 pg. SEMURB. Prefeitura Municipal. Secretaria de
Meio Ambiente e Urbanismo. Anuário de Natal
2017. Natal, RN, 2018. Disponível em: <
https://www.natal.rn.gov.br/semurb/paginas/ctd-
102.html>. Acesso em: 15 jun. 2017. Gehl, J. (2015) Cidade Para as Pessoas. São
Paulo: Editora Perspectiva. 3 ed. Harvey, D. (et al.). (2012) Occupy: movimentos
de protestos que tomaram as ruas. São Paulo:
Editora Boitempo. 64 p. Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-72 13 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Temporary interventions in the public space of the city of Natal - RN: The case of the Eco Praça
movement Temporary interventions in the public space of the city of Natal - RN: The case of the Eco Praça
movement Abstract. The current conformation of cities and the marked distancing of people from public space have
provided the appearance of social movements of different natures that claim new forms of use and
appropriation of space. In this context, the Eco Plaza raça movement appears in Natal-RN as a
temporary intervention project that is based on social mobilization, stimulating the use of underutilized
squares, promoting the transformation in its use and appropriation by the city's residents. This article,
which results from an exploratory research, analyzes these processes and the significance of this
movement as an action of resistance at the local level with an emphasis on the morphology of the squares
and the perception of the agents involved directly and indirectly. Keywords: appropriation of public space, alternative territories, resistance, place, Eco Praça. Editor responsável pela submissão: Vinicius M. Netto Licenciado sob uma licença Creative Commons. Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051
Rede Lusófona de Morfologia Urbana ISSN 2182-72 |
https://openalex.org/W3138686972 | https://docusalut.com/bitstream/20.500.13003/18509/1/sensors-2021-21-02237.pdf | English | null | Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications | Sensors | 2,021 | cc-by | 9,882 |
Citation: Salinas-Bueno, I.;
Roig-Maimó, M.F.;
Martínez-Bueso, P.;
San-Sebastián-Fernández, K.;
Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck
Movements for Cervical
Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. https://
doi.org/10.3390/s21062237 Keywords: camera-based; inertial sensors; neck; cervical rehabilitation; serious game; head-tracker;
therapeutic exercise Received: 30 January 2021
Accepted: 19 March 2021
Published: 23 March 2021 Camera-Based Monitoring of Neck Movements for Cervical
Rehabilitation Mobile Applications https://
doi.org/10.3390/s21062237
Academic Editor: Bert Arnrich
Received: 30 January 2021
Accepted: 19 March 2021
Published: 23 March 2021
Citation: Salinas-Bueno, I.;
Roig-Maimó, M.F.;
Martínez-Bueso, P.;
San-Sebastián-Fernández, K.;
Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck
Movements for Cervical
Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. https://
doi.org/10.3390/s21062237
Academic Editor: Bert Arnrich
Received: 30 January 2021
Accepted: 19 March 2021
Published: 23 March 2021 sensors sensors Camera-Based Monitoring of Neck Movements for Cervical
Rehabilitation Mobile Applications 1, Maria Francesca Roig-Maimó 2,*, Pau Martínez-Bueso 1, Katia San-Sebastián-Fernández 3,
amon Mas-Sansó 2 Iosune Salinas-Bueno 1, Maria Francesca Roig-Maimó 2,*, Pau Martínez-Bueso 1, Katia San-Sebastián-Fernández 3,
Javier Varona 2 and Ramon Mas-Sansó 2 1
Department of Nursing and Physiotherapy, University of the Balearic Islands, Health Research Institute of the
Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.) 1
Department of Nursing and Physiotherapy, University of the Balearic Islands, Health Research Institute of the
Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.)
2
Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma, Spain;
xavi.varona@uib.es (J.V.); ramon.mas@uib.es (R.M.-S.) Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.)
2
Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma, Spain;
xavi.varona@uib.es (J.V.); ramon.mas@uib.es (R.M.-S.) 3
Department of Nursing and Physiotherapy, University of the Balearic Islands, 07122 Palma, Spain;
katia.sansebastian@uib.es 3
Department of Nursing and Physiotherapy, University of the Balearic Islands, 07122 Palma, Spain;
katia sansebastian@uib es *
Correspondence: xisca.roig@uib.es Abstract: Vision-based interfaces are used for monitoring human motion. In particular, camera-based
head-trackers interpret the movement of the user’s head for interacting with devices. Neck pain is
one of the most important musculoskeletal conditions in prevalence and years lived with disability. A common treatment is therapeutic exercise, which requires high motivation and adherence to
treatment. In this work, we conduct an exploratory experiment to validate the use of a non-invasive
camera-based head-tracker monitoring neck movements. We do it by means of an exergame for
performing the rehabilitation exercises using a mobile device. The experiments performed in order
to explore its feasibility were: (1) validate neck’s range of motion (ROM) that the camera-based
head-tracker was able to detect; (2) ensure safety application in terms of neck ROM solicitation
by the mobile application. Results not only confirmed safety, in terms of ROM requirements for
different preset patient profiles, according with the safety parameters previously established, but
also determined the effectiveness of the camera-based head-tracker to monitor the neck movements
for rehabilitation purposes.
Citation: Salinas-Bueno, I.;
Roig-Maimó, M.F.;
Martínez-Bueso, P.;
San-Sebastián-Fernández, K.;
Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck
Movements for Cervical
Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. 1. Introduction Camera-based interfaces provide a hands-free approach to interact with devices. Therefore, they have a straight application in assistive tools for motor-impaired users [1]
but also for rehabilitation purposes [2]. Specifically, head-trackers vision-based interfaces,
a camera-based approach that tracks the motion of the head, could be used for neck
rehabilitation purposes as they demand the movement of the neck joints to interact with
the device. Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Neck pain is one of the most important musculoskeletal conditions in prevalence and
years lived with disability, as it becomes chronic in 30–50% of cases [3,4]. The common
treatment of neck pain includes conservative and pharmacological interventions. Con-
servative treatments often include therapeutic exercise, with the aim of improve mobility,
pain, function and quality of life [5–7]. Therapeutic exercise, usually supervised by a phys-
iotherapist, includes mobility, strengthening, endurance and motor control exercises [5,7,8]. The long-term beneficial effect is achieved by performing the therapeutic exercise constantly
and over time, which requires high motivation and adherence to treatment, especially
when it is done at home. The adherence to the treatment will therefore be essential for
the maintenance of the effects [5]. One potential way to increase adherence is by means
of an exergame, that is, a serious game that aims at physical exercise (in our case, neck Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). https://www.mdpi.com/journal/sensors Sensors 2021, 21, 2237. https://doi.org/10.3390/s21062237 Sensors 2021, 21, 2237 2 of 15 therapeutic exercise) while entertaining the user. The exergame allows therapeutic exercise
performance with assets of motivation, supervision and feedback, which are key factors of
adherence [9,10]. With that aim, we started the design and development of a specific mobile application
that monitors and analyses the fulfilment of neck therapeutic exercises at home (or else-
where). The application includes an exergame individually adapted to the user capabilities
at any time of the rehabilitation process. By means of a camera-based head-tracker, user
head motion is detected, and used to interact with the exergame application in order to
monitor that users perform correctly the neck movements. 1. Introduction The use of the camera has the
advantage that it is not invasive, and the user can move comfortably without external
limitations. In addition, the fact that it is a mobile application allows doing the therapeutic
exercise, with supervision and feedback, available everywhere, anytime, and to anyone. This paper presents the validation experiments performed in order to (1) explore the
feasibility of using the head-tracker interface for neck rehabilitation purposes, in the sense
of the range of motion (ROM) that the head-tracker was able to detect and (2) determine
the safety of the application, as an exploratory safety experiment, in terms of neck ROM
solicitation by the mobile application. 1.1. State-of-the-Art It has been proved in the literature that introducing gamification to therapeutic ex-
ercise in rehabilitation increases its effectiveness and adherence [11–14]. In this sense,
serious exergames have been explored for different rehabilitation purposes, both using
commercial games and devices in a rehabilitation context [15] or designing specific serious
exergames for health and rehabilitation purposes, under more specific and clinical criteria
design [11–14]. Serious exergames have proved to be effective in different neurological and
musculoskeletal diseases [12,16,17]. In recent years, several virtual reality (VR) (immersive
and non-immersive) serious games for rehabilitation have been developed [16–19]. If they
were specifically aimed to a body part, they needed to attach a wearable sensor to the part
of the body, as happened in the work of De Oliveira et al. [17], Rechy-Ramirez et al. [20]
or interact with a full body camera detection [21]. With the aim of using serious gam-
ing with smartphones or mobile devices, with integrated sensors on the mobile phone,
Baranyi et al. [16,22] are developing a serious game system for post-stroke rehabilitation. Regarding specifically neck region, Mihajlovic et al. [23] developed a virtual reality serious
game, but in order to create the immersion on VR a headset needed to be used by the patient. As for neck movements detection with mobile devices, there have been some authors that
have developed neck exercise systems with sensors integrated in mobile devices, i.e., with
camera-based head tracking. Lawanont et al. [24,25] developed a neck movement image
detection integrated in the smartphone sensors. It was able to calculate neck flexion, so it
fulfilled the purpose of monitoring head posture while using smartphones. Yet, it did not
detect or monitor other directions of movement. Thus, the issue of detecting all directions
on neck movements with no sensors on the user, and to use them as an interaction for a
serious exergame for neck rehabilitation with a mobile device remains to explore. 1.2. Camera-Based Head Tracking One common sensor on smartphones and tablets is the front-facing camera, that can
be used to perform the user’s head tracking. Such camera-based head-trackers provide
a way to interact with these devices through the movements of the head. Using a vision-
based head-tracker has several advantages. Mainly, it does not require any calibration or
additional hardware, apart from the components already built in mobile devices. It also
has the additional advantage that it is not invasive, i.e., the user can comfortably move
without the burden imposed by wires or markers. The only requirement is that the main
structures of the face (eyes and nose) have to be fully visible by the front-facing camera. We have previously developed a camera-based head-tracker for mobile devices [26]
that automatically detects and tracks the position of the user’s nose. To track the nose, Sensors 2021, 21, 2237 3 of 15 the system extracts facial features of its surrounding region, and returns the average of all
these features as the nose point. As this region is never occluded by facial hair or glasses,
it can be continuously tracked despite the orientation of the user’s head when he or she
is looking at the screen. We direct the reader to Roig-Maimó et al. [26] for a technical
description of the head-tracker interface. Previous work validated the head-tracker’s viability as a pointing device in target-
selection tasks with able-bodied [27] and motor-impaired users [28]. Once the head-tracker
interface was validated from the point of view of Human-Computer Interaction, in this
work we analyse the feasibility of using it to develop applications for cervical rehabilitation
purposes, as it allows the interaction with devices through the movement of the head. 2. Exploratory Experiment: Neck Range of Motion Tracked by the
Camera-Based Head-Tracker An exploratory experiment was conducted in order to explore the neck ROM that is
effectively tracked by the camera-based head-tracker. With this experiment, we wanted to
determine at what extent the head-tracker was able to track the mobility range of the neck,
in order to determine if it could be used for ROM rehabilitation purposes. p
p
The cervical area has a normal maximum mobility of 45◦of flexion, 45◦of extension,
45◦of lateral flexion (each side) and 70◦of rotation (each side) [29]. See Figure 1 in
order to observe the movements of the neck joint. Functional mobility, understood as the
range of motion used in daily life activities, is 20% to 40% of maximum available cervical
ROM [30,31]. Any kind of change in those ROM would alter the functional mobility of the
neck and spine, which could alter also the functionality of individuals, causing disability
movement [32,33]. Figure 1. Movements of the neck. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages
ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). There were no requirements
or exclusion criteria on prior experience to participate in the experiment. The experiment was conducted on an Apple iPad Air with a front-facing camera
placed in the center on the upper side of the device, in portrait orientation. The software
executed the head-tracker interface and showed on the screen the image captured by the
front-facing camera with the nose point returned by the head-tracker marked with a blue
circle (see Figure 2). An important added value of using the exergame is to enable the user to perform
the exercises alone by means of controlling the correct performance. Therefore, it is very
important to consider the system’s feedback to inform the user and to help him or her to
control the performance. In this sense, it is necessary to explore the neck range of motion
(ROM) that could be effectively tracked by the camera-based head-tracker, as a feasibility
indicator for neck rehabilitation purposes. Figure 1. Movements of the neck. Figure 1. Movements of the neck. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages
ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). 2. Exploratory Experiment: Neck Range of Motion Tracked by the
Camera-Based Head-Tracker There were no requirements
or exclusion criteria on prior experience to participate in the experiment. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages
ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). There were no requirements
or exclusion criteria on prior experience to participate in the experiment. p
p
p
p
p
The experiment was conducted on an Apple iPad Air with a front-facing camera
placed in the center on the upper side of the device, in portrait orientation. The software
executed the head-tracker interface and showed on the screen the image captured by the
front-facing camera with the nose point returned by the head-tracker marked with a blue
circle (see Figure 2). The experiment was conducted on an Apple iPad Air with a front-facing camera
placed in the center on the upper side of the device, in portrait orientation. The software
executed the head-tracker interface and showed on the screen the image captured by the
front-facing camera with the nose point returned by the head-tracker marked with a blue
circle (see Figure 2). An important added value of using the exergame is to enable the user to perform
the exercises alone by means of controlling the correct performance. Therefore, it is very
important to consider the system’s feedback to inform the user and to help him or her to
control the performance. In this sense, it is necessary to explore the neck range of motion
(ROM) that could be effectively tracked by the camera-based head-tracker, as a feasibility
indicator for neck rehabilitation purposes. 4 of 15 Sensors 2021, 21, 2237 Figure 2. Screenshot of the experiment software with annotations on an Apple iPad Air (device in
portrait orientation). Figure 2. Screenshot of the experiment software with annotations on an Apple iPad Air (device in
portrait orientation). Each participant performed the session in an experiment room, seated in upright
position, resting their arms on a table. The iPad with the camera-based head-tracker
running, was placed in front of their face at approximately 37 cm, a distance equivalent
to naturally holding the device by the subject, with the top line of the iPad screen at eye
level [34]. 2. Exploratory Experiment: Neck Range of Motion Tracked by the
Camera-Based Head-Tracker They were asked to move their head slowly as far as possible in the direction being
studied (flexion, extension, right lateral flexion, left lateral flexion, right rotation and left
rotation). See Figure 3. At the moment that the head-tracker lost the position of the
nose (see Figure 3c), an acoustic alert sounded and the participant was asked to stop the
movement. Then, ROM was measured with a goniometer (see Figure 4c), that is a reliable
tool for ROM measurement used in standardized clinical examinations [35–37]. It consisted
of a stationary arm, a movable arm and a fulcrum or axis, as can be seen in Figure 5. (a)
(b)
(c)
Figure 3. Simulated stages of the experiment procedure for the left rotation movement on the
apparatus: (a) participant placed in the initial position with the nose point returned by the head-
tracker marked with a blue circle, (b) the participant starts a rotation movement slowly (the nose
point returned by the head-tracker is marked with a blue circle), (c) moment when the head-tracker
loses the position of the nose (an acoustic alert is triggered) and the participant stops its movement. (c) (a) (b) (a) (b) (c) Figure 3. Simulated stages of the experiment procedure for the left rotation movement on the
apparatus: (a) participant placed in the initial position with the nose point returned by the head-
tracker marked with a blue circle, (b) the participant starts a rotation movement slowly (the nose
point returned by the head-tracker is marked with a blue circle), (c) moment when the head-tracker
loses the position of the nose (an acoustic alert is triggered) and the participant stops its movement. Flexion and extension were measured with the axis over the external auditory mea-
tus, with the stationary arm parallel to ground and the movement arm in line with the
base of nares. Lateral flexion was measured with the axis over spinous process of C7
vertebra, with the stationary arm in line with spinous processes of thoracic vertebrae,
so that arm was perpendicular to ground, and the movement arm in line with occipital
protuberance. Rotation was measured with the axis located over central aspect of head,
with the stationary arm parallel to imaginary line between the two acromial processes,
and the movement arm in line with the tip of the nose. All measurements were conducted
by an experienced physiotherapist. 2. Exploratory Experiment: Neck Range of Motion Tracked by the
Camera-Based Head-Tracker As for rotation,
the head-tracker was able to track the nose position up to about 40◦, moment where the
nose was no longer visible from the front by the front-facing camera. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface
compared to normal maximum mobility. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface
compared to normal maximum mobility. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface
compared to normal maximum mobility. These results proved that the camera-based head-tracker could track the nose position
within functional ROM limits, so it could be useful for the rehabilitation of functional
mobility, as well as other parameters of rehabilitation (speed of movement, motor control,
oculocervical dissociation) within these ranges. This conclusion led us to the design of
a mobile application with an exergame that would aim to rehabilitation of functional
movement and motor control. 3. Validation of the Mobile Application for Monitoring the Neck Movements Once it was proved that the camera-based head-tracker was feasible for rehabilitation
purposes, in the matter of monitoring functional mobility, the application started to be
designed. One of the first steps was to determine its safety, in terms that the software must
not require more ROM, rapid or complex movements than patients were able to perform at
that moment, as they could cause harm and be counterproductive for patients’ recovery. Therefore, a safety validation was needed. 2. Exploratory Experiment: Neck Range of Motion Tracked by the
Camera-Based Head-Tracker Sensors 2021, 21, 2237 5 of 15 (c) (a)
(b)
(c)
Figure 4. Stages of the experiment procedure: (a) participant placed in the initial position, (b) partici-
pant once the acoustic alert sounded and the participant stopped the movement, (c) measurement of
the neck ROM of the participant using the goniometer. (b) (a) (b) (a) (c) Figure 4. Stages of the experiment procedure: (a) participant placed in the initial position, (b) partici-
pant once the acoustic alert sounded and the participant stopped the movement, (c) measurement of
the neck ROM of the participant using the goniometer. Figure 5. Dual-arm universal goniometer. Figure 5. Dual-arm universal goniometer. Each movement was repeated three times, and equally measured (see Figure 4). Testing lasted about 15 min per participant. The total number of measures was 7 participants × 6 directions × 3 repetitions = 126. In Table 1, mean and standard deviation values, as well as proportion of normal
maximum ROM tracked, are given for each movement direction of the cervical area (flexion,
extension, right lateral flexion, left lateral flexion, right rotation, left rotation). s and standard deviation of cervical range of motion measurements, and their relationship with normal Table 1. Mean values and standard deviation of cervical range of motion measurements, and their relationship with normal
mobility range. Table 1. Mean values and standard deviation of cervical range of motion measurements, and their relationship with normal
mobility range. Movement
ROM Detected
Normal Maximum ROM
% of Maximum ROM Tracked
Flexion
29.05◦± 6.25◦
45◦
64.55%
Extension
22.86◦± 6.63◦
45◦
50.79%
Right lateral flexion
27.39◦± 4.64◦
45◦
60.85%
Left lateral flexion
28.10◦± 3.70◦
45◦
62.43%
Right rotation
39.05◦± 6.25◦
70◦
55.78%
Left rotation
38.81◦± 6.70◦
70◦
55.44% As it is shown in Table 1 and Figure 6, the camera-based head-tracker was able to
track the nose position from 50% to 64.5% of the normal maximum cervical mobility ranges. The better detected movements were flexion and lateral flexion, that is, the movements
where nose is more visible for the front-facing camera during the user’s movement. Ex-
tension implies that nose would be seen in a different position as movement advances, so Sensors 2021, 21, 2237 6 of 15 the head-tracker would lose the nose position at about 23◦of extension. 3.1. Materials and Methods For this first safety experiment we focused on the ROM that the software required,
because demanding more movement that a patient was able to perform, or a movement
that reproduced pain, was considered a potential source of unsafe situations. We would
consider the application as safe, in this sense, if the movements asked for the application
and therefore performed by the subject in each direction were within the maximum ROM
that a patient was able to achieve with no pain. As it was expected to be safe for different
patients with different capabilities, or the same patient at different moments of his or her
recovery, it was considered necessary to study safety with different capability profiles. In order to do that, different patient preset profiles were designed. They were designed
by experienced physiotherapists, based on general clinical evolution of ROM and neck
pain data in actual patients [38,39]: •
Profile 1: corresponded to a low cervical mobility person with or without pain associ-
ated with movement. •
Profile 2: corresponded to a lower-medium cervical mobility person, with less or no
pain associated with movement. •
Profile 3: corresponded to an upper-medium mobility person and no pain. Sensors 2021, 21, 2237 7 of 15 •
Profile 4: was supposed to represent a patient with an advanced recovery situation or
a healthy subject, with normal mobility and no pain. •
Profile 4: was supposed to represent a patient with an advanced recovery situation or
a healthy subject, with normal mobility and no pain. •
Profile 4: was supposed to represent a patient with an advanced recovery situation or
a healthy subject, with normal mobility and no pain. •
Profile 4: was supposed to represent a patient with an advanced recovery situation or
a healthy subject, with normal mobility and no pain. Range of motion preset for each profile can be seen in Table 2. Range of motion preset for each profile can be seen in Table 2. Table 2. ROM of the preset profiles. Table 2. ROM of the preset profiles. Profile
Flexion
Extension
Lateral Flexion
Rotation
Profile 1
20◦
15◦
5◦
25◦
Profile 2
30◦
20◦
35◦
40◦
Profile 3
40◦
40◦
45◦
70◦
Profile 4
45◦
45◦
45◦
70◦ We designed an exergame simulating a dart game with targets to be selected using the
movement of the head (see Section 3.1.2 for further description of the game). 3.1. Materials and Methods The configura-
tion of target size, target location, order of targets, time of appearance and disappearance of
the target, gain of the head-tracker and dwell-time criterion for selection were set differently
for each preset profile: •
Profile 1: required horizontal, vertical or diagonal simple movements with low ROM,
with no speed or time pressure. So, configuration for this profile consisted in offering
big, easy targets available all the time, that should be selected in a predetermined
order, with a high gain factor and no dwell-time. As an example, to require a simple
right rotation movement, three big targets available at the same time, that should be
selected left to right, were shown on the screen (see Figure 7a). •
Profile 2: the group of exercises included for this profile were those for profile 1 plus
exercises with smaller targets, complex movements, and higher speed. These exercises
configuration implied more and smaller targets, and a sequential appearance and
disappearance of targets, in the preset order of selection, as to introduce a speed factor. As examples of these exercises, Figure 7b shows the location of targets in a simple
flexion movement, starting with the upper target, and Figure 7c shows a combined
movement: a diagonal. As examples of these exercises, Figure 7b shows the location of targets in a simple
flexion movement, starting with the upper target, and Figure 7c shows a combined
movement: a diagonal. g
•
Profile 3: the group of exercises loaded for this profile were those with smaller targets,
complex movements, movements at a higher speed and motor control requirements. To do so, targets would appear in a random location, with preset time of appearance
and disappearance, and with dwell-time to require steadiness in target selection (see
an example exercise in Figure 7d). •
Profile 4: the group of exercises loaded for this profile were provided with small
targets, complex randomly required movements at a high speed, and motor control
requirements. It did not imply more ROM than the previous profiles, as it focused in
other parameters (speed, reaction time, motor control). The configuration was similar
to profile 3 exercises, but with smaller targets, less time available on screen, less gain
factor and more dwell-time on those with motor control requirement. For the application to be considered as safe, it was supposed to solicit movements
within the maximum ROM preset for each profile (see Table 2). 3.1.1. Participants A total of 24 asymptomatic participants (12 females) were recruited from staff and
postgraduate students from a university campus in Spain. To be included, participants had
to be aged 20 to 64. The average age was 34 years (SD = 13.06). They were excluded if they
had reported or complained of neck, shoulder, and/or head impairments or had pain in
the preceding month. 3.1. Materials and Methods In order to validate
that the application induced the user to correctly perform the neck movements for every
preset profile, it was required that the performed user neck movements were within 80th
percentile of the ROM preset for each movement in the different profiles. 8 of 15 Sensors 2021, 21, 2237 (a)
(b)
(c)
(d)
Figure 7. Examples of exercises for every preset profile: (a) dartboards set to induce a simple
horizontal movement (rotation) with big targets, (b) dartboards set to induce a simple vertical
descending movement (flexion) with small targets, (c) dartboards set in diagonal to induce a combined
movement with small targets, and (d) dartboards set randomly. (a)
(c) (d) (c) Figure 7. Examples of exercises for every preset profile: (a) dartboards set to induce a simple
horizontal movement (rotation) with big targets, (b) dartboards set to induce a simple vertical
descending movement (flexion) with small targets, (c) dartboards set in diagonal to induce a combined
movement with small targets, and (d) dartboards set randomly. 3.1.2. Apparatus The experiment was conducted on an Apple iPad Mini 4 due to ergonomic reasons
related to the device’s weight. All communication with the mobile device was disabled
during testing. The software simulated a dart game (see Figure 8 for details). The study involved a
simple pointing task where the targets to be selected simulated dartboards of different sizes. User input combined the mobile head-tracker for the pointing action and a dwell-time
criterion for selection. 9 of 15 Sensors 2021, 21, 2237 (a)
(b)
Figure 8. Screenshots of the dart game with two dwell-time criterion: (a) 0-ms dwell-time criterion: the target was selected
immediately when the center of the cursor entered inside the target, and (b) 200-ms dwell-time criterion. (a) (b) Figure 8. Screenshots of the dart game with two dwell-time criterion: (a) 0-ms dwell-time criterion: the target was selected
immediately when the center of the cursor entered inside the target, and (b) 200-ms dwell-time criterion. The application started with a login form, which was used to determine the patient
profile. According to the profile that was established, the application showed different tar-
get patterns covering the desired range of motion of the profile (following either horizontal,
vertical, diagonal or random paths). The user got a visual feedback of its motion through
the movement of a cursor displayed in the dart game. To measure the real-time neck mobility performed by subjects while using the applica-
tion, we used wireless ENLAZA inertial sensors (Werium™system [40]). Inertial sensors
included an accelerometer, a gyroscope and a magnetometer which sensed linear accelera-
tion, the turn rate and an accurate angular monitoring along three reference axis. Inertial
sensors are widely used to measure motor activities [41–43]. Specifically, Werium intertial
sensors were previously validated for cervical ROM as well as for other joints [44,45]. The sensors are small and lightweight, so they are barely invasive. Their use would allow
to record full ROM, as we previously stated that the application itself was not able monitor
full ROM. Two sensors were placed on the subject to conduct the real-time measurement,
following the location protocol given by the manufacturer. Sensor 1 was placed on the
forehead of the subject, fixed with an elastic band (see Figure 9a,c). Sensor 2 was placed on
T1-T2 thoracic vertebrae, fixed with double sided fixing tape (see Figure 9b,c). 3.1.3. Procedure The study was conducted according to the guidelines of the Declaration of Helsinki
and approved by the Research Ethics Committee of the University of the Balearic Islands
(Exp.174CER20). Each experiment was conducted by a collaborator of the research team,
with previous training on the procedure. The experiment consisted in performing several
games/matches with the exergame, corresponding to different levels of demand of ROM. Sensors 2021, 21, 2237 10 of 15 10 of 15 Informed consent was obtained from all subjects involved in the study. They were
instructed to play the exergame, following the application instructions, holding the device
still and moving the cursor by moving their head. Subjects were in an experiment room,
seated in a chair with their back supported on the backrest, naturally holding the iPad
in front of their head (see Figure 10), with their elbows resting on a height-adjustable
treatment table. This position (back on the backrest and elbows resting on the table) was
designed to maintain a natural position holding a mobile device while controlling possible
compensation movements. (a)
(b)
(c)
Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (a) (c) (a)
(b)
(c)
Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (a)
(b)
Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. (b) (b) (a) (c) Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (b) (a) (a)
(b)
Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. (a) (b) Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. After sensors were placed, subjects were asked to play the exergame, and to select
targets as quickly and accurately as possible. Every subject was asked to play a match
with the exergame set for each profile. They were allowed to rest as needed between
profiles. Movement in every direction was real-time recorded via the inertial sensors and
Werium software. Any incident observed or informed by the subjects was recorded by the
collaborator. Testing lasted about 30 min per participant. g
p
p
p
The total number of sessions was 24 participants × 4 profiles = 96. 3.1.3. Procedure During every
session, the ROM of the subjects reported by the sensors (flexion, extension, lateral flexion,
rotation) were recorded. 4. Results and Discussion In this section, results for each preset profile are given for all the movement directions
of the cervical area: flexion, extension, right lateral flexion, left lateral flexion, right rotation,
left rotation. Outliers were removed using the Interquartile Range (IQR) method. Results showed that recorded mobility was below the 80th percentile of the established
maximum at all movements and profiles. Even the maximum movement measured stayed
within limits in almost every movement and profile, except for extension. Extension Sensors 2021, 21, 2237 11 of 15 11 of 15 movements in profiles 1 and 2 (see Tables 3 and 4) showed that the maximum recorded
exceeded significantly the preset limits at least once. One possible explanation, from the
observation and data, suggested that the maximum of extension recorded may be due
to moments in which the head-tracker reference was lost, and the manoeuvre done by
the subject to recover the nose tracking was doing a movement out of range of the front-
face camera and back, that could be an extension movement. Nevertheless, extension
movement was within limits at 80th percentile for these profiles. For profiles 3 and 4 (see
Tables 5 and 6), the mobile application would not be able to exceed the limits of ROM
preset due to the head-tracker limits that were determined in the first experiment. Table 3. ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total
flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases
where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for
the profile are marked with an asterisk. Table 3. ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total
flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases
where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for
the profile are marked with an asterisk. Table 3. 4. Results and Discussion ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total
flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases
where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for
the profile are marked with an asterisk. Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
4.39◦
3.40◦
19.17◦
6.91◦
20◦
Extension
8.15◦
5.97◦
26.16◦*
13.15◦
15◦
Right lateral flexion
2.00◦
1.62◦
6.51◦*
3.32◦
5◦
Left lateral flexion
1.45◦
1.09◦
5.49◦*
2.30◦
5◦
Right rotation
7.03◦
5.43◦
23.41◦
11.60◦
25◦
Left rotation
5.71◦
4.21◦
21.51◦
9.34◦
25◦ Table 4. ROM results of Profile 2 (After outlier filtering, the analyzed data for the Profile 2 supposed a 98% of the total
flexion-extension raw data, a 97% of the total lateral flexion raw data, and a 98% of the total rotation raw data). The cases
where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for
the profile are marked with an asterisk. Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
9.18◦
6.84◦
30.98◦*
14.46◦
30◦
Extension
7.74◦
5.77◦
26.75◦*
12.70◦
20◦
Right lateral flexion
2.13◦
1.55◦
7.10◦
3.33◦
35◦
Left lateral flexion
1.78◦
1.39◦
6.29◦
2.85◦
35◦
Right rotation
6.50◦
4.92◦
21.51◦
10.83◦
40◦
Left rotation
5.48◦
4.24◦
20.00◦
8.79◦
40◦
Table 5. ROM results of Profile 3 (After outliers’ filtering, the analyzed data for the Profile 3 supposed a 98% of the total
flexion-extension raw data, a 93% of the total lateral flexion raw data, and a 99% of the total rotation raw data). 4. Results and Discussion Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
10.16◦
7.87◦
33.37◦
16.96◦
40◦
Extension
9.01◦
7.02◦
30.22◦
14.78◦
40◦
Right lateral flexion
2.11◦
1.81◦
7.30◦
3.65◦
45◦
Left lateral flexion
2.31◦
1.74◦
8.00◦
3.61◦
45◦
Right rotation
9.00◦
6.48◦
29.51◦
14.67◦
70◦
Left rotation
6.10◦
4.96◦
21.67◦
10.00◦
70◦ Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
9.18◦
6.84◦
30.98◦*
14.46◦
30◦
Extension
7.74◦
5.77◦
26.75◦*
12.70◦
20◦
Right lateral flexion
2.13◦
1.55◦
7.10◦
3.33◦
35◦
Left lateral flexion
1.78◦
1.39◦
6.29◦
2.85◦
35◦
Right rotation
6.50◦
4.92◦
21.51◦
10.83◦
40◦
Left rotation
5.48◦
4.24◦
20.00◦
8.79◦
40◦ ts of Profile 3 (After outliers’ filtering, the analyzed data for the Profile 3 supposed a 98% of the total
w data, a 93% of the total lateral flexion raw data, and a 99% of the total rotation raw data). Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
10.16◦
7.87◦
33.37◦
16.96◦
40◦
Extension
9.01◦
7.02◦
30.22◦
14.78◦
40◦
Right lateral flexion
2.11◦
1.81◦
7.30◦
3.65◦
45◦
Left lateral flexion
2.31◦
1.74◦
8.00◦
3.61◦
45◦
Right rotation
9.00◦
6.48◦
29.51◦
14.67◦
70◦
Left rotation
6.10◦
4.96◦
21.67◦
10.00◦
70◦ Movement
Mean
Standard Deviation
Maximum
80th Percentile 12 of 15 Sensors 2021, 21, 2237 Table 6. ROM results of Profile 4 (After outliers’ filtering, the analyzed data for the Profile 4 supposed a 99% of the total
flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 98% of the total rotation raw data). Table 6. ROM results of Profile 4 (After outliers’ filtering, the analyzed data for the Profile 4 supposed a 99% of the total
flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 98% of the total rotation raw data). Movement
Mean
Standard Deviation
Maximum
80th Percentile
Preset ROM
Flexion
7.05◦
5.16◦
24.84◦
11.47◦
45◦
Extension
8.70◦
6.16◦
29.67◦
14.12◦
45◦
Right lateral flexion
1.68◦
1.27◦
6.15◦
2.71◦
45◦
Left lateral flexion
1.96◦
1.58◦
6.20◦
3.39◦
45◦
Right rotation
6.40◦
4.80◦
22.07◦
10.37◦
70◦
Left rotation
6.25◦
4.67◦
20.70◦
10.32◦
70◦ Results not only confirmed safety, in terms of ROM requirements for each profile,
according with the safety parameters previously established, but informed also about other
aspects. 4. Results and Discussion One of these findings was that the mobile application required similar maximum
ROM for the different profiles, with differences in flexion: profiles 1, 2 and 3 showed a
slightly increase in mobility demand by the mobile application in flexion. Profile 4 (see
Table 6), on the other hand, did not show this increasing tendency. Profile 4 was not preset
as to continue this increase tendency, but to focus on other rehabilitation parameters. Thus,
it was also expected not to detect an increase of ROM demand for this profile. In addition,
one unexpected finding was the virtual absence of lateral flexion for the interaction with the
mobile application, observed in every profile. Further work is required to clarify whether
it is due to the configuration of the targets on the screen (and so, a mobile application
performance finding), or whether it is a phenomenon linked to the interaction with mobile
devices in general. All these findings, in addition to the results of the intended evaluation, provided
valuable information for future lines of work. Data collected suggested that it would be the
combination of different parameters of the mobile application, and not only ROM, what
would determine the effectiveness of the exergame as a therapeutic exercise application. In order to work gradually and adapt to the objectives of the rehabilitation and the patient’s
situation (functional mobility recovery, motor control, strength, etc.), it would be needed
to combine parameters as required speed of movement, dwell-time for target selection,
number of targets, moment of appearance or disappearance of the targets, etc. If we want
to focus on more ROM demand for the medium and advanced profiles (namely profile
3 and 4), it would be necessary to study the feasibility of working with the gain parameter,
so the mobile application would demand more ROM for the same movement in screen. 5. Conclusions In this paper, we present a evaluation study of a camera-based head-tracker mobile
application for monitoring neck movements for cervical rehabilitation purposes. Due to
the use of the camera, this application has the advantage that it does not need any contact
sensor and the user can move freely, without any external limitation. The objective of this
paper is to present the technical feasibility and a first safety evaluation of the camera-based
head-tracker to monitor the neck movements. First, we explored at what extent the head-tracker was able to monitor the user’s
neck movements. On that question, the study found that camera-based head-tracker
is able to monitor from the 50% to the 64.5% of the full cervical range of motion. This
result proved that a camera-based head-tracker was a feasible tool for cervical rehabilitation
purposes, within a functional mobility range of motion. Secondly, an exploratory validation
experiment has determined the safety of the designed head-tracker mobile application. We checked that is possible to use the head-tracker for neck movement detection in an
exergame for cervical rehabilitation purposes and, that is safe in terms of the required neck
range of motion demanded by the exergame for each preset patient profile. At this point,
we can conclude that the camera-based exergame did not require more range of motion
than the preset profile user was capable to perform. Sensors 2021, 21, 2237 13 of 15 13 of 15 As the objective of this paper was to present the technical feasibility and a first
safety study, participants in the presented studies were healthy subjects. In order to
continue with the validation of the exergame mobile application using a camera-based
head tracker as a sensor, further work needs be conducted, including clinical research
studies, with actual patients. In addition, we point out that this research could serve as a base for future studies on
the use of camera-based head-trackers for other healthcare purposes, as we proved that
is able to monitor the user’s head movements by means of the front-facing camera of a
mobile device. Author Contributions: conceptualization, I.S.-B., K.S.-S.-F. and M.F.R.-M.; methodology, I.S.-B.,
K.S.-S.-F. and R.M.-S.; software, M.F.R.-M. and R.M.-S.; validation, K.S.-S.-F. and I.S.-B.; formal analy-
sis, I.S.-B., M.F.R.-M. and R.M.-S.; investigation, I.S.-B., K.S.-S.-F. and P.M.-B.; data curation, M.F.R.-M. and R.M.-S.; writing—original draft preparation, I.S.-B., M.F.R.-M. and R.M.-S.; writing—review and
editing, I.S.-B., M.F.R.-M., R.M.-S., P.M.-B. and J.V.; supervision, I.S.-B., M.F.R.-M., R.M.-S. 5. Conclusions and P.M.-B.;
project administration, I.S.-B. and J.V. All authors have read and agreed to the published version of
the manuscript. Author Contributions: conceptualization, I.S.-B., K.S.-S.-F. and M.F.R.-M.; methodology, I.S.-B.,
K.S.-S.-F. and R.M.-S.; software, M.F.R.-M. and R.M.-S.; validation, K.S.-S.-F. and I.S.-B.; formal analy-
sis, I.S.-B., M.F.R.-M. and R.M.-S.; investigation, I.S.-B., K.S.-S.-F. and P.M.-B.; data curation, M.F.R.-M. and R.M.-S.; writing—original draft preparation, I.S.-B., M.F.R.-M. and R.M.-S.; writing—review and
editing, I.S.-B., M.F.R.-M., R.M.-S., P.M.-B. and J.V.; supervision, I.S.-B., M.F.R.-M., R.M.-S. and P.M.-B.;
project administration, I.S.-B. and J.V. All authors have read and agreed to the published version of
the manuscript. Funding: This research was funded by the Spanish Government with project TIN2016-81143-R
(MINECO/AEI/ERDF, EU) and grant number PID2019-104829RA-I00/AEI/10.13039/501100011033. Institutional Review Board Statement: The study was conducted according to the guidelines of the
Declaration of Helsinki and approved by the Research Ethics Committee of the University of the
Balearic Islands (Exp.174CER20). Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Data Availability Statement: The data presented in this study are available on request from the
corresponding author. The data are not publicly available due to data privacy restrictions. Data Availability Statement: The data presented in this study are available on request from the
corresponding author. The data are not publicly available due to data privacy restrictions. Acknowledgments: The authors acknowledge the Ministerio de Economía, Industria y Competitivi-
dad (MINECO), the Agencia Estatal de Investigacion (AEI), and the European Regional Development
Funds (ERDF) for their support to the project TIN2016-81143-R (MINECO/AEI/ERDF, EU) and the
Spanish Government for its support by the Project EXPLainable Artificial INtelligence systems for
health and well-beING (EXPLAINING) (PID2019-104829RA-I00/AEI/10.13039/501100011033). We
also thank the University of the Balearic Islands, the Department of Nursing and Physiotherapy,
and the Department of Mathematics and Computer Science for their support. Conflicts of Interest:
The authors declare no conflict of interest. The funders had no role in the
design of the study; in the collection, analyses, or interpretation of data; in the writing of the
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https://openalex.org/W4294997145 | https://dergipark.org.tr/tr/download/article-file/985439 | English | null | The Effect of Carbonmonoxide Sources and Meteorologic Changes in Carbonmonoxide Intoxication: A Retrospective Study | DergiPark (Istanbul University) | 2,020 | cc-by-sa | 2,886 | ABSTRACT Objective: Carbon monoxide (CO) poisoning is frequently seen in
emergency departments (ED) especially in cold weather. We
investigated the relationship of some of the meteorological factors
with the sources of CO poisoning. Amaç: Karbonmonoksit (CO) zehirlenmelerine, özellikle soğuk
havalarda olmak üzere acil servis birimlerinde sıklıkla karşılaşılır. Çalışmamızda, bazı meteorolojik faktörlerin CO zehirlenmesinin
kaynakları ile ilişkisini araştırdık. Yöntem: Retrospektif gözlemsel çalışmamızda, son üç yılda acil
servise CO zehirlenmesi ile başvuran 1153 hastayı dahil edildi. Bölgenin atmosferik basıncı, rüzgarın yönü ve hızı, nem düzeyi ve
hava sıcaklığı değerleri ve CO zehirlenme tipi karşılaştırıldı. Methods: In this retrospective observational study, we included
1153 patients who were admitted to ED due to CO poisoning in a
three years period. Atmospheric pressure, wind direction and
speed, humidity level and air temperature of the region at
exposure time were compared with CO poisoning type. Bulgular: Hastaların yaş ortalaması 39,5±16,3; kadın cinsiyet %65,7
(n=761) idi. Karbonmonoksit kaynağının kaynağı en sık doğalgaz
ısıtıcıları (n=628; %54,4); daha sonra ocak (n=393; %34,1), şofben
(n=94; %8,4) ve yangındı (n=38; %3,3). En sık görülen rüzgar yönü
kuzey-kuzeydoğu yönü (poyraz) idi. Atmosferik basınç tüm
zehirlenme tiplerinde benzerdi. Yangınlarda nem düzeyleri
istatistiksel anlamlı düşüktü ve hava sıcaklığı anlamlı yüksekti. Rüzgar hızı yangın tipinde en hızlı ve şofben tipinde en yavaştı. Bulgular: Hastaların yaş ortalaması 39,5±16,3; kadın cinsiyet %65,7
(n=761) idi. Karbonmonoksit kaynağının kaynağı en sık doğalgaz
ısıtıcıları (n=628; %54,4); daha sonra ocak (n=393; %34,1), şofben
(n=94; %8,4) ve yangındı (n=38; %3,3). En sık görülen rüzgar yönü
kuzey-kuzeydoğu yönü (poyraz) idi. Atmosferik basınç tüm
zehirlenme tiplerinde benzerdi. Yangınlarda nem düzeyleri
istatistiksel anlamlı düşüktü ve hava sıcaklığı anlamlı yüksekti. Rüzgar hızı yangın tipinde en hızlı ve şofben tipinde en yavaştı. Sonuç: Karbonmonoksit zehirlenmeleri ciddi morbidite ve
moraliteye neden olabilen acil servis başvuru nedenlerindendir. Başlıca nedeni ev ısıtıcılarıdır. Risk altındaki insanlar CO
zehirlenmeleri hakkında ve önemli meteorolojik değişikliklerde
ısıtıcaların
riskleri
hakkında
bilgilendirilmelidir. Zehirlenme
bulguları görüldüğünde acil servise başvurulmalıdır. A
ht
K li
l
At
f
ik b
CO
hi l
i
kl k Results: Mean age of the patients was 39.5±16.3; females were
65.7% (n=761) of the patients. Most frequent source of CO was
natural gas heaters (n=628; 54.4%); others were stove (n=393;
34.1%), geyser (n=94; 8.4%) and blaze (n=38; 3.3%). Most frequent
direction of the wind was North-North-East (euroclydon). Atmospheric pressure was similar in all of the poisoning types; in
blaze, humidity levels was significantly lower, air temperature was
significantly higher. ABSTRACT Wind speed was faster in blaze and slowest in
geyser type poisoning. Conclusion: Carbon monoxide poisoning is an important cause of
emergency visits which can result in serious morbidity or mortality. Main sources are home heating systems. People should be
informed about the risks of these heaters and symptoms of CO
poisoning and, also in case of important meteorological changes. They should apply to an ED in case of occurrence of intoxication
symptoms. Anahtar Kelimeler: Atmosferik basınç, CO zehirlenmesi, sıcaklık,
rüzgar, yangın Keywords: Atmospheric pressure, CO intoxication, temperature,
wind, humidity Keywords: Atmospheric pressure, CO intoxication, temperature,
wind, humidity KARBONMONOKSİT KAYNAKLARININ VE METEOROLOJİK DEĞİŞİKLİKLERİN
KARBONMONOKSİT ZEHİRLENMELERİNE ETKİSİ: RETROSPEKTİF ÇALIŞMA Duygu Yılmaz1,
Umut Yücel Çavuş2,
Sinan Yıldırım3,
Bahar Gülcay Çat Bakır4*,
Gözde Besi Tetik5,
Onur Evren
Yılmaz6,
Mehtap Kaynakçı Bayram7 1Manisa Turgutlu State Hospital, Department of Emergency Medicine, Manisa, Turkey. 2Ankara Education and Research Hospital, Department of
Emergency Medicine, Ankara, Turkey. 3Çanakkale State Hospital, Department of Emergency Medicine, Çanakkale,Turkey. 4Mersin City Education and
Research Hospital, Department of Emergency Medicine, Mersin, Turkey. 5Gaziantep Şehitkamil State Hospital, Department of Emergency Medicine,
Gaziantep, Turkey. 6Medical Park Hospital, Department of Plastic and Reconstructive Surgery, İzmir, Turkey. 7Kayseri City Education and Research
Hospital, Department of Emergency Medicine, Kayseri, Turkey. ÖZ Research Article | Araştırma Makalesi THE EFFECT OF CARBON MONOXIDE SOURCES AND METEOROLOGIC
CHANGES IN CARBON MONOXIDE INTOXICATION: A RETROSPECTIVE
STUDY THE EFFECT OF CARBON MONOXIDE SOURCES AND METEOROLOGIC
CHANGES IN CARBON MONOXIDE INTOXICATION: A RETROSPECTIVE
STUDY KARBONMONOKSİT KAYNAKLARININ VE METEOROLOJİK DEĞİŞİKLİKLERİN
KARBONMONOKSİT ZEHİRLENMELERİNE ETKİSİ: RETROSPEKTİF ÇALIŞMA Published Online/Online Yayın: 20.02.2020 ● Bu eser, Creative Commons Atıf-Gayri Ticari 4.0 Uluslararası Lisansı ile lisanslanmıştır. Telif Hakkı © 2020 Kocaeli Ü Bu eser, Creative Commons Atıf-Gayri Ticari 4.0 Uluslararası Lisansı ile lisanslanmıştır. Telif Hakkı © 2020 Kocaeli Üniversitesi Tıp Fakültesi Dekanlığı Yılmaz et al., CO Intoxication Due to Meteorologic Changes Results One thousand one hundred fifty-three patients were
included the study; females were 65.7% (n=761) of the
patients. The mean age of the patients was 39.5±16.3. The mean age of males and females were similar
(p=0.676). The most frequent source of CO was natural
gas heaters (n=628; 54.4%); others were stove (n=393;
34.1%), geyser (n=94; 8.4%) and blaze (n=38; 3.3%). It is known in the literature that storms and sudden
weather changes lead to epidemic CO intoxications.10 To
the best of our knowledge the only study that
investigated
the
meteorological
parameters
like
humidity, air pressure and wind speed was Tiekuan Du et
al.’s study.11 The most frequent direction of the wind was North-
North-East (euroclydon), the second was north winds
(Figure 1). In this retrospective study, we investigated the
relationship of some of the meteorological factors with
the sources of CO poisoning. Figure 1. The relationship of carbon monoxide source and wind
direction Statistical Analysis The statistical analyses were performed by SPSS 15.0 for
Windows package program. The continuous variables are
expressed as mean±SD, categorical variables are
expressed as n (%). The normal distribution is
determined by histogram and One-Sample Kolmogorov
Smirnov test. Comparison of means was evaluated by
Mann-Whitney-U test if any of the groups is not normally
distributed; if both of the groups are normally
distributed, Student’s t-Test is used. p<0.05 is accepted
as significant. Introduction demographic data of the patients were obtained from
the hospital registration records. Our primary outcome
was the frequency of CO sources. Secondary outcomes
were the frequency of the wind directions and the most
common months of CO poisoning. Carbon monoxide (CO) poisoning is an important public
health problem. The emergency visits increase due to CO
intoxication caused by use of stove, geyser and other
heating devices especially in cold weather. The analysis was performed in Ankara, 870-meter-high
above the sea, in the middle of Turkey. The city is located
between the northern latitudes of 39° 50´ and 40° 00´and
the longitudes of 32° 35´ and 33° 00´. Generally, the
continental climate prevails in Ankara. Carbon monoxide was first described by a French
chemist de Lassone in 1776.1 Carbon monoxide has more
than 210 fold affinity in binding to hemoglobin than
oxygen.2 Carbon monoxide combines with hemoglobin to
produce carboxyhemoglobin, which is ineffective for
delivering oxygen to tissues that finally causes tissue
damage.3 The mechanism of CO-induced death is
thought to be high affinity binding of CO to hemoglobin
and myoglobin, resulting in tissue hypoxia that inhibits
cytochrome oxidase synergistically with CO.4 It causes
tissue damage in all organs, especially brain, heart and
kidney which are very sensitive to hypoxia.5 Cardiac
effects, ranging from mild and transitory injury to
necrosis and contractile dysfunction has been known in
patients
with
carbon
monoxide
poisoning.6
The
myocardial tissue is highly vulnerable to oxygen
deprivation, thus causing a substantial reduction of
contractility and cardiac output, which ultimately
contribute to the direct worsening injury of CO on
cardiomyocytes.7 The most common symptoms of carbon
monoxide poisoning are headache, nausea, vomiting,
dizziness, fatigue, and a feeling of weakness. Infants may
be irritable and malnourished. Neurological symptoms
are confusion, disorientation, visual disturbance, syncope
and seizure.8 The most important prognostic factor is the
exposure duration. Chronic intoxications has worse
prognosis.9 The atmospheric pressure, wind direction and speed,
humidity level and air temperature of the region at
exposition time are recorded from General Directorate of
Meteorology. Age and gender of patients, the source of
CO, admission time and date are recorded. Discussion The most common reason of CO intoxication in our study
was natural gas heaters with 54.4%; the second reason
was stove with 34.1%. Natural gas heaters are the most
commonly used domestic heating system in our study
region; so, the most common cause of CO poisoning was
natural gas heaters. Region, ethnic and socio-cultural
factors affect the poisoning type.12 Frequency of CO
source type varies by location. In some regions, the
geyser is the most common cause with a ratio between
68.3% and 77.5%; but in some regions, stove is the most
frequent source with a ratio between 85.9% and
89.7%.13-17 Figure 2. The frequency of carbon monoxide poisoning in
months In our study, the CO poisoning rate was found to be 74%
from December to March, while this rate was found to
be between 38.9% and 64.6% in the previous months in
our country.14,17-21 The frequency varies, but the main
result is a significant increase in CO poisoning in cold
weather especially in ice storms.22-24 The Centers for
Disease Control and Prevention (CDC) reports also
support our results that the CO exposure occurs mostly
in winter and at least in July and August.25,26 Figure 2. The frequency of carbon monoxide poisoning in
months The mean atmospheric pressure, air temperature, wind
speed and humidity levels at exposure time according to
the source of CO were expressed in Table 1. The
atmospheric pressure was similar in all of the poisoning
types; in blaze, humidity levels was significantly lower, air
temperature was significantly higher. The wind speed
was faster in blaze and slowest in geyser type poisoning. The box-plot graphics of meteorological data according
to CO source were given in Figure 3. y
g
In our study, atmospheric pressure was similar in all
types of poisoning. Tiekuan Du et al. reported that air
pressure is not associated with CO poisoning, similar to
our results. They reported that the only factor affecting
CO poisoning is air temperature; CO poisoning frequency
increases as temperature decreases.11 This result is
partially similar to our study result because we found
that the air temperature in CO poisoning associated with
the natural gas heater was the lowest. However, the
mean temperature was still very low (2.1°±7.1°)
compared to winter months. On the other hand, the air
temperature was significantly higher at blaze (7.2°±10.0°)
but the temperature still indicated cold weather. Methods This retrospective observational study is carried out after
local ethical committee approval (Dışkapı Yıldırım Beyazıt
Educational and Research Hospital, Approval number:
01/46, Date: 27.02.2012). The study hospital was a third-degree education and
research hospital with an annual emergency visit of
250.000 patients. Patients over the age of 18, who were
admitted to ED due to stove, natural gas, water heater
and smoke-induced CO poisoning with the symptoms of
headache, nausea, vomiting, dizziness, syncope, chest
pain and dyspnea were investigated in a three year
period. Patients diagnosed with CO poisoning were
included
in
the
study. Patients
with
normal
carboxyhemoglobin (COHb) levels are excluded. The Figure 1. The relationship of carbon monoxide source and wind
direction 2 Yılmaz et al., CO Intoxication Due to Meteorologic Changes Yılmaz et al., CO Intoxication Due to Meteorologic Changes The most common exposure was in January (Figure 2). The visits have significantly decreased after June. Discussion In case
of blaze, humidity levels were significantly low and air
temperature was significantly higher. Tiekuan Du et al. also investigated other parameters, but they reported
that there is no correlation of wind speed and humidity;11
but in our study we showed that wind speed was faster
in blaze and slowest in geyser type poisoning. In addition,
the humidity level in our study was the highest in geyser
type CO poisoning and the lowest in blaze. Table 1. The relationship of carbon monoxide source and
meteorological data Table 1. The relationship of carbon monoxide source and
meteorological data
Carbon
monoxide
Source
Air atmospheric
pressure
Humidity
rate
Air
temperature
Wind
speed
(mean±SD)
(mean±SD)
(mean±SD)
(mean±SD)
Natural
gas heater
(n=627)
1014±8
80±16
2.1°±7.1°
9.8±8.3
Stove
(n=393)
1013±8
81±14
2.9°±6.0°
10.6±8.6
Geyser
(n=94)
1014±7
85±14
2.2°±5.8°
7.4±6.8
Blaze
(n=38)
1014±5
65±24
7.2°±10.0°
12.1±8.2
Figure 3. The distribution of meteorological data according to
carbon monoxide source Table 1. The relationship of carbon monoxide source and
meteorological data
Carbon
monoxide
Source
Air atmospheric
pressure
Humidity
rate
Air
temperature
Wind
speed
(mean±SD)
(mean±SD)
(mean±SD)
(mean±SD)
Natural
gas heater
(n=627)
1014±8
80±16
2.1°±7.1°
9.8±8.3
Stove
(n=393)
1013±8
81±14
2.9°±6.0°
10.6±8.6
Geyser
(n=94)
1014±7
85±14
2.2°±5.8°
7.4±6.8
Blaze
(n=38)
1014±5
65±24
7.2°±10.0°
12.1±8.2
Figure 3. The distribution of meteorological data according to
carbon monoxide source Figure 3. The distribution of meteorological data according to
b
id The retrospective nature was a limitation of our study. The main sources of CO poisoning are home heating
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https://openalex.org/W4316015511 | https://researchonline.ljmu.ac.uk/id/eprint/18887/1/GCB%20Bioenergy%20-%202023%20-%20Shepherd%20-%20Novel%20Miscanthus%20hybrids%20%20Modelling%20productivity%20on%20marginal%20land%20in%20Europe%20using.pdf | English | null | Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception | Global change biology. Bioenergy/GCB bioenergy | 2,023 | cc-by | 14,233 | Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe
using dynamics of canopy development determined by light interception Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe
using dynamics of canopy development determined by light interception LJMU Research Online LJMU Research Online Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E,
‐
Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan,
M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der
Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Donnison, I, Kiesel, A,
Clifton Brown, J and Hastings, A
‐ Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E,
‐
Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan,
M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der
Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Donnison, I, Kiesel, A,
Clifton Brown, J and Hastings, A
‐ Abstract New biomass crop hybrids for bioeconomic expansion require yield projections to
determine their potential for strategic land use planning in the face of global chal-
lenges. Our biomass growth simulation incorporates radiation interception and
conversion efficiency. Models often use leaf area to predict interception which
is demanding to determine accurately, so instead we use low-cost rapid light in-
terception measurements using a simple laboratory-made line ceptometer and
relate the dynamics of canopy closure to thermal time, and to measurements of Novel Miscanthus hybrids: Modelling productivity on
marginal land in Europe using dynamics of canopy
development determined by light interception Anita Shepherd1
| Danny Awty-Carroll2
| Jason Kam3 | Chris Ashman2
|
Elena Magenau4
| Enrico Martani5 | Mislav Kontek6
| Andrea Ferrarini5
|
Stefano Amaducci5 | Chris Davey2 | Vanja Jurišić6 | Gert-Jan Petrie7 |
Mohamad Al Hassan8
| Isabelle Lamy9 | Iris Lewandowski4 |
Emmanuel de Maupeou10 | Jon McCalmont1
| Luisa Trindade8
|
Kasper van der Cruijsen8 | Philip van der Pluijm10 | Rebecca Rowe11
|
Andrew Lovett12 | Iain Donnison2 | Andreas Kiesel4
| John Clifton-Brown2,13
|
Astley Hastings1 Anita Shepherd1
| Danny Awty-Carroll2
| Jason Kam3 | Chris Ashman2
|
Elena Magenau4
| Enrico Martani5 | Mislav Kontek6
| Andrea Ferrarini5
|
Stefano Amaducci5 | Chris Davey2 | Vanja Jurišić6 | Gert-Jan Petrie7 |
Mohamad Al Hassan8
| Isabelle Lamy9 | Iris Lewandowski4 |
Emmanuel de Maupeou10 | Jon McCalmont1
| Luisa Trindade8
|
Kasper van der Cruijsen8 | Philip van der Pluijm10 | Rebecca Rowe11
|
Andrew Lovett12 | Iain Donnison2 | Andreas Kiesel4
| John Clifton-Brown2,13
|
Astley Hastings1 Anita Shepherd1
| Danny Awty-Carroll2
| Jason Kam3 | Chris Ashman2
|
Elena Magenau4
| Enrico Martani5 | Mislav Kontek6
| Andrea Ferrarini5
|
Stefano Amaducci5 | Chris Davey2 | Vanja Jurišić6 | Gert-Jan Petrie7 |
Mohamad Al Hassan8
| Isabelle Lamy9 | Iris Lewandowski4 |
Emmanuel de Maupeou10 | Jon McCalmont1
| Luisa Trindade8
|
Kasper van der Cruijsen8 | Philip van der Pluijm10 | Rebecca Rowe11
|
Andrew Lovett12 | Iain Donnison2 | Andreas Kiesel4
| John Clifton-Brown2,13
|
Astley Hastings1 1Biological Sciences, University of Aberdeen, Aberdeen, Scotland, UK 2Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
3Terravesta, Lincoln, UK 5Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy 6Department of Ag Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia 8Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands 11NERC Centre for Ecology and Hydrology, Lancaster Environment Centre, Lancaster, UK
12 12School of Environmental Sciences, University of East Anglia, Norwich, UK Article http://researchonline.ljmu.ac.uk/ For more information please contact researchonline@ljmu.ac.uk For more information please contact researchonline@ljmu.ac.uk http://researchonline.ljmu.ac.uk/ Received: 30 November 2022 | Accepted: 21 December 2022
DOI: 10.1111/gcbb.13029 Received: 30 November 2022 | Accepted: 21 December 2022 R E S E A R C H A R T I C L E R E S E A R C H A R T I C L E Article Citation (please note it is advisable to refer to the publisher’s version if you
intend to cite from this work)
Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E,
‐
Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al
Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J,
Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Citation (please note it is advisable to refer to the publisher’s version if you
intend to cite from this work) Citation (please note it is advisable to refer to the publisher’s version if you
intend to cite from this work) Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E,
‐
Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al
Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J,
Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E,
‐
Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al
Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J,
Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, LJMU has developed LJMU Research Online for users to access the research output of the
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the original work is properly cited.
© 2023 The Authors. GCB Bioenergy published by John Wiley & Sons Ltd. 1 | INTRODUCTION definition of marginal land is different things to different
crops and farmers. ‘Less productive’ is a more acceptable
term than marginal to growers, not inferring it is their fault
(pers. comms. Jason Kam, Terravesta). There is no single
definition, but most farms are said to have 10% less pro-
ductive (marginal) land area (Clifton-Brown et al., 2017)
which robust miscanthus plants could capitalize on, since
plant nutrients are self-contained in the rhizome and re-
cycled. This study assumes that the land is the least pro-
ductive 10% of land that farmers would be willing to take
out of food production to diversify their farms. Lovett
et al. (2014) advised that 1.4 million ha of less productive
agricultural land of the UK could be used for biomass pro-
duction without compromising food production. An acceleration in investment of biomass crops pro-
vision and use is required to meet net zero targets. The
European Commission and the UK government have set a
long-term goal to develop a low carbon economy by 2050
(Scarlat et al., 2015) where the new bioeconomy's focus
is on growth opportunities in bio-based sectors while
considering global challenges (e.g. raw material supply
insecurity) and resource and environmental constraints. Scarlat et al. (2015) voiced concerns about competing sec-
tors in Europe with bioenergy for land use. This requires
solutions to challenges, such as the sustainability of bio-
mass raw material and efficiency in biomass use, which
could be met using miscanthus for bioenergy. This is be-
cause miscanthus is highly sustainable, having a low car-
bon footprint, absorbing its nutrients in the rhizome for
re-use and depositing leaf litter to decompose into soil
(Shepherd, Clifton-Brown, et al., 2020). It is also one of
the most efficient biomass crops to convert into bioetha-
nol (Heaton et al., 2019). Competing sectors with biomass
for land use require growing biomass crops without tak-
ing away land resources for food. The answer could lie
in using marginal lands, lands under-productive for food
production. However, that in itself is a grey area since the Miscanthus is a genus of tropical C4 perennial grasses
with origins in Eastern Asia. Selections of naturally occur-
ring and synthetic hybrids have sufficient cold tolerance
for a wide range of European climates. It is a productive,
non-invasive perennial grass for biomass which is capa-
ble of maintaining commercial yields for about 20 years
(Anderson et al., 2011). K E Y W O R D S biomass, light absorption, light interception, miscanthus, sacchariflorus, seeded hybrid,
simulation, sinensis Funding information Bio-Based Industries Joint
Undertaking, Grant/Award Number:
745012; Biotechnology and Biological
Sciences Research Council, Grant/
Award Number: BB/V011553/1; © 2023 The Authors. GCB Bioenergy published by John Wiley & Sons Ltd. | 1
wileyonlinelibrary.com/journal/gcbb GCB Bioenergy. 2023;00:1–18. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Onlin SHEPHERD et al. Supergen Bioenergy Hub, Engineering
and Physical Sciences Research
Council, Grant/Award Number: EP/
S000771/1; UK Energy Research
Centre, Grant/Award Number: EP/
S029575/1; Aston University, Grant/
Award Number: RG15855 Supergen Bioenergy Hub, Engineering
and Physical Sciences Research
Council, Grant/Award Number: EP/
S000771/1; UK Energy Research
Centre, Grant/Award Number: EP/
S029575/1; Aston University, Grant/
Award Number: RG15855 biomass. We apply the model to project the European biomass potentials of new
market-ready hybrids for 2020–2030. Field measurements are easier to collect,
the calibration is seasonally dynamic and reduces influence of weather variation
between field sites. The model obtained is conservative, being calibrated by crops
of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020–2030
based on 10% land use conversion of the least (productive) grassland and arable
for farm diversification, which show a European potential of 80.7–89.7 Mt year−1
biomass, with potential for 1.2–1.3 EJ year−1 energy and 36.3–40.3 Mt year−1 car-
bon capture, with seeded Miscanthus sacchariflorus × sinensis displaying high-
est yield potential. Simulated biomass projections must be viewed in light of the
field measurements on less productive land with high soil water deficits. We are
attempting to model the results from an ambitious and novel project combin-
ing new hybrids across Europe with agronomy which has not been perfected on
less productive sites. Nevertheless, at the time of energy sourcing issues, seed-
propagated miscanthus hybrids for the upscaled provision of bioenergy offer an
alternative source of renewable energy. If European countries provide incentives
for growers to invest, seeded hybrids can improve product availability and bio-
mass yields over the current commercial miscanthus variety. or pesticide in maturity. This results in low field mainte-
nance, suitable for busy growers, remote fields and urban
neighbours where chemical spraying is not desirable. agricultural land and less productive land, less suitable for
food crops (Lewandowski et al., 2016). To understand the
potential contribution of Miscanthus to EU targets for do-
mestic biomass production, it is critical to be able to model
biomass growth under varying environmental conditions
on less productive lands. Model development requires
high-quality input data, one such leading experiment is
the GRACE project (https://www.grace-bbi.eu/) and the
only project to provide intensely and frequently measured
data on crop performance on less productive land on a
transect of field sites across Europe. Even with favourable policies in some European
countries, upscaling of miscanthus as a cellulosic peren-
nial biomass has been slow. Barriers include uncertainty
of yield with poor or slow establishment (Zimmerman
et al., 2013), bulkiness for storage and transport and low
quality of product for its processing chain (Clifton-Brown
et al., 2017). Poorly established crops are more suscepti-
ble to Fusarium and miscanthus blight (Lewandowski
et al., 2000). High moisture, ash and silica result in a low
quality product for combustion, this can be modified by
the timing of senescence and harvest. Earlier flowering
times can improve biomass quality by triggering active se-
nescence before temperatures fall in autumn with better
nutrient remobilization from the shoot to the rhizome and
convey cold resistance (Jensen et al., 2017). Post-winter
harvests improve miscanthus quality criteria for thermal
conversion to energy and crop sustainability through re-
mobilization of nutrients to the underground rhizome
(Jensen et al., 2017). A recent survey of miscanthus grow-
ers (Von Hellfeld et al., 2022) showed a major bottleneck
to miscanthus uptake was viewed by growers as the cost
of logistics, transporting to crop to the processing plant
countrywide when the processing plants are in very spe-
cific locations. Clifton-Brown et al. (2017) mention lack of
supply chain coordination as a barrier to growth. Growers
responses (Von Hellfeld et al., 2022) also mentioned a lack
of financial incentives and policies for the perennial bio-
mass crop industry. A more reliable crop establishment
would avoid unwanted planting gaps, patchiness and
yield losses (Hastings et al., 2017), and a shorter time to
establishment in cool temperate climates would reach
maximum economic harvest faster. 2 | MATERIALS AND METHODS We use the leading miscanthus growth model, MiscanFor
(Hastings, Clifton-Brown, Wattenbach, Mitchell, &
Smith, 2009; Shepherd, Littleton, et al., 2020), a process-
based model that uses soil properties and meteorological
data to predict crop growth through a series of algorithms,
running on a daily timestep. The model processes predict
the timing of various stages of growth in a mature mis-
canthus crop. These are emergence of the shoots, the first
leaf, the maximum leaf area, flowering start and stop, the
onset of senescence (ripening) and senescence comple-
tion. Using calibrations from empirical data the model
predicts the rate of leaf expansion, the rate of evapotran-
spiration and soil moisture content, rate of photosynthe-
sis and rate of leaf fall and senescence. All these rates are
modified by air temperature, soil moisture level, nutrient
level and solar radiation. For bioenergy, it calculates net
power station energy produced and bioenergy carbon
capture and storage (BECCS) potential. The model is de-
scribed in Hastings, Clifton-Brown, Wattenbach, Mitchell,
and Smith (2009) and Shepherd, Littleton, et al. (2020). A
block diagram of the model growth processes is shown in
Figure 1 It is hoped the devel-
opments in new seed-propagated miscanthus hybrids and
improved agronomic methods can improve establishment,
reducing some of the barriers to biomass upscaling. Seed-
propagated hybrids which can be grown from seed into
rhizome plugs for planting at a faster rate than propagat-
ing from rhizome to rhizome (Clifton-Brown et al., 2019). The current commercial miscanthus (Miscanthus × gigan-
teus or M × g) is rhizome-propagated, a slow and land-
intensive process, which means a delay to growers when
they order new crops. One hectare of rhizome plugs cloned
has a multiplication rate of 1:20, providing rhizomes for
around 20 ha of new plantation, whereas seed-based hy-
brids have multiplication rates of 1:2000 for several hy-
brids with multiplication of M. sinensis higher stated at
1:5000–10,000 (Clifton-Brown et al., 2019). So how much biomass can those hybrids provide? What is their potential across Europe in terms of biomass,
energy and carbon capture and storage (CCS)? We aim
to use site measurements from these international field
trials to calibrate a biomass crop model to determine the
European potential for biomass from these new hybrids,
and introduce a novel method in their parameterization
for determining biomass. 1 | INTRODUCTION Miscanthus is a thermally supe-
rior biomass crop compared to commonly used maize or
wheat straw, it is also a pragmatic solution to farm prob-
lems (Shepherd, Clifton-Brown, et al., 2020). It has a low
C footprint (Hastings et al., 2017), requiring no fertilizer SHEPHERD et al. | 3 3 2.1 Databases were obtained and formatted for Europe-wide
spatial simulations. To maximize their contribution to the food resource
security element of the European bioeconomy, second-
generation biomass crops should be grown on lower-grade Potential land that could be used for the cultivation of
biomass crops in Europe was investigated. The Corine land 4 |
FIGURE 1 Schematic of the MiscanFor model. SHEPHERD et al. 4 plant growth during 2020, to provide measurements for
parameterizing and calibrating a model and extrapolating
the results in space and time period. This work focusses on the seasonal biomass and har-
vest potential of three novel miscanthus hybrids plus the
current commercial crop M. × giganteus (shortened here
to M × g). The novel hybrids are a seed-propagated M. sinensis × sinensis (shortened here to M. sin × sin), a seed-
propagated M. sacchariflorus × sinensis (shortened here to
seed M. sac × sin, marketed as ‘Aphrodite’) and a clonal
M. sacchariflorus × sinensis (shortened here to rhizome M. sac × sin, marketed as ‘Athena’). These hybrids were se-
lected for the field trials by the breeders using best infor-
mation available at the time of selection. Criteria included
(1) evidence of good yield performance traits on a range of
sites in UK and EU with contrasting environmental con-
ditions; (2) seed production and propagation ability; and
(3) diverse morphologies (heights and stem diameters)
relative to impacts on harvest logistics and downstream
processing operations. FIGURE 1 Schematic of the MiscanFor model. cover map from Copernicus (Buettner, 2014) was used to
create a mask of areas unsuitable for the cultivation such
as bare rock, or areas that should not be used for cultiva-
tion such as forests, wetlands and shrubland. Only arable
and pasture classes were considered suitable. In addition,
any areas with high carbon soils, typically above 15% or-
ganic matter or peatland were considered unsuitable. The field trial involved intensive crop measurements
at European sites (Table 1) throughout the growing sea-
son of 2020 for crops harvested in March 2021; 2020 was
the third year of growth, crops having been planted during
2018. For this simulation work, field measurements were
used from the most frequently (two-weekly) sampled four
sites and four hybrids. Further details on the whole field
trial can be read in Awty-Carroll et al. (2022). The soil properties were obtained from the harmonized
world soil data base from IIASA (Wieder et al., 2014). 2.1 We
only used the dominant soil for each grid block. These
soil parameters were used to calculate the wilting point,
field capacity and soil carbon to a depth of up to 1 m for
each grid pixel. The RCP2.6 future climate scenario from
the HADGEM 3 model from the UK Met Office (Martin
et al., 2011) for the period 2020–2030 in monthly time
steps and on a 0.5 degree grid was used as driving climate
data. For each hybrid in the field, four replicate blocks were
measured. M. sin × sin is planted at double the density
(30,000 plants ha−1) of the other hybrids (15,000 plants
ha−1) as recommended by its developer Wageningen
University. in the UK at Trawsgoed (TWS) near Aberystwyth is nor-
mally used for pasture. The shallow stony sandy loam has
lead contamination and low water holding capacity. TWS
site's low lying position at 72 m asl means that crops ex-
perience more temperature extremes than in most of the
UK, including more severe late spring and early autumn
frosts. TWS has the lowest plant available water (50 mm)
of all the field sites. In southern Germany, the field trial
was planted at a high-altitude site (706 m asl) Oberer
Lindernhof (OLI) which has a shortened growing sea-
son. Over winter, it snows regularly, and temperatures of
down to −20°C are reached. OLI has been used for years
by cereal breeders to test for overwinter cold tolerance
and resistance to late spring and early frosts [e.g. wheat
and rye for bioethanol (Rosenberger et al., 2002); durum
wheat (Sieber et al., 2014)]. The site in Croatia near Zagreb
is limited by local clay soils that have low enzyme activity
which suffer from rainfall extremes—too much in sum-
mer and too little in spring (Magenau et al., 2022). The site
in Northern Italy near Piacenza (PAC) is the least produc-
tive of the sites but continuous arable has compacted and
depleted the soil organic carbon (Awty-Carroll et al., 2022)
which can potentially be improved by growing perennials
such as Miscanthus. SCH experiences the lowest annual
precipitation of the field trial sites, 473 mm. CHV has
heavy metals contaminating its soils from surrounding
heavy industry, plus copper sulphate fungicide and low
soil water retention (Awty-Carroll et al., 2022). For more
detailed mean climate data, see Magenau et al. (2022). Site
Lat, Long (decimal deg)
Altitude
(m asl)*
Annual precipitation
(mm)
Plant available
water (mm)
Mean temp
(degree)
Soil texture
TWS Trawscoed, Wales
52°24′59.8′′ N, 4°04′02.6′′ W
72
1311
50
10.7
Shallow stony sandy loam
OLI Oberer Lindenhof, Germany
48°28′42.1′′ N, 9°18′41.0″ E
706
863
148
8.7
Clay loam
ZAG Zagreb, Croatia
45°49′47.9′′ N, 15°58′33.5′′ E
117
891
158
11.7
Clay and silt loam
PAC1 Piacenza lowland site, Italy
44°84′50.4′′ N, 9°60′60.7″ E
73
820
166
13.9
Compacted loam
PAC2 Piacenza upland site Italy
44°84′50.4′′ N, 9°71′02.4″ E
578
804
140
12.8
Compacted loam
SCH Schiphol, Netherlands
52°18′45.2′′ N, 4°39′55.3″ E
−4
473
147
10.7
Peat and clay reclaimed land
CHV Chanteloup, France
48°58′34.9′′ N, 2°01′57.9″ E
42
537
67
11.9
Sandy loam 2.2 | Field data, hybrids and
site locations The field trial sites (Table 1) chosen for their frequent
measurement for modelling are sites nearby Trawscoed
(labelled in the text TWS), Oberer Lindenhof (labelled
OLI); Zagreb (labelled ZAG); Piacenza lowland site (la-
belled PAC); for locations of field sites, see figure 1 in
Awty-Carroll et al. (2022). Further sites used for validation
comparison with modelled values were Hoofdoorp near
Schiphol airport (labelled SCH), Chanteloup near Paris
(labelled CHV) and Piacenza upland site (labelled PAC2). Climate data for modelling at the site level were provided
by the WS-GP 1 weather stations (Delta-T Devices Ltd), soil
data taken from soil core sampling (soil texture and bulk
density were used to derive the capillary pressure taken at
time-zero in 2017 using the Campbell method, as defined
in Hastings, Clifton-Brown, Wattenbach, Mitchell, and
Smith (2009) which allowed calculation of plant available
water), together with the crop measurements. At each site, an automatic weather station (GP1;
Delta-T Devices) measured in field environmental param-
eters: hourly solar radiation, rainfall, wind and air tem-
perature that determine crop growth processes. The project whose data we are using, aims to develop
the technology for upscaling miscanthus production on
land with low productivity to avoid competition with
the food sector for land use. To achieve this one its work
packages includes multi-location field trials of many mis-
canthus hybrids across European sites. Of the 14 hybrids
it investigates, four hybrids were selected in this study for
intensive growth measurements in four widely distributed
locations to create equations for crop modelling. These
measurements were scheduled during the third year of Land marginality—the field trials were performed on
less productive/lower-grade lands (also referred to as mar-
ginal lands) that are less suitable for arable food crops. Marginal land is defined (Tóth et al., 2016) as experiencing
one or more of environmental stresses (drought, flooding,
stoniness, steep slope, exposure to wind and sub-optimal
aspect), low nutrients and/or contaminated soils. The site SHEPHERD et al. | 5 5 2.3.2 | Seasonal dynamics of light
interception (PAR) by the canopy Monsi and Saeki (1953) published the first mathematical
model for radiation intercepted by the leaf canopy based
on the Beer–Lambert Law: | in Shepherd, Littleton, et al. (2020) uses the RUE of
2.4 g MJ−1 as a maximum because validation shows this
produces realistic modelled versus observed aboveground
yield. RUE is reduced by soil water deficit (Clifton-Brown
et al., 2004) and temperature (Hastings, Clifton-Brown,
Wattenbach, Mitchell, & Smith, 2009). In the MiscanFor
model, downregulation via too high or too low tempera-
ture is applied to maximum RUE via the temperature vari-
ation factor (Farage et al., 2006) because RUE depends on
the temperature at leaf formation and the temperature of
photosynthesis. Downregulation of RUE via water deficit
is applied via coefficients representing the evaporation
of rainfall intercepted by leaf and leaf transpiration and
evaporation through soil, all limited via water deficit. The
process is similar to the one used in SWAT2000 (Neitsch
et al., 2005). In the model, these separate coefficients are
determined and then combined into a RUE downregula-
tion coefficient. and below the leaf canopy. These measures are used to cal-
culate the ‘light ratio’, the measured fraction of radiation
transmitted though the canopy (i.e. under the canopy and
not absorbed by the plant as a portion of radiation above
the canopy), and hence 1 − ‘light ratio’ is the fraction of
light absorbed, which can replace the term ‘1 − exp (−ext. coeff × LAI)’. Inserting this term into Equation (1) Inserting this term into Equation (1) (3)
Plant biomass increase (g)=RUE×(1−}light ratio’)
×cumulative PAR measured (3
Plant biomass increase (g)=RUE×(1−}light ratio’)
×cumulative PAR measured increase (g)=RUE×(1−}light ratio’) (3)
×cumulative PAR measured (3) and rearranging, (4)
RUE=plant biomass increase∕
((1−}light ratio’)×cumulative PAR) (4) and we can measure this over time increments to determine
how the RUE changes during the growth period. Plant biomass increase over a time interval (e.g. g dry
matter per day) is the product of cumulative radiation in-
tercepted by the canopy (e.g. MJ PAR day−1) and the con-
version efficiency (RUE, e.g. g MJ−1 PAR): (
Plant biomass increase=RUE×cumulative PAR
× fraction of light absorbed (1) Standing crop biomass (for comparison against simu-
lated biomass) was determined from a subsampling ap-
proach devised and explained fully in Nunn et al. (2017),
consisting of fortnightly destructive harvests (known as
‘serial cuts’) of randomly selected shoots per plot (10 for
M. sac × sin and 20 shoots for smaller M. sin × sin plants),
cut at 10 cm above soil surface. These subsamples were
rescaled by multiplying serial dry weight by the ratio of
the final 10-stem weight measurement and the quadrat
harvest dry weight taken on the same day. Units were ex-
pressed in terms of t ha−1. Because the brown and green
leaf biomass and stem biomass were measured separately
at each serial cut throughout the season in 2020, canopy
dynamics (expansion and senescence) could be identified. The product of a RUEmax and the RUE downregulation
coefficient produces the RUE which can be calculated in
the field using Equation (1). When changes in crop bio-
mass can be detected with sufficient accuracy over short
intervals (e.g. weekly or fortnightly), the dynamics of RUE
in the field can be related to environmental constraints
and plant developmental stages to derive coefficients that
can be used for downregulation. 6 2.3.1 | Maximum radiation use
efficiency and its environmental
down regulation Miscanthus is a genus of tropical C4 perennial grasses
with origins in Eastern Asia. Selections of naturally oc-
curring and synthetic hybrids have sufficient cold toler-
ance for a wide range of European climates. Radiation
use efficiency (RUE) is an estimate of net whole grow-
ing season photosynthesis. Field measurements of RUE
have been derived multiple times for M × g in ‘largely’ non
water limiting temperate conditions in Ireland (Clifton-
Brown et al., 2000), Wales (Davey, Jones, et al., 2017) and
in Netherlands (van der Werf et al., 1992). They average
2.4 g above round dry matter MJ−1 of intercepted pho-
tosynthetically active radiation (PAR). Although there
are several publications with higher RUE estimates, the
MiscanFor model described in Hastings, Clifton-Brown,
Wattenbach, Mitchell, and Smith (2009) and updated 6 SHEPHERD et al. 2.3.3 | Seasonal dynamics of
aboveground biomass Plant biomass increase=RUE×cumulative PAR
× fraction of light absorbed 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Cond each hybrid. The RUE has to be treated the same across all
sites of the same hybrid, so the line of best fit is taken for
measured values across all field sites for a representative
hybrid RUE. applied the model spatially. There are two versions of the
MiscanFor model, a single site version and a spatial ver-
sion with exactly the same processes but with the capabil-
ity to use databases at variable scale and extent. For the
spatial model, climate, elevation, soil, land use and land
constraint databases were prepared for Europe at 1 km
resolution. The crop biomass processes and parameters for
the validated site model were input to the spatial model. applied the model spatially. There are two versions of the
MiscanFor model, a single site version and a spatial ver-
sion with exactly the same processes but with the capabil-
ity to use databases at variable scale and extent. For the
spatial model, climate, elevation, soil, land use and land
constraint databases were prepared for Europe at 1 km
resolution. The crop biomass processes and parameters for
the validated site model were input to the spatial model. 3.1 | Method 1 A plot of measured RUE through the season (Figure 2)
using the M. sin × sin hybrid is representative of the find-
ings for all hybrids. It shows a high variability in 2-week
interval measured RUE between sites and a high standard
error between replicates with no statistical significance. Each site's climate which modifies RUE did not produce 2.4 2.4 (2)
Radiation below canopy=Radiation above canopy
⋅exp (−ext. coeff×LAI) (2) For each hybrid and each site: The 2020 time series of
RUEmeasured (Equation 4) concerning intercepted light for
the different hybrids was plotted against simulated RUE
(for M × g in the pre-modified model), which had been
downregulated via limitations for soil and leaf water via
deficit and photosynthesis via leaf expansion temperature. Leaf area index (LAI) is variable so not easy to mea-
sure for calibration, and calculating LAI first in order to
then calculate light interception, aggregates uncertainty
by having two calculations when one could be used. We
replaced the Monsi–Saeki calculation using a direct mea-
surement of light intensity with a line ceptometer (an
array of 10 photodiodes spaced along a 1 m stick) above The comparison of RUE from measurement of all sites
and simulated RUE allows us to determine the amount of
reduction or increase to apply to the simulated RUE for 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for ru | 7 SHEPHERD et al. | 7 2.5.2 | Method 2b: Logistic light interception-
degree day relationship The fraction of light interception from top and bottom
of the canopy (1 − ‘light ratio’) was plotted against accu-
mulated degree day for all field sites, and a logistic curve
fitted. The resulting algorithm to determine light intercep-
tion from cumulative degree days was used to determine
biomass via Equation (1). 2.5 | Photosynthesis simulation method
2: Replacing LAI with light interception The energy produced by a miscanthus assuming a
medium size power plant burning miscanthus bales uses
the method of Hastings, Clifton-Brown, Wattenbach,
Mitchell, Stampfl, and Smith (2009). Carbon capture po-
tential (CCS) is based on an assumption of 90% efficiency
(Albanito et al., 2019) of capture post-combustion at bio-
mass electricity plants. From Equation (1), biomass increase = light intercep-
tion × cumulated PAR × RUE. RUE varies with each hybrid as some have more vigour
than others. PAR varies for each site, making a comparison of hy-
brids difficult, and what we want to do is reduce environ-
mental influences to look at the biological operation of the
hybrids. In a previous UKRI-funded project (Shepherd,
Littleton, et al., 2020), the IMAGE IAM which makes
socio-economic decisions had determined land area to
locate biomass crops to provide sufficient biomass for car-
bon capture schemes to retain global temperature increase
under 2°C. IMAGE projected the same global area as con-
verting 10% of grassland and 10% of less productive arable
land. The industry-supported field trials we are using are
based on less productive arable, so we assume that bio-
mass crops would be marketed for such use. The biomass
growth calibrations determined from the crop measure-
ments on less productive land have been used to produce
projections for Europe, taking 10% of each spatial grid
square of grassland and arable land use as less productive. We have used this method to produce aggregated European
totals rather than using marginal land use databases be-
cause the definition of marginal land changes depending
on the crop or land use, and because land use databases
are based on current/past land use, and we are producing
future projections with a proportion of land conversion to
biomass determined by a socio-economic IAM. Moreover,
the IAM land area output is related to the RCP 2.6 climate
scenario, used in this study, to determine the biomass land
area necessary for sufficient BECCS decarbonization to
meet the Paris Agreement (United Nations, 2015) limit on
global temperature increase under 2°C. The light interception fraction however has the po-
tential to work in a simulation common to all hybrids,
is dependent on cumulative degree days, and when light
interception fraction-degree days data are plotted, the
temperature influence is standardized. This can be useful
when you have measurements collected from different cli-
mate zones for a single hybrid. 2.5.1 | Method 2a: Third-order polynomial
light interception-degree day relationship 2.5.1 | Method 2a: Third-order polynomial
light interception-degree day relationship The fraction of intercepted light interception from the top
and bottom of the canopy (1 − ‘light ratio’) was plotted
against accumulated degree day for all field sites, and a
third-order polynomial curve of the relationship fitted. The resulting algorithm to determine light interception
from cumulative degree days was used to determine bio-
mass via Equation (1). 2.5.2 | Method 2b: Logistic light interception-
degree day relationship 2.6 After satisfactorily validating the MiscanFor model for
different sites and years with varying soils and climate, we 8 |
SHEPHERD et al
FIGURE 2 Variability of measured radiation use efficiency (RUE, g MJ−1) in M. sin × sin across four field sites (a) TWS: Trawscoed
Wales, (b) OLI: Oberer Lindenhof Germany, (c) ZAG: Zagreb Croatia, (d) PAC: Piacenza Italy, and with Std Error bars of four replicates at
each field site sampling date. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Lib SHEPHERD et al. wnloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions ( FIGURE 2 Variability of measured radiation use efficiency (RUE, g MJ−1) in M. sin × sin across four field sites (a) TWS: Trawscoed
Wales, (b) OLI: Oberer Lindenhof Germany, (c) ZAG: Zagreb Croatia, (d) PAC: Piacenza Italy, and with Std Error bars of four replicates at
each field site sampling date. In a previous project, OPTIMISC, establishment issues
were also noted as being problematic for comparative
measurement of hybrids (Nunn et al., 2017). Magenau
et al. (2022) also refer to the fact that by the third year
at colder locations such as OLI and TWS, the establish-
ment of miscanthus takes up to 6 years (citing Christian
et al., 2008), while in warmer climates, maximum yields
are reached after 2 years (Clifton-Brown et al., 2000). In
Croatia, establishment was hampered by a heavy clay and
less productive soil conditions, so that plants in the third
year were not fully established. any common relationship for a single hybrid to use extract
for modelling and shows that RUE is not static, but dy-
namic with climate conditions. Therefore, we conclude
that a constant reduction in RUE is not the answer. It
was decided to discontinue this method. Ideally, we need
a method more based on the drivers of the variability in
RUE and the characteristics of the hybrid and reducing
the impact of climate. 3.3 | Method 2b: Logistic fitted light
interception curve See the Terms and Conditions URE 3 Field observations with fitted logistic relationship between accumulated light interception and degre g
p
g
p
g
y
p
hybrids M. sin × sin (a), M × g (b), seeded M. sac × sin (c), rhizome M. sac × sin (d). Fitted curves are based on all-site data. In (c) light
absorption for the best performing crop at Piacenza is displayed alongside the average-site data for seeded M. sac × sin due to establishment
issues at various sites. Variability of observation in all plots denoted by standard deviation of the four sampled replicates. M × g,
Miscanthus × giganteus; M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. TABLE 2 Curve fit parameter statistics of observed light interception and fitted logistic values with data aggregated from four
measurement sites. Logistic fitted curve
Seed M. sin × sin
Rh. M × g
Seed M. sac × sin
Seed M. sac × sin
potentiala
Rh. M. sac × sin
r2 correlation
0.98
0.98
0.93
0.99
0.98
RMSE
12.61
12.98
26.87
2.94
13.89
Mean difference
−0.04
−0.02
−0.03
0.003
−0.02
Relative error
−5.42
−3.06
−5.46
0.01
−3.46
Maximum error
0.22
0.31
0.40
0.05
0.26
No. of values
44
44
44
12
44
Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis; Rh.: rhizome;
RMSE: root mean square error. aPotential = data from best performing crop at Piacenza only. Logistic fitted curve established as well as other hybrids and shows relatively
little variability. relationship using only the data from the best perform-
ing crop at PAC. In the light interception plot for seeded
M. sac × sin (Figure 3c), observed data and logistic fitted
curves based on all-site data are shown and also the PAC
site best performing crop, from which we see a far steeper
growth of light interception as the canopy has a more
rapid closure with a well-established crop. We refer to re-
sults from the latter as ‘Seed M. sac × sin potential’, statis-
tics being included in Table 2 which reflect the consistency Considering such an expensive, measurement inten-
sive, international project to determine the potential of
new hybrids including seed-propagated lines, the poor
establishment of seeded M. 3.3 | Method 2b: Logistic fitted light
interception curve A third-order polynomial was fitted to describe the rela-
tionship between the radiation intercepted by the canopy
and the accumulated degree days across all sites for each
hybrid (Supplementary Material S1). Figure 3 plots for each hybrid show the fitted logistic
curves for the fraction of light interception from the top
and bottom of the canopy against accumulated degree
days for data measurements from all field sites. Standard
deviation of the four replicate plot measurements at a sin-
gle site and in a single sampling have been included for
each data point. Seeded hybrid M. sac × sin had the greatest variabil-
ity in light interception and growth across field sites
(Supplementary Materials S1 and S2c). The widely vary-
ing values are due to poor plug plant establishment at
some sites and frost damage on the same plot as crops
established well with a more rapid canopy closure (Awty-
Carroll et al., 2022). First-year overwintering was partic-
ularly affected by climate and repeated frosts in Wales
UK, which affected the second-year growth of seeded M. sac × sin hybrids. Field gap filling during establishment
prevented compound yield losses. The lowest yielding
third-year site was the Wales UK and the highest in low-
land northern Italy. The logistic curves are the best fit (Table 2) and they
are also the correct shape for the growth curve starting off
with a shallow increase and ending at a plateau. All hy-
brids show better fitted curve agreement using a logistic
relationship, but the seeded M. sac × sin hybrid had the
greatest variance in establishment (reflected in the sta-
tistical variability). The other seeded hybrid M. sin × sin | 9
HEPHERD et al. IGURE 3 Field observations with fitted logistic relationship between accumulated light interception and degree days for separate
ybrids M. sin × sin (a), M × g (b), seeded M. sac × sin (c), rhizome M. sac × sin (d). Fitted curves are based on all-site data. In (c) light
bsorption for the best performing crop at Piacenza is displayed alongside the average-site data for seeded M. sac × sin due to establishment 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Li | 9 SHEPHERD et al. wnloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. a rapid rise in growth, they did not occur late enough to
delay a high rate of increase in biomass. of data when very well-established replicates are used
instead of replicates of low establishment success, this
treatment of data only pertains to the seeded M. sac × sin
hybrid because of its greater establishment problems. The standing crop biomass field measurements show
how M × g crops at ZAG suffered in a drought and were
poorly established at TWS. The simulated biomass, resulting
from a calibration using mean measurements from all less
productive sites, will be higher than the measured biomass
at poorly established sites because calibration values are in-
creased by the better performing sites. To show the poten-
tial of a hybrid, well-established plants should be used for
calibration measurements, therefore since the hybrid with
the poorest establishment is the seeded M. sac × sin, this has
been calibrated for its best established calibration field mea-
surements at the PAC field site in green. The second thing to
improve the variability of measurements from sites is to de-
termine best agronomy practise, to ensure well-established
plants at all sites, then repeat an study such as this. 3.3 | Method 2b: Logistic fitted light
interception curve sac × sin at sites was an issue
that warranted an alternative model calibration to deter-
mine the crop potential for seeded M. sac × sin; hence,
we re-visited the light interception-degree days logistic 10 SHEPHERD et al. 10 | 11 SHEPHERD et al. 11 TABLE 3 Statistics of observed and
simulated biomass for selected hybrids
and sites using logistic light interception
curve. Logistic light interception
M. sin × sin
M × g
Seed M. sac × sin
Rh. M. sac × sin
TWS
OLI
ZAG
PAC
r2 correlation
0.98
0.98
0.85
0.86
RMSE
23.86
16.38
35.18
42.40
Mean difference
−0.59
0.21
−0.86
4.34
Relative error
−9.29
2.08
−7.84
31.37
Maximum error
4.23
3.87
10.18
13.19
No. of values
17
17
17
17
Abbreviations: OLI: Oberer Lindenhof; PAC: Piacenza; Rh.: rhizome; RMSE: root mean square error;
TWS: Trawscoed; ZAG: Zagreb. Logistic light interception Abbreviations: OLI: Oberer Lindenhof; PAC: Piacenza; Rh.: rhizome; RMSE: root mean square error;
TWS: Trawscoed; ZAG: Zagreb. FIGURE 5
(a, b) Two validations
using simulated versus measured harvest
biomass across all hybrids: (a) from
different field sites 2021 harvest and (b)
from the same field sites as calibrations
2022 harvest (four replicates). and shows how the validated model has improved upon
the unmodified model (in blue) which was calibrated for
M × g only. The validation data provide satisfactory re-
sults (r2 0.54, RMSE 28.7). Figure 5b shows validations
at the same field sites for 2022, the next harvest after
the calibration growing season. This showed a poor r2 of
0.0005, but was due to three outliers shown in red of very
low measured harvest yield (each an average of four rep-
licates), much lower than other hybrids in the same field
under the same environmental conditions and was not
connected to the modelling. If we take the three outliers
away, the results are satisfactory (Table 4, r2 0.68, RMSE
12.65). selected sites and hybrids derived from a logistic light in-
terception curve. (Statistics on every site and hybrid, for
third-order polynomial and logistic derived relationships,
can be found in Table S3 of Supplementary information.)
Biomass resulting from the logistic method for determin-
ing light interception was more accurately simulated than
from the third-order polynomial method; hence, only the
logistic method was taken forward for validation and final
simulation. The aim of the modelling is to determine the biomass
incremental change using daily climatic data and accu-
mulate these increments over a whole growing season
to predict final biomass yield. To validate the model, we
compared simulations to measured harvest yields from
different sites or from different years to the calibration
data, across any of the hybrids. 3.4 | Resulting biomass from light
interception curves Figure 4 shows the resulting calibrations of measured bio-
mass compared against simulations determined from the
calculated light interception resulting from third-order
polynomial and logistic relationships with degree days,
showing how the logistic simulations shown in red have
a better agreement with the field measurements than
both the unmodified model and the third order polyno-
mial simulation. Early season frosts occurrences were
checked against the growth curves (displayed on Figure 4
M. sin × sin plots), but as the timing of frosts were before MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; O Table 3 shows a statistical comparison of the seasonal
time series of observed and simulated crop biomass from FIGURE 4 Simulated biomass, from logistic light interception-degree day relationships plus the original model using leaf area index
estimation, compared against measured standing crop biomass for each hybrid and for each site. nelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License rary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are m/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by nditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable C Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Com OA articles are governed by the applicable Creative Commons License FIGURE 4 Simulated biomass, from logistic light interception-degree day relationships plus the original model using leaf area index
estimation, compared against measured standing crop biomass for each hybrid and for each site. FIGURE 4 Simulated biomass, from logistic light interception-degree day relationships plus the original model using leaf area index
estimation, compared against measured standing crop biomass for each hybrid and for each site. 12 Clifton-Brown, Wattenbach, Mitchell, & Smith, 2009), al-
though it is accepted that in harvest:peak ratio, it can vary a
little between the hybrids. During 2020–2030, mean annual
harvest yield ranges from 0 to 11 t ha−1 year−1. This is shown
in Figure 6a,b for M. sac × sin and M. sin × sin, respectively,
with black areas displaying where either the bioenergy land
use is constrained by national parks, forestry, mountains,
etc. or yield is zero, due to frost or drought crop kill. The crop biomass processes and parameters for the
validated site model were input to the spatial model
(Equation 5, Table 5) to run simulations across Europe to
determine the European-wide potential of the hybrids. The Europe-wide simulations for each hybrid display
similarly in map form, the differences being in the spa-
tially aggregated totals; hence, spatial results are displayed
using the seed-propagated hybrids M. sin × sin and M. sac × sin. The mean peak annual biomass during 2020–
2030 ranges from 0 to 18 t ha−1 year−1. The mean annual
harvest yield was calculated at 67% of peak yield (Hastings, Growth is closely related to water availability, so north-
erly and central European regions with lower water defi-
cit and warm growing season temperatures in central
Europe have the highest simulated peak yield and harvest
yield, on a per hectare basis Switzerland for example con-
tains areas with the highest yields in Europe. Ultimately
though, spatial area availability matters, so countries with
larger areas of grassland and unproductive arable for con-
version which are not biomass land use constrained will
have the largest aggregated yields. Figure 7 shows the
areas of highest harvest biomass projected for the seeded
hybrids, this is a small difference of yield in tonnes per
hectare but will aggregate spatially. M. sac × sin has the ad-
vantage over most areas; however, M. sin × sin appears to
be the hybrid to use in warmer drier areas. TABLE 4 Validation statistics (relating to Figure 5) for the
different sites (V1 relating to Figure 5a) and next year 2022 harvest
data at calibration sites (V2 relating to Figure 5b) (three field data
outliers removed). V1
V2
r 2 correlation coef
0.67
0.68
Root mean square error
27.2
12.65
Mean difference
−0.2
0.004
Relative error
−2.2
0.03
Maximum error
4.1
3.0
No. | 11 The two validations were
done at different times, first using 2021 measured harvest
data from other field sites' (SCH site near Amsterdam,
CHV site near Paris and a Piacenza second site PAC2)
and second after the 2022 harvests, data from the same
sites as the calibration were used, shown in Figure 5a,b,
respectively. Figure 5a displays the validation data (in
green) and also calibrations (in black) for various hybrids, For the best (logistic) photosynthetic simulation of bio-
mass, we determined that the core photosynthesis proce-
dure is to substitute Equation (5) into Equation (1), where
RUE is 2.35 g MJ−1. Fraction of light interception is by the applicable Creative Commons License (5)
theta1 + ((theta2 −theta1)∕(1 + exp(DDcum −theta3)∕theta4)) (5)
)) where the parameters for the different hybrids are listed in
Table 5. where the parameters for the different hybrids are listed in
Table 5. 12 | SHEPHERD et al. sac × sin for mean
annual harvest biomass (t ha−1 year−1)
over 2020–2030 for Europe. M. sac × sin,
Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. FIGURE 8
Standard deviation
of annual harvest dry matter biomass
for Europe 2020–2030 (simulated
using seed-propagated M. sac × sin
potential). M. sac × sin, Miscanthus
sacchariflorus × sinensis. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Lib 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are g SHEPHERD et al. | 13 13 FIGURE 7
Spatial distribution
of highest yielding seeded hybrids M. sin × sin hybrid and M. sac × sin for mean
annual harvest biomass (t ha−1 year−1)
over 2020–2030 for Europe. M. sac × sin,
Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. m/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-co FIGURE 8
Standard deviation
of annual harvest dry matter biomass
for Europe 2020–2030 (simulated
using seed-propagated M. sac × sin
potential). M. sac × sin, Miscanthus
sacchariflorus × sinensis. FIGURE 8
Standard deviation
of annual harvest dry matter biomass
for Europe 2020–2030 (simulated
using seed-propagated M. sac × sin
potential). M. sac × sin, Miscanthus
sacchariflorus × sinensis. the other hybrids only flowered at the Zagreb latitude. The
OPTIMISC miscanthus field trial found little evidence
of spread of Miscanthus by seed fertile flowering hybrids
(Kalinina et al., 2017), because volunteer seedlings rarely
establish and successfully overwinter (Hastings et al., 2017),
breeding of sterile triploid seeded hybrids which eliminate
invasive risk remains a long-term goal for Miscanthus breed-
ers. Breeding for late or absent flowering reduces invasive
risk because plants fail to produce seed before winter frosts
(Hastings et al., 2017). Creeping rhizomes have been ob-
served in several M. sacchariflorus genotypes, it is therefore
recommended to exclude creeping genotypes from commer-
cialization to avoid the problem (Lewandowski et al., 2016). which are, in turn, related to variance in soil type and cli-
mate. 4 | DISCUSSION 4 Athena, Aphrodite and M × g have the same genetic back-
ground but the difference is in the origin of the parent ma-
terial for these hybrids. Germplasm collected from Asia
(303 accessions of M. sinensis, M. sacchariflorus, M. floridu-
lus, collected from 158 diverse locations with varied agro-
nomic traits) has been used in the Defra-BBSRC supported of values
10
11 Higher uncertainty in yield (Figure 8) has been shown
to be due to higher water deficits (Shepherd et al., 2021) theta1
theta2
theta3
theta4
M. × sinensis
1
0
1000
149.287
M. × giganteus
0.96
0.096
1120.14
190.779
Seeded M. sac × sin ‘Aphrodite’—all site
calibration
0.95
0.095
1114.45
177.901
Seeded M. sac × sin ‘Aphrodite’ potential—
best site calibration
0.95
0.095
925.33
85.702
Rhizome M. sac × sin ‘Athena’
0.95
0.095
986.769
103.178
TABLE 5 Light interception
parameters for hybrids. FIGURE 6 (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–2030 for Europe (simulated using growth calibrated
for seed-propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin,
Miscanthus sinensis × sinensis. TABLE 5 Light interception
parameters for hybrids. theta1
theta2
theta3
theta4
M. × sinensis
1
0
1000
149.287
M. × giganteus
0.96
0.096
1120.14
190.779
Seeded M. sac × sin ‘Aphrodite’—all site
calibration
0.95
0.095
1114.45
177.901
Seeded M. sac × sin ‘Aphrodite’ potential—
best site calibration
0.95
0.095
925.33
85.702
Rhizome M. sac × sin ‘Athena’
0.95
0.095
986.769
103.178 wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License FIGURE 6 (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–2030 for Europe (simulated using growth calibrated
for seed-propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin,
Miscanthus sinensis × sinensis. FIGURE 6 (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–2030 for Europe (simulated using growth calibrated
for seed-propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin,
Miscanthus sinensis × sinensis. FIGURE 6 (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–2030 for Europe (simulated using growth calibrated
for seed-propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin,
Miscanthus sinensis × sinensis. | 13
SHEPHERD et al. FIGURE 7
Spatial distribution
of highest yielding seeded hybrids M. sin × sin hybrid and M. Uncertainty in rapidly scaling-up biomass energy
supply, especially in dry climates and in regions where fu-
ture climate change could result in drier conditions, has
important policy implications in bioenergy effectiveness
for lowering atmospheric carbon (Littleton et al., 2022). Despite different climate and soil datasets, the uncertainty
we obtained for European biomass projections is of the
same range and spatial distribution as obtained in Hastings,
Clifton-Brown, Wattenbach, Mitchell, and Smith (2009). The European aggregated mean annual totals for bio-
mass (Table 6) show a European capacity to produce nearly
90 Mt year−1 of miscanthus harvest yield from the conver-
sion of 10% of less productive grassland and 10% of less
productive arable land. This would provide 1.34 EJ year−1
energy in electricity generation and a carbon capture po-
tential (CCS) of 40 Mt year−1. FIGURE 7
Spatial distribution
of highest yielding seeded hybrids M.
sin × sin hybrid and M. sac × sin for mean
annual harvest biomass (t ha−1 year−1)
over 2020–2030 for Europe. M. sac × sin,
Miscanthus sacchariflorus × sinensis; M.
sin × sin, Miscanthus sinensis × sinensis. 4 | SHEPHERD et al. 14 TABLE 6 European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate
period 2020–2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt
year−1 (SD)
Electrical energy
produced EJ year−1
Carbon capture
Mt year−1
M. × sin × sin
87.19 (0.051)
1.30
39.24
M × g
81.28 (0.048)
1.20
36.57 TABLE 6 European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate
period 2020–2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt
year−1 (SD)
Electrical energy
produced EJ year−1
Carbon capture
Mt year−1
M. × sin × sin
87.19 (0.051)
1.30
39.24
M × g
81.28 (0.048)
1.20
36.57
Seeded M. sac × sin ‘Aphrodite’—all site calibration
80.72 (0.047)
1.20
36.32
Seeded M. sac × sin ‘Aphrodite’ potential—best site calibration
89.66 (0.052)
1.34
40.36
Rhizome M. sac × sin ‘Athena’
89.66 (0.052)
1.34
40.35
Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. The calibrations were based on field trials grown on less
productive land, where the definition of environmental re-
striction on growth is in keeping with the use of lower-grade
arable land and grassland conversion to growing biomass. Climate projections from the RCP2.6 climate scenario have
been used, assuming a 2°C or lower global temperature in-
crease and associated bioenergy land use change which as-
sumes biomass crops for bioenergy with CCS being rolled
out at scale in the next 10–20 years (Littleton et al., 2022). GIANT project, a European miscanthus breeding program
(Huang et al., 2019). Various diploid M. sinensis and tetra-
ploid M. sacchariflorus were collected that could be used as
parents to breed high-yielding sterile triploid hybrids to ad-
dress potential concern about plant invasiveness. Field tri-
als in Europe with miscanthus over the past 25 years have
demonstrated that interspecies hybrids such as M × g com-
bine high yield potentials and low inputs in a wide range of
soils and climates (Clifton-Brown et al., 2017). Despite the
main current commercial hybrids, M. sac × sin and M × g,
having similar parent material, they have different phe-
nological characteristics. For example, different charac-
teristics being the late ripening of M. 4 | sac × sin (seeded and
rhizome), and M × g having intermediate flowering and se-
nescence when compared (Magenau et al., 2022). y
All hybrids use the same climate, soil and land use da-
tabases, the only differences are from the biomass calibra-
tions from field trials. Seeded M. sin × sin and rhizome M. sac × sin European harvest potential show promise to out-
perform the current commercial crop M × g. Seeded M. sin × sin is planted at double density and therefore being
seed-propagated requires more plugs than the M. sac × sin
and rhizome-propagated plants. It was planted at the
recommended rate advised by its developer; however, in-
creasing the density of M. sin × sin hybrids has previously
not increased the yield (Ouattara et al., 2020). This is the
shortest hybrid and height has a much stronger effect on
yield than stem count (Awty-Carroll et al., 2022; Davey,
Robson, et al., 2017) but increasing density could result in
lower yields in the longer term due to overcrowding (in-
terplant competition). Rhizome M. sac × sin will have the
same problem as M × g of slower propagation and avail-
ability. Meanwhile, seeded M. sac × sin based on a calibra-
tion of poorly and well-established crops performed a little
lower than the current commercial crop, but its potential
based on well-established plants, already mature at third
year in a warmer climate, outperforms most miscanthus
hybrids and shows the same yield potential as rhizome M. sac × sin (the rhizome version was well established, sup-
porting what could be expected of the seeded version). The methods chosen demonstrate that simply reduc-
ing RUE by a constant rate through the season does not
work since RUE is not constant; being influenced greatly
by environmental conditions, it is different between sites. Thus, a more seasonally dynamic process is required and
one based on the phenological characteristics of a hybrid
while reducing the variation from the climate of each field
site is required to determine a relationship related to RUE
which is common to all sites. 4 | The aim was to parameterize a model in a way that will
work for any hybrid; therefore, a modelling process was
found which will suit all hybrids at all sites, retain a stan-
dardized model coding and processes and change only the
crop parameter file rather than change the way that photo-
synthesis is represented in the model code for each hybrid. Since for this projects we had measured values of light
interception, we extracted a direct relationship with cumu-
lative degree days, therefore bypassing a previous calcula-
tion for leaf area in the model, and that a single relationships
could be used for each hybrid that was applicable at each
site. This simplified the model and avoided using environ-
mental influences in the algorithm (temperature, water and
light), although their direct effects were reflected in estab-
lishment levels of the plant, canopy closure and light inter-
ception, but not as a variable within the 2-week measuring
frequency as was required for predicting measured RUE. 3.4.1 | A note on invasiveness The M. sin × sin hybrid was the only hybrid to reach flow-
ering at all four locations (Magenau et al., 2022); however, 14 |
SHEPHERD et al. TABLE 6 European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate
period 2020–2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt
year−1 (SD)
Electrical energy
produced EJ year−1
Carbon capture
Mt year−1
M. × sin × sin
87.19 (0.051)
1.30
39.24
M × g
81.28 (0.048)
1.20
36.57
Seeded M. sac × sin ‘Aphrodite’—all site calibration
80.72 (0.047)
1.20
36.32
Seeded M. sac × sin ‘Aphrodite’ potential—best site calibration
89.66 (0.052)
1.34
40.36
Rhizome M. sac × sin ‘Athena’
89.66 (0.052)
1.34
40.35
Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. 14 |
SHEPHERD et al. TABLE 6 European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate
period 2020–2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt
year−1 (SD)
Electrical energy
produced EJ year−1
Carbon capture
Mt year−1
M. × sin × sin
87.19 (0.051)
1.30
39.24
M × g
81.28 (0.048)
1.20
36.57
Seeded M. sac × sin ‘Aphrodite’—all site calibration
80.72 (0.047)
1.20
36.32
Seeded M. sac × sin ‘Aphrodite’ potential—best site calibration
89.66 (0.052)
1.34
40.36
Rhizome M. sac × sin ‘Athena’
89.66 (0.052)
1.34
40.35
Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. If it were also possible to link onto
other projects such as the PBC4GGR, carbon fluxes will
be combined with similar measurements to this study to
understand the dynamics of RUE, which could provide
further information on the dynamics of photosynthesis
and respiration. Nevertheless, to see the limitations is not to downplay
the successes of the field trials and the modelling. The
GRACE project field trials developed phenological proto-
cols and trained international teams to collect data that
can used to assess light interception and conversion and is
a particular benefit of European projects. The modelling
found generic equations for light interception dynamics
with thermal time despite the different site conditions. In summary, the benefit of applying a relationship be-
tween light interception measurement and degree days
is that it is dynamic through the season, reduces uncer-
tainty, is easier to measure in the field, and for calibra-
tion standardizes weather variation between field sites,
with differences being largely phenotypic based. Using
light interception-degree day curves includes variation
between hybrids in phenological timing. Calibrating data
against standing crop biomass includes different rates of
leaf litter drop between hybrids. A conservative model, calibrated by crops of varying
establishment and varying maturity, accompanied by out-
put resulting from a calibration showing the potential of
a well-established mature crop, is a more realistic predic-
tor of a variable landscape when spatial aggregations are
required. It is projected that 10% land use conversion of
less productive grassland and arable with seeded hybrids
could provide 1.3 exajoule of power annually in Europe,
where 1 exajoule is equivalent to 174 million barrels of oil
(Koppelaar, 2012). Less productive land in temperate climates and time
to maturity are linked, with crops establishing slower
and take longer to maturity, for example. at TWS 4–5 year
is required for full establishment of miscanthus (pers. comm. Professor John Clifton-Brown). Thus, a longer
funded period for the project measurements would have
been desirable with a five growing season project. A com-
mon assumption in modelling is that crops are mature,
when in reality aggregating spatial yield in the landscape
includes crops at varying age and yield potential and
therefore lowers the accumulated total, which is why a
conservative projection is a realistic predictor. on meta-analysis work in the United States, Sharma
et al. (2022) show, M × g yield increases at a decreasing
rate till the seventh year, beyond which, yield starts de-
creasing at an increasing rate. However, work in the UK
by Shepherd, Clifton-Brown, et al. (2020) shows M × g
yields to continue increasing at a decreasing rate to
10 years and beyond with expanding rhizome and infilling
of crop stems. Regarding the 2-week sampling frequency
of the crop biomass and light interception measurements,
frequency is limited by manpower but nuanced details
can be lost easily especially at the temporal resolution
of 2-weekly biomass. It is however important to keep in
mind the novelty of this project and the scale and coor-
dination across several European sites and field teams to
achieve simultaneous sampling across the season was an
ambitious undertaking. The development of miscanthus
varies by climate zone. Third-year miscanthus will be ma-
ture in southern Europe while still developing in temper-
ate latitudes. This means that we are inevitably dealing
with a varying development of crops that we calibrate over
Europe locations and climate zones, and also dealing with
a variation of crop establishment level. The standard de-
viation map of simulated harvest yield will also show a
high variability in areas prone to higher soil water deficit
and variable soil types and quality. This is a project to de-
termine the potential for miscanthus on less productive
lands, calibrations from field measurements will produce
projections of yields lower than the those obtained on
prime arable land. However, on prime land best agro-
nomic practices are applied for the current commercial
cultivar of miscanthus, these field measurements and
projections are ambitious, newly developed and best agro-
nomic practices have yet to be developed. Ongoing work
is needed to develop agronomic methods for the best es-
tablishment and least risk to the seeded hybrids, since this
holds potential for improved yield over the current com-
mercial crop plus improved plant upscaling. Agronomy
for seeded M. sac × sin is currently being investigated in
the UK by the Perennial Biomass Crops 4 Greenhouse Gas
Reduction (PBC4GGR) project. The next steps could be to repeat the measurements a
later year in a follow on project, using the same plus ad-
ditional locations. This is particularly important regard-
ing plant maturity. 4.1 | Model and measurement limits and
next steps These calibrations result in conservative model estimates
based on third-year field trial measurements. Based SHEPHERD et al. 15 on meta-analysis work in the United States, Sharma
et al. (2022) show, M × g yield increases at a decreasing
rate till the seventh year, beyond which, yield starts de-
creasing at an increasing rate. However, work in the UK
by Shepherd, Clifton-Brown, et al. (2020) shows M × g
yields to continue increasing at a decreasing rate to
10 years and beyond with expanding rhizome and infilling
of crop stems. Regarding the 2-week sampling frequency
of the crop biomass and light interception measurements,
frequency is limited by manpower but nuanced details
can be lost easily especially at the temporal resolution
of 2-weekly biomass. It is however important to keep in
mind the novelty of this project and the scale and coor-
dination across several European sites and field teams to
achieve simultaneous sampling across the season was an
ambitious undertaking. The development of miscanthus
varies by climate zone. Third-year miscanthus will be ma-
ture in southern Europe while still developing in temper-
ate latitudes. This means that we are inevitably dealing
with a varying development of crops that we calibrate over
Europe locations and climate zones, and also dealing with
a variation of crop establishment level. The standard de-
viation map of simulated harvest yield will also show a
high variability in areas prone to higher soil water deficit
and variable soil types and quality. This is a project to de-
termine the potential for miscanthus on less productive
lands, calibrations from field measurements will produce
projections of yields lower than the those obtained on
prime arable land. However, on prime land best agro-
nomic practices are applied for the current commercial
cultivar of miscanthus, these field measurements and
projections are ambitious, newly developed and best agro-
nomic practices have yet to be developed. Ongoing work
is needed to develop agronomic methods for the best es-
tablishment and least risk to the seeded hybrids, since this
holds potential for improved yield over the current com-
mercial crop plus improved plant upscaling. Agronomy
for seeded M. sac × sin is currently being investigated in
the UK by the Perennial Biomass Crops 4 Greenhouse Gas
Reduction (PBC4GGR) project. Less productive land in temperate climates and time the spatial limit of the databases and the components of
the land mask do not allow us to view variation between
fields, maps only allow for regional viewing at a 1 km
resolution. 1707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and impact of centralized versus distributed BECCS with domestic
biomass production in Great Britain. GCB Bioenergy, 11, 1234–
1252. https://doi.org/10.1111/gcbb.12630 doi.org/10.1111/gcbb.13026 Buettner, G. (2014). CORINE land cover and land cover change
products. In I. Manakos & M. Braun (Eds.), Land use and land
cover mapping in Europe: Practices & trends. Remote sensing
and digital image processing (pp. 55–74). Springer. Christian, D. G., Riche, A. B., & Yates, N. E. (2008). Growth, yield
and mineral content of Miscanthus × giganteus grown as a bio-
fuel for 14 successive harvests. Industrial Crops and Products, Clifton-Brown, J., Harfouche, A., Casler, M. D., Dylan Jones, H.,
Macalpine, W. J., Murphy-Bokern, D., Smart, L. B., Adler, A.,
Ashman, C., Awty-Carroll, D., Bastien, C., Bopper, S., Botnari,
V., Brancourt-Hulmel, M., Chen, Z., Clark, L. V., Cosentino,
S., Dalton, S., Davey, C., … Lewandowski, I. (2019). Breeding
progress and preparedness for mass-scale deployment of pe-
rennial lignocellulosic biomass crops switchgrass, miscanthus,
willow and poplar. GCB Bioenergy, 11, 118–151. https://doi. org/10.1111/gcbb.12566 Clifton-Brown, J., Harfouche, A., Casler, M. D., Dylan Jones, H.,
Macalpine, W. J., Murphy-Bokern, D., Smart, L. B., Adler, A., ORCID Anita Shepherd
https://orcid.org/0000-0003-1902-5147
Danny Awty-Carroll
https://orcid. org/0000-0001-5855-0775
Chris Ashman
https://orcid.org/0000-0001-5736-6327
Elena Magenau
https://orcid.org/0000-0003-3859-9402
Mislav Kontek
https://orcid.org/0000-0001-9042-5499
Andrea Ferrarini
https://orcid. org/0000-0001-9390-7004
Mohamad Al Hassan
https://orcid. org/0000-0002-2297-3394
Jon McCalmont
https://orcid.org/0000-0002-5978-9574
Luisa Trindade
https://orcid.org/0000-0003-1541-2094
Rebecca Rowe
https://orcid.org/0000-0002-7554-821X
Andreas Kiesel
https://orcid.org/0000-0003-0806-2532
John Clifton-Brown
https://orcid. org/0000-0001-6477-5452 Anita Shepherd
https://orcid.org/0000-0003-1902-5147
Danny Awty-Carroll
https://orcid. org/0000-0001-5855-0775
Chris Ashman
https://orcid.org/0000-0001-5736-6327
Elena Magenau
https://orcid.org/0000-0003-3859-9402
Mislav Kontek
https://orcid.org/0000-0001-9042-5499
Andrea Ferrarini
https://orcid. org/0000-0001-9390-7004
Mohamad Al Hassan
https://orcid. org/0000-0002-2297-3394
Jon McCalmont
https://orcid.org/0000-0002-5978-9574
Luisa Trindade
https://orcid.org/0000-0003-1541-2094
Rebecca Rowe
https://orcid.org/0000-0002-7554-821X
Andreas Kiesel
https://orcid.org/0000-0003-0806-2532
John Clifton-Brown
https://orcid. org/0000-0001-6477-5452
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//
id
/0000 0001 9863 7613 Clifton-Brown, J. C., Neilson, B., Lewandowski, I., & Jones, M. B. (2000). The modelled productivity of Miscanthus × giganteus (Greef et
Deu.) in Ireland. Industrial Crops and Products, 12, 97–109. Clifton-Brown, J. C., Stampfl, P. F., & Jones, M. B. (2004). Miscanthus
biomass production for energy in Europe and its potential con-
tribution to decreasing fossil fuel carbon emissions. Global
Change Biology, 10, 509–518. Davey, C. L., Jones, L. E., Squance, M., Purdy, S. J., Maddison, A. L.,
Cunniff, J., Donnison, I., & Clifton-Brown, J. (2017). Radiation
capture and conversion efficiencies of Miscanthus sacchariflo-
rus, M. sinensis and their naturally occurring hybrid M. × gi-
ganteus. GCB Bioenergy, 9, 385–399. https://doi.org/10.1111/
gcbb.12331 Astley Hastings
https://orcid.org/0000-0001-9863-7613 Davey, C. L., Robson, P., Hawkins, S., Farrar, K., Clifton-Brown, J. C.,
Donnison, I. S., & Slavov, G. T. (2017). Genetic relationships be-
tween spring emergence, canopy phenology, and biomass yield
increase the accuracy of genomic prediction in Miscanthus. Journal of Experimental Botany, 68(18), 5093–5102. https://doi. /10 1093/j b/
339 DATA AVAILABILITY STATEMENT The data that support the findings of this study are avail-
able from the corresponding author upon reasonable
request. Clifton-Brown, J., Hastings, A., Mos, M., McCalmont, J. P., Ashman,
C., Awty-Carroll, D., Cerazy, J., Chiang, Y.-C., Cosentino, S.,
Cracroft-Eley, W., Scurlock, J., Donnison, I. S., Glover, C.,
Gołąb, I., Greef, J. M., Gwyn, J., Harding, G., Hayes, C., Helios,
W., … Flavell, R. (2017). Progress in upscaling Miscanthus bio-
mass production for the European bio-economy with seed-
based hybrids. GCB Bioenergy, 9, 6–17. https://doi.org/10.1111/
gcbb.12357 CONFLICT OF INTEREST The authors have no conflicts of interest to declare. The authors have no conflicts of interest to declare. ACKNOWLEDGEMENTS We would like to thank the industry partner Terravesta,
developers of Miscanthus throughout the UK, the Dutch
company Van Dinter Semo, developers of M. sin × sin
hybrids, and all collaborators and the members of the
GRACE project funded by the Bio-based Industries Joint
Undertaking, grant agreement no. 745012. The authors
thank EPSRC, BBSRC and UK Supergen Bioenergy Hub
(EP/S000771/1) who funded and supported this research. The work was made possible by a Supergen Bioenergy
hub fellowship, funding ref. RG15855—UKRI (EPSRC)
via Aston University and the survey was carried out as
part of project SUMMER—seed-propagated upscaling of
Miscanthus—modelling and environmental response. This work was also made possible by BBSRC funding
(BB/V011553/1) for the Perennial Biomass Crops for
Greenhouse Gas Removal (PBC4GGR) Demonstrator pro-
ject, and was also undertaken as part of the UK Energy
Research Centre research programme. Funded by the UK
Research and Innovation Energy Programme under grant
number EP/S029575/1. Anderson, E., Arundale, R., Maughan, M., Oladeinde, A., Wycislo,
A., & Voigt, T. (2011). Growth and agronomy of Miscanthus
× giganteus for biomass production. Biofuels, 2(2), 167–183. https://doi.org/10.4155/bfs.10.80 Awty-Carroll, D., Al Hassan, M., Ashman, C., Magenau, E.,
Martani, E., Kontek, M., van der Pluijm, P., de Maupeou, E. ,
McCalmont, J., Davey, C., van der Cruijsen, K., Jurišić , V.,
Amaducci, S., Lamy, I., Kam, J., Hoogendam, A., Dolstra, O.,
Ferrarini, A., Lewandowski, I., … Clifton-Brown, J. (2022). Establishment and yield performance over three years of four-
teen inter- and intra-species Miscanthus hybrids planted using
novel agronomies at 7 European sites. GCB Bioenergy. https://
doi.org/10.1111/gcbb.13026 Finally, re-
garding limitations for viewing the European projections, Future work should be to establish the best agronomy
practise to establish biomass crops on less productive
land, investigate their low carbon footprint with land use
change to biomass crops and ability to sequester carbon
on less productive soils. Unlike wind or solar power production, energy from
biomass does not have a reduction dependent on weather
or season. At the time of writing, when Europe is strug-
gling to source energy, seed-propagated hybrids of mis-
canthus offer a substantial alternative source of energy
from hybrids with an increase in production availability
over traditional rhizome hybrids. 16 SHEPHERD et al. 16 Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Con Lovett, A., Sünnenberg, G., & Dockerty, T. (2014). The availability of
land for perennial energy crops in Great Britain. GCB Bioenergy,
6, 99–107. https://doi.org/10.1111/gcbb.12147 6, 99–107. https://doi.org/10.1111/gcbb.12147 Hastings, A., Clifton-Brown, J., Wattenbach, M., Mitchell, C. P., & Smith, P. (2009). The development of MISCANFOR,
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https://openalex.org/W2805063276 | https://hal-amu.archives-ouvertes.fr/hal-02143617/file/s41598-018-23549-2.pdf | English | null | The Cish SH2 domain is essential for PLC-γ1 regulation in TCR stimulated CD8+ T cells | Scientific reports | 2,018 | cc-by | 8,318 | To cite this version: Geoffrey Guittard, Ana Dios-Esponera, Douglas C. Palmer, Itoro Akpan, Valarie A. Barr, et al.. The Cish SH2 domain is essential for PLC-gamma 1 regulation in TCR stimulated CD8(+) T cells. Scientific Reports, 2018, 8 (5336), 10.1038/s41598-018-23549-2. hal-02143617 Distributed under a Creative Commons Attribution 4.0 International License The Cish SH2 domain is essential
for PLC-γ1 regulation in TCR
stimulated CD8+ T cells Geoffrey Guittard1,3, Ana Dios-Esponera1, Douglas C. Palmer2, Itoro Akpan1, Valarie A. Barr
Asit Manna1, Nicholas P. Restifo2 & Lawrence E. Samelson1 Geoffrey Guittard1,3, Ana Dios-Esponera1, Douglas C. Palmer2, Itoro Akpan1, Valarie A. Barr1,
Asit Manna1, Nicholas P. Restifo2 & Lawrence E. Samelson1 Received: 23 November 2017
Accepted: 6 March 2018
Published: xx xx xxxx Cish, participates within a multi-molecular E3 ubiquitin ligase complex, which ubiquitinates target
proteins. It has an inhibitory effect on T cell activation mediated by PLC-γ1 regulation, and it functions
as a potent checkpoint in CD8+ T cell tumor immunotherapy. To study the structural and functional
relationships between Cish and PLC-γ1 during CD8+ T cell activation, we tested mutants of the Cish-SH2
(R107K) and D/BC (L222Q, C226Q) domains. We confirmed that Cish-SH2-specific binding was essential
for PLC-γ1 ubiquitination and degradation. This domain was essential for the Cish-mediated inhibition
of Ca2+ release upon TCR stimulation. No effect on inhibition of cytokine release was observed with
SH2 or D/BC mutants, although the absence of Cish led to an increased release of IFN-γ and TNF-α. Using imaging we showed that Cish was expressed mostly in the cytoplasm and we did not see any
Cish clustering at the plasma membrane upon stimulation. We conclude that the Cish-SH2 domain is
essential for PLC-γ1 regulation in TCR-stimulated CD8+ T cells. Cish (cytokine-inducible SH2 containing protein) belongs to the SOCS (Suppressor of Cytokine signaling) fam-
ily of E3-ligases. Emerging evidence indicates that SOCS family members can play critical roles in both innate
and adaptive immune responses by mediating negative-feedback inhibition of cytokine signaling1. Lack of Cish
expression in cytotoxic CD8+ T cells and NK cells improves their anti-tumor properties2–4. Understanding the
precise molecular mechanisms for Cish function is thus of great interest and might suggest possibilities for new
targeted cancer therapies. g
p
We previously observed that Cish is expressed following T cell antigen receptor (TCR) stimulation2. We also
showed that Cish is involved in negative regulation of TCR signaling. Cish can bind PLC-γ1 constitutively and
negatively regulates its phosphorylation and activation. This interaction leads to PLC-γ1 ubiquitination and sub-
sequent degradation. Thus our data identified Cish as a new key negative regulator of TCR signaling and immune
function2.h There are eight SOCS family members, SOCS1–7 and Cish. HAL Id: hal-02143617
https://amu.hal.science/hal-02143617v1
Submitted on 28 Nov 2019 L’archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d’enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés. HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License www.nature.com/scientificreports www.nature.com/scientificreports Received: 23 November 2017
Accepted: 6 March 2018
Published: xx xx xxxx Materials and Methods Cells and culture. 293 T Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supple-
mented with 10% fetal bovine serum, and 1% penicillin-streptomycin. Cells were incubated at 37 °C in 5% CO2. E6-1 Jurkat cell lines were cultured in RPMI supplemented with 10% fetal bovine serum and 1%
penicillin–streptomycin. mented with 10% fetal bovine serum, and 1% penicillin streptomycin. Cells were incubated at 37 C in 5% CO2. E6-1 Jurkat cell lines were cultured in RPMI supplemented with 10% fetal bovine serum and 1%
penicillin–streptomycin. Mice. Cish−/− mice were generated and genotyped, as previously described2. Mice were housed according to
the guidelines of the Animal Care and Use Committee at the National Institutes of Health (NIH). Transfection 293 T cells. 293 T cells were transfected using a calcium-phosphate transfection method. Briefly, for transfection, 2.5 × 106 cells were plated 24 hrs prior to transfection in a 10-cm dish. On the day of
transfection, a 500 μL aqueous mixture of DNA (5 μg max per construct plus pcDNA3 empty vector, to reach
20 μg total DNA per dish) and CaCl2 (62 μl of 2M CaCl2) was added dropwise to 500 μL of 2X HBS (42 mM
HEPES, 274 mM Nacl, 10 mM KCL, 1.8 mM Na2PO4) (pH 6.95–7.00). 10 mL of fresh medium was then added to
the 293 T cells, and the HBS/DNA mixture was added dropwise to the cells. 24 hrs later the medium was replaced
with 10 mL of fresh media. Cloning. The Cish WT expression retroviral vector has already been described2 and encodes N-terminal
Flag-tagged (3×) Cish, self-cleaving furin-2A (f2A) peptide, and congenic marker Thy1.1 driven by the intrinsic
LTR promoter. We generated the SH2 domain R107K10 and the SOCS-Box D/BC (L222Q, C226Q) mutations11 in
the same backbone vector (Genesynthesis Company). Cish and Cish mutant constructs were expressed in pmTur-
quoise2-C1 (Addgene #6056012) vectors (Kind gift of Dorus Gadella). In-fusion kit from Clontech was used and
cloning was performed according to manufacturer’s instructions. Transfection of Jurkat cells, fixation and immunostaining. Jurkat T cells were transfected using
the Amaxa T-kit. Cells were allowed to spread on coverslips as described earlier13. Briefly, poly-lysine cov-
ered four-chambered glass coverslips (LabTek II, Nunc/Nalgene) were coated with 10 μg/ml of antibody
(anti-CD3-Ucht1) from BD Pharmigen (custom concentration of Catalog # 550367). Materials and Methods The chambers were loaded
with 300 μl of normal media without phenol red supplemented with 25 mM HEPES, pH 7.0, and warmed. Cells
were resuspended in the same buffer, plated into the bottom of the chamber and incubated at 37 °C. After 3 min,
cells were fixed in 2.4% paraformaldehyde for 30 min. The cells were permeabilized with TritonX-100, incubated
with blocking buffer for 30 min and then incubated with primary antibodies for 60 min, followed by washes
and 60 min incubation with either mouse isotype specific or anti-rabbit Alexa conjugated secondary antibod-
ies (ThermoFisher Grand Island NY). Primary antibodies used for immunostaining: pLAT 132 - rabbit poly-
clonal IgG from Invitrogen (Catalog # 44–224) - used at 4.38 μg/ml, pY (4G10) - mouse monoclonal IgG2B from
Millipore (Catalog # 05–321) - used at 1.1 μg/ml. Secondary antibodies used for immunostaining: Alexa Fluor 647
- goat anti mouse monoclonal IgG2B from Thermo Fisher Scientific (Catalog # A21242) - used at 4 μg/ml, Alexa
Fluor 568 - goat anti rabbit IgG from Thermo Fisher Scientific (Catalog #A11036) - used at 2 μg/ml. Imaging. Confocal imaging was performed as previously described14. Microscope images of fixed cells were
captured using a Leica SP8 laser-scanning confocal microscope using a 63×, 1.4 numerical aperture (NA) objec-
tive (Leica Microsystems Inc, Buffalo Grove IL). 2- to 3-μm z-stacks with a spacing of 0.3 μm were taken of the
area contacting the coverslip. Image processing. Leica AF software was used to produce images of fixed cells. Adobe PhotoShop and
Illustrator (Adobe Systems Inc, San Jose CA) were used to prepare composite figures. Scale bars were cut from the
original images and then were pasted in a more visible position on the final composite image. T cell transduction. Retroviral T cells transduction was performed as previously described2. Briefly, WT and
CISH KO CD8+ T-cell blasts were obtained from lymph nodes by negative selection (Mouse CD8+ T cell Isolation
Kit, STEM CELL, #19853) and activated with 2 μg/ml CD3, 2 μg/ml CD28 mAbs and 100 U IL2 for 1 day. The
virus-containing supernatant form Plat-E packaging cells was added to 24-well non-tissue culture treated plates
coated with Retronectin and anti-CD3 mAb and then centrifuged at 2500 rpm at 32 °C for 120 min. Viral particles
were removed and then T-cell blasts were added in regular medium containing IL-2. The Cish SH2 domain is essential
for PLC-γ1 regulation in TCR
stimulated CD8+ T cells Each of these proteins has a conserved struc-
ture with a central Src homology 2 (SH2) domain, an amino-terminal domain of variable length and a
carboxy-terminal 40-amino-acid module known as the SOCS box. The SOCS box interacts with several ubiq-
uitination machinery enzymes: elongin B/C, cullins, ring-box 2 (Rbx2) and an E2 ubiquitin transferase1. This
complex forms an E3 ubiquitin ligase complex. Thus SOCS proteins exert their inhibitory role by mediating
protein degradation. The central SH2 domain appears critical for binding target molecules, thereby enabling the
E2-E3 complex to ubiquitinate them5. Cish was the first identified member of the SOCS family. It was discovered
as a gene product induced in response to various cytokines (IL-2, 3, 5 and EPO) that activate STAT56,7. Cish was
shown to bind via its SH2 domain to cytokine receptors after ligand-mediated phosphorylation8,9. Cish can act as
a negative-feedback regulator of the STAT5 pathway by binding in this manner, thereby masking STAT5 docking
sites9,10. 1Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health,
Bethesda, Maryland, 20892-4256, USA. 2Surgery Branch, Center for Cancer Research, National Cancer Institute,
National Institutes of Health, 9000 Rockville Pike, Building 10/CRC, Room 3W-3840, Bethesda, MD, 20892, USA. 3Present address: INSERM, U1068, CNRS UMR7258, Aix-Marseille Université UM105, Institut Paoli-Calmettes,
Centre de Recherche en Cancérologie de Marseille, 13009, Marseille, France. Geoffrey Guittard and Ana Dios-
Esponera contributed equally to this work. Correspondence and requests for materials should be addressed to G.G. (email: geoffrey.guittard@inserm.fr) or L.E.S. (email: SamelsonL@mail.nih.gov) SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 1 www.nature.com/scientificreports/ In order to define the structural and functional relationships between Cish and PLC-γ1 during CD8+ T cell
activation, we used both SH2 domain (Cish SH2*) and D/BC SOCS box (Cish D/BC*) Cish mutants to check
for their impact on PLC-γ1 and CD8+ T cell function. Underlying our study is our desire to identify a dominant
negative mutant of Cish, which would be of great interest to understand more precisely the regulation of Cish and
might give some insight into approaches that would specifically target Cish for inhibition. www.nature.com/scientificreports/ www.nature.com/scientificreports/ material was pre-cleared with 4 μg of normal mouse IgG bound to 20 μl of Protein A/G Plus-Agarose beads (Santa
Cruz Biotechnology) for 1 hr at 4 °C. The precleared samples were incubated with 4 μg of the indicated antibody
(FLAG M2, Cish, GFP or PLC-γ1) previously conjugated to 30 μl Protein A/G Plus-Agarose beads. After incuba-
tion for 2 hr at 4 °C, the immunoprecipitates were washed three times with ice-cold lysis buffer. p
p
yf
Transduced CD8+ T cells, prior to simulation, were rested overnight in regular RPMI medium (supplemented
with 10% fetal bovine serum, 1% penicillin-streptomycin and 50 μM β-mercaptoethanol). For ubiquitination
experiments, 293 T cells were treated for 4 hrs with proteasome inhibitor MG-132 at 20 mM (Calbiochem
#474790). Samples were resolved by 10% SDS–polyacrylamide gel electrophoresis or 5% gels for ubiquitinyl-
ation experiments. Blots were incubated overnight at 4 °C with the corresponding primary antibody directed
against ZAP-70 (Cell Signaling Technology #2705), β-actin (Cell Signaling Technology #4970), CISH (Cell
Signaling Technology #8731), PLC-γ1 (Cell Signaling Technology #2822). For immunoprecipitations, PLC-γ1
(Santa Cruz Biotechnology #sc-7290), ubiquitin (Santa Cruz Biotechnology #sc-8017), or FLAG M2 (Sigma
#F3165 or anti-GFP (Roche# 11814460001) were used. GFP-HRP conjugate (Miltenyi biotec #120-002-105) and
HA−Peroxidase (Sigma #H6533-1VL) were used for Western blotting. Blots were incubated with horseradish
peroxidase–conjugated secondary antibodies (Millipore) for 1 hr at room temperature. ECL (enhanced chemi-
luminescence; SuperSignal West Pico and SuperSignal West Femto, Pierce) was used to visualize protein bands,
which were quantified with ImageJ software (NIH). Cytokine stimulation. Cultured T cells were restimulated for 6 hr with different concentrations of
anti-CD3ε (#624092, BD Pharmingen) and 2 μg/ml anti-CD28 (#553294, BD Pharmingen) with addition of
protein transport inhibitor (2 μl/ml, BD GolgiStop, #51-2092KZ, BD Biosciences). For intracellular staining,
cells were surface stained with fixed LIVE/DEAD (Molecular Probes), then fixed and permeabilized (Cytofix/
Cytoperm Plus Fixation/Permeabilization kit, BD Biosciences) to evaluate intracellular cytokine production by
flow cytometry with the following antibodies: antitumor necrosis factor-α-PE-Cy7 (1:300, #557644, eBioscience),
anti-IFN-γ-Pacific blue (1:500, #487311, eBioscience) and anti-Thy1.1-APC (1:2000, (#202526, Biolegend). Cytometry. Cytometry was performed as previously described15. Cell acquisition was performed on
FACSCalibur (Becton Dickinson, Franklin Lakes, NJ, USA) or LSRFortessa (BD Biosciences) flow cytometers. Data analysis was performed using FlowJo software (Tree Star, Inc., Ashland, OR, USA). Calcium flux measurement. www.nature.com/scientificreports/ Cells were incubated in RPMI containing 5 mM Indo-1 dye (#I1223,
Invitrogen) and 0.5 mM Probenicid (#P8761, Sigma) for 45 min at 37 °C. Cells were washed with RPMI,
re-suspended in RPMI, and incubated at 37 °C for 5 min before Ca2+ measurement. Biotinylated anti-CD3ε (5 μg/
ml) was added, and a baseline reading was taken for 30 sec before cross-linking with streptavidin (20 μg/ml). Samples were analyzed with an LSRFortessa (BD Biosciences) with a UV laser, and data were analyzed with
FlowJo software. Calcium increases were monitored as the ratio of Indo-1 (blue) and (violet) emission, and dis-
played as a function of time. Responses were quantified from three experiments using the area under curve
(AUC) function of PrismGraph. Data availability. The datasets generated during and/or analyzed during the current study are available from
the corresponding author on reasonable request. Data availability. The datasets generated during and/or analyzed during the current study are available from
he corresponding author on reasonable request. Ethical approval and informed consent. Mice used in this manuscript were maintained under
pathogen-free conditions at an American Association for the Accreditation of Laboratory Animal
Care-accredited facility. Mice were housed in accordance with the recommendations in the Guide for the Care
and Use of Laboratory Animals of the National Institutes of Health under animal study proposals approved by the
NCI-Bethesda Animal Care and Use Committee (ASP#LCMB-013). Materials and Methods After a short centrifugation,
1500 rpm for 5 min, cells were used 3 days after the transduction. Cell, stimulation, lysis, immunoprecipitation and Western blotting analysis. For stimulation of
naïve purified CD8+ T cells, cells were re-suspended in RPMI alone at 50 × 106 cells per 100 μL. CD8+ T cells
were then incubated for 15 min at 4 °C with biotinylated anti-CD3ε (10 μg/mL 2C11 BD Pharmingen #553060). Cells were washed twice in RPMI, incubated with RPMI for 5 min at 37 °C, and then stimulated for the indicated
time by adding streptavidin (20 μg/ml final concentration). After rapid centrifugation, cells were lysed at 4 °C
for 10 min in 1% NP-40 lysis buffer (50 mM Tris pH 7.4, 150 mM NaCl, 5 mM EDTA, protease inhibitor cocktail
[Roche# 11836170001], 1 mM Na3VO4, 0.1% SDS, adding 200 mM N-ethylmaleimide [NEM] for ubiquitinyla-
tion experiments). Lysates were centrifuged at 13000 rpm for 10 min at 4 °C. For immunoprecipitation, soluble SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 2 Results Cish is expressed upon TCR stimulation and regulates PLC-γ1 expression. As previously
described, the Cish protein is expressed at a very low amount at steady state and increases upon TCR stimulation2. To more precisely study Cish expression, we stimulated blast CD8+ T cells for the indicated times using increas-
ing amounts of plate-bound antibody (Fig. 1A). Interestingly, Cish expression is maximal at 4 hrs of stimulation
(Fig. 1A). Indeed, for all concentrations tested, a decrease in Cish expression is detected between 4 and 6 hrs. Using α-CD3 concentrations above 2 μg/ml does not seem to increase Cish expression. g
μg
p
We also have showed that Cish is necessary for the ubiquitination of PLC-γ1 upon TCR activation2. In order to
test the impact of Cish expression on PLC-γ1 degradation, we stimulated CD8+ T blast cells from WT or Cish KO
mice using increasing amounts of plate-bound α-CD3 for 4hrs (Fig. 1B). As expected, we observed that PLC-γ1
expression decreased in the presence of Cish expression in WT CD8+ T cells (Fig. 1B,C) or in 293 T cells trans-
fected with Cish and PLC-γ1 (Suppl. Figure 1). The expression of PLC-γ1 is higher in stimulated Cish KO CD8+
T cell compared to WT T cells, suggesting a direct effect of Cish on PLC-γ1 expression and the degradation that
is dependent on TCR stimulation. Cish SH2 and D/BC domains are essential for PLC-γ1 ubiquitination. Each SOCS protein has a con-
served structure with a central SH2 domain, an amino-terminal domain of variable length and a carboxy-terminal
40-amino-acid module that is known as the SOCS box. The central SH2 domain appears critical in binding target
molecules, enabling the E2-E3 complex to ubiquitinate them, but the structural and functional relationships
between Cish and PLC-γ1 during CD8+ T cell activation remain unknown5. To better understand the Cish
domains required for its interaction with PLC-γ1 we used mutations known to disable the SH2 domain (R107K)
or to disable the SOCS box D/BC domain (L222Q, C226Q)10,11 (Fig. 2A). Because we have previously learned SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 3 www.nature.com/scientificreports/ Figure 1. (A) and (B) Blast T cells from the indicated mice were stimulated with increasing concentration of
anti-CD3 coated antibody during the indicated time. Cell lysates were analyzed by immunoblotting for Cish,
PLC-γ1 and Zap-70 (Loading control). Numbers below the band indicate PLCγ1 expression quantification. (C) Quantification of PLC-γ1 expression from 3 experiments. Results Non-stimulated conditions represent 100% of
PLC-γ1 expression. Bars show mean + SEM out of 3 independent experiments. Statistical significance was
determined by two-tailed Student’s t test. *P ≤ 0.05. (NS = Non-stimulated). Figure 1. (A) and (B) Blast T cells from the indicated mice were stimulated with increasing concentration of
anti-CD3 coated antibody during the indicated time. Cell lysates were analyzed by immunoblotting for Cish,
PLC-γ1 and Zap-70 (Loading control). Numbers below the band indicate PLCγ1 expression quantification. (C) Quantification of PLC-γ1 expression from 3 experiments. Non-stimulated conditions represent 100% of
PLC-γ1 expression. Bars show mean + SEM out of 3 independent experiments. Statistical significance was
determined by two-tailed Student’s t test. *P ≤ 0.05. (NS = Non-stimulated). that PLC-γ1 was ubiquitinated in the presence of Cish we were able to test the effect of Cish mutant expres-
sion on PLC-γ1 ubiquitination2. Cultured 293 T cells were transfected with a vector expressing Cish WT, Cish
SH2* or Cish D/BC* and a vector expressing PLC-γ1-YFP and/or Ubiquitin-HA. We then immunoprecipitated
PLC-γ1-YFP and blotted for HA (Fig. 2B). We observed that expression of the D/BC mutant decreased PLC-γ1
ubiquitination minimally compared to expression of Cish WT. However, expression of Cish containing the SH2
mutation resulted in a major decrease in the ubiquitination of PLC-γ1 (Fig. 2B). This result is consistent with a
model whereby the SH2 domain is critically important for the ubiquitination of the targeted PLC-γ1. The Cish SH2 domain is essential for PLC-γ1 binding. To evaluate more precisely the question of how
the domains of Cish affected its physical binding to PLC-γ1, we transfected 293 T cells with vectors expressing
Cish WT, Cish SH2* or Cish D/BC* in combination with PLC-γ1-YFP. We then immunoprecipitated Cish from
these cells and blotted for GFP (PLC-γ1) (Fig. 2C). These data revealed an interaction of Cish WT and D/BC*
with PLC-γ1 but a decreased interaction between Cish SH2* and PLC-γ1 suggesting that the SH2 domain was
required for optimal interaction between Cish and PLC-γ1. q
p
γ
To study the Cish/ PLC-γ1 interaction in resting and stimulated T cells we transduced activated Cish KO
CD8+ T cells with retroviral N-terminal FLAG-tagged construct expressing Cish WT, SH2* or D/BC*. After
resting the transduced T cells we stimulated them with a α-CD3 antibody for five minutes and compared these
cells with unstimulated T cells (Fig. 2D). Results To measure the physical interactions of Cish and PLC-γ1, we immuno-
precipitated Cish using the Flag M2 antibody, performed electrophoresis and blotted for PLC-γ1. As observed in
experiments with 293 T cells, the Cish WT protein and the D/BC* mutant interacted with PLC-γ1, but we clearly
saw a decrease in PLC-γ1 binding to Cish with the SH2 mutation. We concluded that mutation of the SH2 domain
of Cish, but not a mutation to the D/BC domain diminished the ability of Cish to physically interact with PLC-γ1. The Cish SH2 domain is essential for calcium release inhibition. Once activated, PLC-γ1 hydrolyses
PtdIns (4,5)P2 to Inositol tri-phosphate (IP3) and diacylglycerol (DAG), which are responsible for intracellular
Ca2+ release and PKC activation, respectively. To evaluate the impact of CISH WT, SH2* and D/BC* expression
on calcium release from CD8+ T cells we reconstituted Cish KO CD8+ T cells with retroviruses expressing either
an N-terminal FLAG-Cish WT, or Cish with SH2* or D/BC* mutations (Fig. 3A,B). We examined the impact
of PLC-γ1–dependent changes in cytosolic Ca2+ flux upon TCR stimulation in these transduced CD8+ T cells SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 4 www.nature.com/scientificreports/ B. C. Cish
YFP
HA
YFP
250
150
150
37
150
WCL
IP
YFP
+
+ + +
+
+ + +
PLC-γ1 YFP
HA-ub
NT
Cish WT
Cish D/BC*
Cish SH2*
A. +
+ + +
PLC-γ1 YFP
NT
Cish WT
Cish D/BC*
Cish SH2*
Cish
YFP
YFP
IP
FLAG M2
WCL
Cish KO background
NT
Cish WT
Flag M2
Cish D/BC*
Flag M2
Cish SH2*
Flag M2
NS
5min
NS
5 min
NS
5min
NS
5min
CD3 10µg/ml
IP
Flag M2
WCL
PLC-γ1
Cish
PLC-γ1
Flag M2
100
37
100
37
150
150
37
D. 1
0.6 0.15
1
0.9 0.3
Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected
with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/
BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody)
was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and
YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily
set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome
inhibitor, MG-132. Results (D) Immunoprecipitation
of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and
without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected
with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/
BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody)
was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and
YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily
set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome
inhibitor, MG-132. Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell
lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value
of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. (D) Immunoprecipitation
of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and
without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. (Fig. 3A,B). As previously described, Cish KO CD8+ T cells transduced with an empty vector demonstrated an
increase in Ca2+ release when compared to cells transduced with WT (Cish WT)2. This result confirmed that
Cish WT constitutive expression was sufficient to inhibit Ca2+ release. Importantly, transduction of Cish SH2*
in Cish KO CD8+ T cells failed to decrease Ca2+ release. This finding was consistent with the data shown above
indicating the functional importance of the SH2 domain in binding PLC-γ1. Importantly, transduction of Cish
WT and Cish D/BC* constructs in Cish KO CD8+ T cells had similar effects on PLC-γ1 as indicated by the Ca2+
decrease. These observations indicate that the SH2 domain of Cish is essential for Ca2+ release inhibition, most
likely through PLC- γ1 binding. Cish SH2* and D/BC* do not impair cytokine inhibition. We already showed that Cish expression lead
to a decreased release of certain cytokines such as IFN-γ and TNF-α in CD8+ T cells2. Results Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell
lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value
of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. (D) Immunoprecipitation
of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and
without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. A. B. Cish
YFP
HA
YFP
250
150
150
37
150
WCL
IP
YFP
+
+ + +
+
+ + +
PLC-γ1 YFP
HA-ub
NT
Cish WT
Cish D/BC*
Cish SH2*
D. 1
0.6 0.15 C. Cish
YFP
37
150
WCL
+
+ + +
PLC-γ1 YFP
NT
Cish WT
Cish D/BC*
Cish SH2*
Cish
YFP
YFP
IP
FLAG M2
WCL
Cish KO background
NT
Cish WT
Flag M2
Cish D/BC*
Flag M2
Cish SH2*
Flag M2
NS
5min
NS
5 min
NS
5min
NS
5min
CD3 10µg/ml
IP
Flag M2
WCL
PLC-γ1
Cish
PLC-γ1
Flag M2
100
37
100
37
150
150
37
D. 1
0.9 0.3 D. C. Cish KO background +
+ + +
PLC-γ1 YFP
NT
Cish WT
Cish D/BC*
Cish SH2*
Cish
YFP
YFP
IP
FLAG M2
WCL
150
150
37
1
0.9 0.3 Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfecte Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected
with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/
BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody)
was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and
YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily
set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome
inhibitor, MG-132. Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell
lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value
of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. Results (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of
indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed
by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression
of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at
indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Cells were then labeled
for surface Thy1.1 and intracellular TNF-α or IFN-γ. The flow cytometry analysis of Thy1.1+ T cell populations
is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show
mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed
Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). 0.24
19.0
20.3
60.5
0
102
103
104
0
-10 2
102
103
TNF-α
Cish KO + empty 0.49
9.86
12.3
77.4
0
102
103
104
0
-10 2
102
103
0.45
7.57
10.6
81.3
0
102
103
104
0
-10 2
102
103
Cish KO + Cish D/BC*
Cish KO + Cish SH2* 0.44
8.73
12.5
78.4
0
102
103
104
0
-10 2
102
103
0
-10 2
102
103
0.45
7.57
10.6
81.3
0
102
103
104
0
-10 2
102
103
IFN-γ
Cish KO + Cish WT
Cish KO + Cish D/BC* Cish KO + Cish D/BC* D. D. Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of
indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed
by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression
of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at
indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Cells were then labeled
for surface Thy1.1 and intracellular TNF-α or IFN-γ. Results To evaluate the impact
of CISH WT, SH2* and D/BC* expression on cytokine expression, we again reconstituted Cish KO CD8+ T
cells with a retrovirus expressing N-terminal FLAG-Cish WT, SH2* or D/BC*. We then stimulated cells with
plate-bound α-CD3 and soluble α-CD28 for 6 hrs, and checked by FACS for intracellular expression of IFN-γ and
TNF-α (Fig. 3C,D). We observed a decrease in IFN-γ and TNF-α expression in Cish KO CD8+ T cells expressing
either Cish WT, Cish D/BC* or Cish SH2* constructs compared to Cish KO T cells transduced with an empty
vector (Fig. 3C,D). At low-dose of anti-CD3 stimulation (0.1 μg/ml), there was little difference in cytokine inhi-
bition between cells expressing Cish WT or Cish D/BC* for production of either cytokine. However, expression SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 5 www.nature.com/scientificreports/ p
/
C. A. Cish WT + empty
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2*
1
10
19
28
37
46
55
64
73
82
91
100
109
118
127
136
145
154
163
172
181
190
199
208
217
226
235
244
253
262
271
280
289
298
307
)
c
e
S
(
e
m
i
T
n
o
it
a
l
u
m
it
s
Indo Violet/Blue
3.5
3
2.5
2
1.5
1
0.5
0
0.24
19.0
20.3
60.5
0
102
103
104
0
-10 2
102
103
0.44
8.73
12.5
78.4
0
102
103
104
0
-10 2
102
103
0.49
9.86
12.3
77.4
0
102
103
104
0
-10 2
102
103
0.45
7.57
10.6
81.3
0
102
103
104
0
-10 2
102
103
TNF-α
IFN-γ
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2*
D. B. Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of
indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed
by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression
of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at
indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Results Cells were then labeled
for surface Thy1.1 and intracellular TNF-α or IFN-γ. The flow cytometry analysis of Thy1.1+ T cell populations
is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show
mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed
Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). C. A. Cish WT + empty
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2*
1
10
19
28
37
46
55
64
73
82
91
100
109
118
127
136
145
154
163
172
181
190
199
208
217
226
235
244
253
262
271
280
289
298
307
)
c
e
S
(
e
m
i
T
n
o
it
a
l
u
m
it
s
Indo Violet/Blue
3.5
3
2.5
2
1.5
1
0.5
0
B. A. Cish WT + empty
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2*
1
10
19
28
37
46
55
64
73
82
91
100
109
118
127
136
145
154
163
172
181
190
199
208
217
226
235
244
253
262
271
280
289
298
307
)
c
e
S
(
e
m
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it
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3.5
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B. A. B. C. 0.24
19.0
20.3
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0
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103
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102
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IFN-γ
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2* C. 0.24
19.0
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0
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103
TNF-α
IFN-γ
Cish KO + empty
Cish KO + Cish WT
Cish KO + Cish D/BC*
Cish KO + Cish SH2*
D. Figure 3. Results The flow cytometry analysis of Thy1.1+ T cell populations
is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show
mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed
Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). of the Cish SH2* resulted in TNF-α expression not statistically different than TNF-α expression with the empty
vector. The effect of the Cish SH2* protein was more restrained producing lower IFN-γ levels than cells express-
ing the empty vector, but higher levels than cells expressing either Cish WT or Cish D/BC*. Higher dose stimulus
(1 μg/ml anti-CD3) eliminated any differences of cytokine release from cells expressing the different constructs. Thus, the Cish SH2 domain is essential for binding to PLC-γ1 and this binding is important for PLC-γ1 ubiquiti-
nation and for Ca2+ inhibition. However, mutation of the Cish SH2 domain has only a subtle effect on inhibition
of cytokine release in the assays we performed. 6 SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 www.nature.com/scientificreports/ /scientificreports/
SH2 mutant
Cish Turq
PLC YFP
pY
Merged
mTurq alone
WT Cish Turq
D/BC mutant
Cish Turq
B. A. Figure 4. (A) and (B) Evaluation of PLC-γ1 and phosphotyrosine in TCR-induced microclusters after
αCD3 stimulation in Jurkat T cells transfected with empty mTurq2-C1, Cish WT-mTurq2-C1, Cish-D/BC*-
mTurq2-C1 or Cish-SH2*-mTurq2-C1 as indicated. (A) Representative confocal images from transfected
Jurkat cells dropped on to stimulatory coverslips, fixed after three minutes, immunostained for PLC-γ1 and
phosphotyrosine (pY), and the areas of the clusters were calculated (B). Statistical significance was determin
by two-tailed Student’s t test. *P ≤ 0.05, ***P ≤ 0.001. SH2 mutant
Cish Turq
PLC YFP
pY
Merged
mTurq alone
WT Cish Turq
D/BC mutant
Cish Turq
A. A. mTurq alone WT Cish Turq B. B. Figure 4. (A) and (B) Evaluation of PLC-γ1 and phosphotyrosine in TCR-induced microclusters after
αCD3 stimulation in Jurkat T cells transfected with empty mTurq2-C1, Cish WT-mTurq2-C1, Cish-D/BC*-
mTurq2-C1 or Cish-SH2*-mTurq2-C1 as indicated. (A) Representative confocal images from transfected
Jurkat cells dropped on to stimulatory coverslips, fixed after three minutes, immunostained for PLC-γ1 and
phosphotyrosine (pY), and the areas of the clusters were calculated (B). Statistical significance was determined
by two-tailed Student’s t test. *P ≤ 0.05, ***P ≤ 0.001. Cish WT or mutants construct expression is sufficient to inhibit PLC-γ1 clusters. Discussion
l Stimulation of the T cell for the calcium release is measured in seconds and minutes, while
activation for the cytokine assay is six hours. The more prolonged assay might allow sufficient function from the
Cish proteins to affect cytokine production. pf
y
p
By genetically coupling Cish to the Turquoise fluorescent protein we were able to show that Cish was
expressed predominately in the cytoplasm. We did not observe any Cish clustering at the plasma membrane or
co-localization with PLC-γ1 or any other tyrosine-phosphorylated proteins upon T cell stimulation. Any effect of
the Cish protein might thus occur prior to PLC-γ1 recruitment to microclusters or is so rapid at that site as to be
not visible in our assay. We confirmed our previous observation that the area of microclusters containing PLC-γ1
in Cish-deficient T cells decreased in the presence of Cish, whereas the absence or presence of Cish had no effect
on the area of microclusters detected using anti- phosphotyrosine antibodies. When we reconstituted the Cish
KO cells with either of the SH2 or D/BC mutations, we observed a decrease in the PLC-γ1 microcluster area as we
did with WT Cish reconstitution. As with the cytokine assay, the mutated protein likely had sufficient functional
capacity to affect clustering of the PLC-γ1 molecule. f
Immunotherapy has led to unprecedented responses in patients with advanced-stage tumors with the use of
checkpoint inhibitors and adoptive cellular therapy16,17. Additionally, T cells can be engineered to express CAR
T cell and adoptively transferred to patients18. All of these strategies target cell surface molecules to improve T
cell anti-tumor function. We propose to identify and target intracellular molecules to improve T cell anti-tumor
properties2,19. We previously showed that genetic deletion of the Cish molecule, an intracellular protein regulatory
molecule, was an efficient strategy to improve CD8+ T cell function and others have shown the importance of
Cish in NK anti-tumor properties2,3. In the current study, we performed initial structure-function studies on Cish
in an attempt to discover a region of the protein that would be essential to its inhibitory properties and that could
be targeted for immunotherapy development. Perhaps due to the complexity of Cish regulation, we were unable to
identify an appropriate dominant negative mutant of Cish that consistently inhibited Cish in all assays. Discussion
l In an earlier publication we demonstrated that following TCR-mediated T cell activation, the SOCS family mol-
ecule, Cish, binds to PLC-γ1 leading to its degradation, thus regulating early T cell signaling and its functional
consequences. The aim of our current study was to further define the structural and functional relationships
between Cish and PLC-γ1 during CD8+ T cell activation. We show here that Cish is expressed for a very short
period of time that peaks after 4 hrs of TCR stimulation. Previous data using a pulse chase assay in other cell
models showed that the Cish half-life was very short (1 hr)11. These data indicate that Cish expression is tightly
regulated in cells and especially in CD8+ T cells through an as yet unknown mechanism. To study the relationship of Cish protein structure to its function we then used mutants of the Cish SH2 and
SOCS-Box domains. We showed that SH2-specific binding was essential for the Cish-mediated PLC-γ1 ubiquit-
ination and degradation. The Cish D/BC domain mutant caused a small decrease in ubiquitination. The impact
of these mutations on CD8+ T cells functions was also tested and we showed that an intact Cish SH2 domain was
essential for full inhibition of Ca2+ release. Expression of a Cish molecule with this mutation resulted in the same
level of calcium release as was observed in Cish KO T cells without any Cish-expressing construct. Reconstitution
with Cish having a D/BC mutation did not differ from reconstitution with a WT construct in the calcium assay.ii f
In cytokine release functional assays, we reproduced our original findings that activation of Cish-deficient T
cells resulted in more cytokine release than was observed from similarly activated Cish KO cells re-constituted
with WT Cish protein. Levels of IFN-γ and TNF-α produced by the KO cells were significantly different than
that produced by the reconstituted cells. We also showed that reconstitution of the KO cells with the Cish SH2
mutant resulted in a slight increase in cytokine expression (TNF-α greater than IFN-γ) compared to the WT
while expression of the Cish D/BC mutant brought down the level of cytokine expression to that seen in cells
reconstituted with WT Cish. The difference in the results of the calcium and cytokine assays may reflect the length
of time of the assay. Discussion
l In light of
this observation, we believe that a more efficient strategy to target Cish, and perhaps other intracellular proteins
for immunotherapy, is to generate genetic deletion of the protein of interest in lymphocytes. Results In our previ-
ous study, we also observed that Cish KO CD8+ T cells, upon T cell activation, showed more PLC-γ1 recruit-
ment to microclusters as detected by phosphotyrosine content compared to WT CD8+ T cells2. However we
were unable to image Cish localization in those experiments due to the poor visualization of Cish protein using
antibody-mediated immunofluorescence2. In order to localize Cish during T cell activation we generated a chi-
meric Cish molecule by cloning Cish WT, SH2* and D/BC* constructs into a pmTurquoise2-C1 vector12. We
expressed these constructs and the empty pmTurquoise2-C1 vector in Jurkat T cells (Supplemental Fig. 2A). The
pmTurquoise2-C1 empty vector was expressed diffusely in cytoplasm and nucleus. WT Cish mTurq was seen in
the cytoplasm of both activated and unactivated cells. When transfected Jurkat cells expressing WT or mutant
Cish were activated on coverslips coated with α-CD3 for 3 min, we were unable to see differences in localization
of the Cish WT, SH2* and D/BC* constructs. No Cish constructs were found in any clusters upon activation
(Supplemental Fig. 2B). Thus Cish is expressed in the cytoplasm and not in a specific subcellular compartment of SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 7 www.nature.com/scientificreports/ the cell; it is not recruited to the plasma membrane. We also tried immunofluorescence staining of FLAG-tagged
retroviral constructs of Cish, transduced into Cish KO activated blast T CD8+ cells with anti-Cish or anti
Flag-Tag, but were unable to detect the Cish constructs (data not shown). g
g
(
)
We then co-expressed Cish WT, SH2* and D/BC* proteins in combination with PLC-γ1-YFP in Jurkat T cells
to test the effect of the various Cish constructs on microcluster formation. In this experiment, we observed fewer
PLC-γ1-YFP clusters in cells transfected with Cish WT-mTurq2 compared to cells transfected with mTurq2 and
stimulated with α-CD3 (Fig. 4A,B). This result confirms our previous results, and demonstrates that cytoplasmic
Cish-mTurq2 is functional. Unexpectedly mutation of the SH2 or D/BC domains did not reverse PLC-γ1-YFP
inhibition of cluster formation. These mutations were somewhat more efficient than Cish WT in inhibiting
PLC-γ1-YFP cluster formation. However, the size of clusters detected by anti-phosphotyrosine staining was not
affected by transfection of the various Cish constructs, demonstrating that the effect on PLC-γ1 was specific. References
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14. Barr, V. A. et al. Development of nanoscale structure in LAT-based signaling complexes. Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-23549-2.h Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-23549-2 Competing Interests: The authors declare no competing interests. Competing Interests: The authors declare no competing interests. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and
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https://openalex.org/W2050182606 | https://earth-planets-space.springeropen.com/counter/pdf/10.1186/BF03352546 | English | null | VLBI observation of narrow bandwidth signals from the spacecraft | Earth, planets and space | 2,014 | cc-by | 6,151 | 1.
Introduction the rim of the Moon, we apply very long baseline interfer-
ometry (VLBI) technique in VRAD (the differential VLBI
radio sources) mission of Japanese lunar exploration project
SELENE (SELenological and ENgineering Explorer) in ad-
dition to a conventional 2-way Doppler and newly applied
4-way Doppler measurement (e.g., Hanada et al., 2002;
Namiki et al., 1999). By measuring the difference of arriv-
ing time of the same wave front of a radio signal from the
spacecraft (s/c) at two or more separated antennas, VLBI
can precisely determine the position and the velocity of the
s/c in the direction perpendicular to LOS in contrast to the
Doppler measurement. The lunar gravity field has been investigated by Doppler
measurement for the last 40 years. Recently its global map-
ping has been done by “Clementine” (Zuber et al., 1994)
and “Lunar Prospector” (LP) (Konopliv et al., 2001). Al-
though these observations contributed to knowing the low
degree gravity field and the detail structure of the nearside,
the gravity field of the rim of the Moon was not clearly in-
vestigated like the nearside. This is because the Doppler
measurement is sensitive to the direction of the line of sight
(LOS). Over the rim of the Moon, the gravity force from
the Moon acts mainly in the direction perpendicular to LOS
and we cannot estimate the gravity field precisely only by
Doppler measurements. The internal structure, which is
conventionally derived from the gravity and the topographic
data (Bratt et al., 1985), is interesting especially for the rim
of the moon. For example, the observational fact that a crust
of the far side is older and thicker than that of the nearside
is one of the important phenomena related to the thermal
evolution of the moon, and there may be new facts under
the rim region of the Moon which give us a key to clear up
the cause of the dichotomy. In order to improve the low
order and degree components of gravity field especially for The VLBI technique has been applied to tracking of a
s/c since 1960s (e.g. Border et al., 1992; Sagdeyev et al.,
1992). These VLBI observations of the s/c were success-
ful, and recently it has been used for deep space missions
of NASA and ESA (Antreasian et al., 2002; Thornton and
Border 2003). However, a large amount of VLBI data pre-
vented the real time processing. Copy right c⃝The Society of Geomagnetism and Earth, Planetary and Space Sci-
ences (SGEPSS); The Seismological Society of Japan; The Volcanological Society
of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sci-
ences; TERRAPUB. (Received May 7, 2004; Revised October 13, 2004; Accepted October 13, 2004) (Received May 7, 2004; Revised October 13, 2004; Accepted October 13, 2004) We carried out a series of VLBI observations of Nozomi by using a dedicated narrow bandwidth VLBI system. The three carrier waves with frequency interval of 515 kHz were recorded in 3 channels of the system and
correlated by a software method. As a result of the correlation, the residual fringe phases of the main carrier
wave are obtained for every 1.3 seconds. We can also continuously track them for 100 minutes. The variation
of the residual fringe phase is +/−150 degrees. Moreover, we can derive succesively the group delay for every
100 seconds by using these three carrier waves. The RMS of the group delays is 13 nsec and its average is
well accorded with the delay determined by the range and Doppler measurements within an error of 2 nsec. Consequently, we confirmed the validity of the narrow bandwidth VLBI system, and it could be expected that
this system, in addition to range and Doppler measurements, can be applied to three-dimensional tracking of a
spacecraft and the precise gravity measurement of the Moon and the planets. Key words: VLBI, spacecraft, narrow bandwidth, group delay, SELENE. Key words: VLBI, spacecraft, narrow bandwidth, group delay, SELENE. Earth Planets Space, 56, 1041–1047, 2004 Earth Planets Space, 56, 1041–1047, 2004 VLBI observation of narrow bandwidth signals from the spacecraft Fuyuhiko Kikuchi1, Yusuke Kono2, Makoto Yoshikawa3, Mamoru Sekido4, Masafumi Ohnishi5,
Yasuhiro Murata3, Jinsong Ping6, Qinghui Liu6, Koji Matsumoto6, Kazuyoshi Asari6,
Seiitsu Tsuruta6, Hideo Hanada2, and Nobuyuki Kawano6 1Department of Astronomical Science, Graduate University for Advanced Studies,
2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan
2Division of Radio Astronomy, National Astronomical Observatory, 2-21-1 Osawa, Mitaka, Tokyo 181-8588, Japan
3Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency,
3-1-1 Yoshinodai, Sagamihara, Kanagawa 229-8510, Japan
4Kashima Space Reserch Center, National Institute of Information and Communications Technology,
893-1 Hirai, Kashima, Ibaraki 314-8510, Japan
5Fujitsu Limited, 1-9-3 Nakasen Mihama-ku, Chiba 261-8588, Japan
6Division of Radio Astronomy, National Astronomical Observatory, 2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan 6Division of Radio Astronomy, National Astronomical Observatory, 2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1042 Fig. 1. Block diagram of the narrow bandwidth receiving system. the Moon emit three carrier waves in S band and one in X
band, and differential VLBI observation between the two
sub-satellites is carried out. When we derived the fringe
phase with an accuracy of 10 degrees by using differential
VLBI, the relative position of two sub-satellites around the
moon will be decided with an accuracy of 20 cm for the
2000 km baseline (Kono et al., 2003). This accuracy will
be contributed on determination of the low degree coeffi-
cients of the spherical harmonics of the lunar gravity field
(Matsumoto et al., 2002). In association with this plan, we
have developed a narrow bandwidth sampling and recording
system for VLBI and a correlation software for processing
of the data obtained in the VRAD mission. Fig. 1. Block diagram of the narrow bandwidth receiving system. which are ajusted to the bandwidth of the S-RTP, are mixed
to the signals to compensate the phase difference between
channels in front of the video converter. Using the systems mentioned above, VLBI observations
for tracking of LP were carried out (Kono et al., 2003). In
these observations, a phase delay was estimated within an
error of a few degrees for a short period, however a group
delay could not be estimated because only one frequency
signal was used in LP. For applying VLBI to the gravity
measurement of the Moon, we must obtain the phase delay
for longer period within an error of a few degrees and deter-
mine the group delay without cycle ambiguity. In order to
confirm the performance and capability of our narrow band-
width VLBI system and analysis software, we conducted a
fringe phase tracking and group delay determination for a
few hours by VLBI observation of Japanese explorer No-
zomi, which transmitted a main carrier wave and two sub
carriers with frequencies of 515 kHz apart from that of the
main carrier. In this article, a detail of the VRAD system,
and the result of the fringe phase tracking and the group
delay measurement of Nozomi are shown. 2.
VRAD System
2.1
Back-end system where Rsc(t) is the predicted position vector of the s/c
and Rref (t) represents the position vector of the reference
station. t is the time based on the reference station, c is the
velocity of light, and τgrav is general relativistic delay. We
obtain τref (t) from an iterative procedure as follows, 2.2
Correlation software A correlation software has been also developed for this
system. The software is composed of modules of VLBI
delay estimation and cross-correlation which includes a bit-
shift, a fringe-stopping and a fractional bit correction. 2.2.1
Delay model for a s/c in finite distance
In a
conventional correlator, a geometric delay is calculated as-
suming plane waves coming from the extra galactic radio
sources. However, the assumption of the plane wave is not
valid in the case of a s/c at a finite distance from the Earth. So we modified the delay model from the plane wave to a
spherical wave to estimate the geometric delay for the s/c. In our method, the propagation times from the s/c to each
ground station are calculated directly by using the light time
equation. The propagation time from the s/c to the reference
station is expressed as follows, 2.2.1
Delay model for a s/c in finite distance
In a
conventional correlator, a geometric delay is calculated as-
suming plane waves coming from the extra galactic radio
sources. However, the assumption of the plane wave is not
valid in the case of a s/c at a finite distance from the Earth. τref (t) = | Rsc(t −τref (t)) −Rref (t)|
c
+ τgrav
(1) (1) 1.
Introduction Moreover, frequency allo-
cation of the downlink signals was not appropriate for pre-
cise group delay measurement and limited the accuracy of
angular component of the position of the s/c to several tens
to nano radians (Thornton and Border 2003). In order to de-
tect a small motion of an s/c generated by the regional grav-
itational acceleration of the Moon, multi-frequency VLBI
(MFV) was proposed (Kono et al., 2003). In MFV method,
radio transmitters on board two small sub-satellites around 1041 3.
VLBI Observation of Nozomi Nozomi is the Japanese explorer that had two swing-
bys by the earth in December 2002 and June 2003 so as
to be injected into a Mars orbit in 2004 (Yoshikawa et
al., 2001). During the period between these two swing-
bys, the onboard high gain antenna could not point to the
Earth due to some operational problems. In this period,
range and Doppler measurements could not be conducted
with sufficient SNR. To overcome this problem, the No-
zomi team of JAXA (Japan Aerospace Exploration Agency)
and the VLBI group of NICT (National Institute of In- 2.1
Back-end system We also took part in the
to 27, 2003, by using our VLBI
scopes involved in this observati
KASHIMA (KSM), and MIZUS
these telescopes are shown in Tab
Usually the differential VLBI o
and a QSO is carried out to remov
phase and propagation delay cau
sphere, and the ground systems. observation was not applied in o
long-term behavior of fringe phas
sitions well known, for example 1
were observed before and after th
calibrating the clock offset and th
t ti
X b
d i
l f
Q Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Station
Antenna diameter (m)
System noize temperature (K)
Longitude
Latitude
USUDA
64
70
138◦21′57′′E
36◦07′45′′N
KASHIMA
34
85
140◦39′36′′E
35◦57′06′′N
MIZUSAWA
10
130
141◦07′56′′E
39◦08′00′′N
MIZUSAWA
20
150
141◦07′57′′E
39◦08′01′′N Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Fig. 2. Block diagram of the correlation process of the software. formation and Communications Technology) collaborated
to determine the Nozomi orbit by using the VLBI tech-
nique. We also took part in the observation from May 13
to 27, 2003, by using our VLBI systems. The radio tele-
scopes involved in this observation were USUDA (USD),
KASHIMA (KSM), and MIZUSAWA (MZS). Details of
these telescopes are shown in Table 2. p
Usually the differential VLBI observation between an s/c
and a QSO is carried out to remove the fluctuations in fringe
phase and propagation delay caused by ionosphere, tropo-
sphere, and the ground systems. However, the switching
observation was not applied in our observation to detect a
long-term behavior of fringe phase. Several QSOs with po-
sitions well known, for example 1842+681 and 1849+670,
were observed before and after the tracking of Nozomi for
calibrating the clock offset and the clock rate between VLBI
stations. X band signals from QSOs were recorded in 4
channels of the K5 system, in which the sampling rate and
quantization were 4 MHz and 2 bit, respectively (Kondo et
al., 2002). Fig. 2. Block diagram of the correlation process of the software. from an iterative procedure in the same way as τref (t). Finally the geometric delay between the reference and the
slave station is obtained as follows, 3.1
Signals of Nozomi τgeometric(t) = τslv(t) −τref (t)
(5) Between the two swing-by events, the downlink signal
of Nozomi was either in telemetry mode or in ranging
mode. There was only one carrier wave in the teleme-
try mode. In contrast, the downlink signal consists of a
main carrier wave, two range tones, and some ambiguity
tones in the ranging mode. We observed Nozomi in rang-
ing mode to estimate the group delay. The frequency of the
main carrier wave fcarrier was 8411 MHz and those of the
two range tones were fcarrier+/−fcarrier/214 ( fcarrier/214
is about 515 kHz). The ambiguity tones with frequencies
of fcarrier+/−fcarrier/2n+14 (n = 1, 2. . .) were added ev-
ery 100 seconds for 40 seconds to solve the ambiguity of
the range tones. However, the carrier to noise ratios (C/N)
of the ambiguity tones were so weak that these tones could
not be detected. The main carrier wave and the two range
tones were separately recorded in three channels of S-RTP
station. To compensate the phase difference between these
three channels, the phase calibration signals at every 60 kHz
were mixed with the IF signals in front of the video con-
verter. (5) τgeometric(t) = τslv(t) −τref (t) 2.2.2
Correlation process
The correlation process is
made by FX mode. The signal recorded at the 1st station is
Fourier transformed for every parameter period (PP). On
the other hand, the signal recorded at the 2nd station is
bit-shifted, fringe-stopped and corrected for the fractional
bit by using the predicted geometric delay calculated from
Eq. (5). After these corrections, the signal of the 2nd station
is Fourier transformed. Finally, each Fourier component
is cross-correlated and a residual fringe phase is obtained. Block diagram of the process is shown in Fig. 2. In many
cases, the downlink signal from a s/c is a narrow bandwidth
carrier wave. So, we use only several tens of Hz around the
center frequency of the carrier wave to obtain a high SNR
in the course of calculating the residual fringe phase. 2.1
Back-end system In radio astronomical and geodetic VLBI surveys, usu-
ally wide bandwidth signals (from several MHz to GHz)
from radio stars have been recorded by a fast sampling-
rate system. This is because the signal-to-noise ratio (SNR)
and the accuracy of the group delay depend on signal band-
width. However, the wide bandwidth signals are not ef-
fective for real-time tracking of a s/c because they consume
higher power in the s/c and they need longer time to obtain a
result from the large amount of data. For these reasons, we
have developed a narrow bandwidth sampling and record-
ing system for VLBI, called S-RTP station, for an s/c VLBI
tracking. The performances of this system are listed in Ta-
ble 1 and block diagram of this system is shown in Fig. 1. After the frequency down conversion and the video con-
version of the signals by using K4 or Mark-4 systems, the
S-RTP station samples and digitizes the video signals, and
now a hard disk drive is used for recording sampled data
instead of the tape recorder in the old system. Moreover,
the phase calibration signals at every several tens of kHz, τ i+1
ref (t) =
| Rsc(t −τ i
ref (t)) −Rref (t)|
c
+ τgrav
(2)
τ 0
ref (t) = | Rsc(t) −Rref (t)|
c
+ τgrav
(3) (2) (3) τ 0
ref (t) is an initial value of τref (t). On the other hand,
the propagation time from the s/c to the slave station is
expressed as follows, τslv(t) = | Rsc(t −τref (t)) −Rslv(t −τref (t) + τslv(t))|
c
+τgrav
(4) (4) +τgrav where Rslv(t) is the position vector of the slave station and
τref (t) is given from the Eq. (1). τslv(t) can be obtained F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1043 Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Station
Antenna diameter (m)
System noize temperature (K)
Longitude
USUDA
64
70
138◦21′57′′
KASHIMA
34
85
140◦39′36′′
MIZUSAWA
10
130
141◦07′56′′
MIZUSAWA
20
150
141◦07′57′′
Fig. 2. Block diagram of the correlation process of the software. formation and Communications
to determine the Nozomi orbit
nique. 3.2
Result of correlation The difference of the ASD for three
baselines would be attributed to the difference of the param-
eters of the ground systems: system temperature, diameter
of the antenna, coherence factor, and aperture efficiency of
the antenna. The ratios of the ASD expected from the nomi-
nal value of the parameters of the ground systems are 11 for
USD-KSM/KSM-MZS, 5 for USD-KSM/MZS-USD, and 3
for MZS-USD/KSM-MZS. These values are roughly con-
sistent with Fig. 5. While τ is longer than 10 seconds for
USD-KSM and 30 seconds for KSM-MZS and MZS-USD,
the fluctuation of the atmosphere became dominant and the
ASD hardly decreased. The ASD of the residual fringe
phases caused by the atmospheric fluctuation varies from
10−12 to 10−13 according to the atmospheric condition, and
1.5 × 10−13 from Fig. 5 corresponds to the value of clear
day. In addition, the ASD for longer than 200 seconds was
not calculated. This is because the observation period of
about 6,000 seconds is not enough to obtain the ASD for
longer than 200 seconds. Fig. 3. The residual fringe phases of the main carrier wave for USD-KSM
baseline. These clock parameters were corrected before the correla-
tion of the signals from Nozomi. g
3.2.2
Estimation of residual fringe phase
The fre-
quency of the carrier waves from Nozomi changed slightly
by a few Hz in 1 PP of 1.3 seconds. So the Fourier compo-
nents of only +/−10 Hz around the center frequency of the
carrier wave were used to calculate the residual fringe phase
with a high SNR. The frequency resolution was 0.76 Hz for
1 PP. The residual fringe phases for USD-KSM baseline
calculated by using the whole recorded bandwidth and only
+/−10 Hz around the center frequency of the main carrier
wave are shown in Fig. 3. The root mean square (RMS) of
the residual fringe phase for the period of 120 seconds de-
creased from 39 to 8 degrees by this method. The averaged
SNR of the main carrier wave is about 40 for 40 seconds
integration. Moreover, we could continuously track the residual
fringe phases of the main carrier wave for most obser-
vations of all baselines, i.e. USD-KSM, KSM-MZS, and
MZS-USD. The residual fringe phases of the main carrier
waves in each baseline from 07:00:00 to 08:40:00 on May
27, 2003 in UT and the closure phases are shown in Fig. 4. 3.2
Result of correlation 3.2.1
Clock offset and clock rate
The correlation of
the signal from QSO was also carried out by the same soft-
ware. Correlation process of the QSO was similar to the
conventional method and the delay model was the same
as the Consensus model (McCarthy, 2003). As a result of
the correlation and the group delay analysis, the clock off-
set and the clock rate were estimated within an error of 20
pico seconds (psec) and of 0.001 psec/second, respectively. F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1044 -150
-100
-50
0
50
100
150
200
250
300
07:00:00
07:30:00
08:00:00
08:30:00
Residual fringe phase [degree]
2003/5/27 [UT]
USUDA-KASHIMA
KASHIMA-MIZUSAWA
MIZUSAWA-USUDA
closure phase
Fig. 4. The residual fringe phases of the main carrier wave for 3 baselines and the closure phases. USUDA-KASHIMA
KASHIMA-MIZUSAWA
MIZUSAWA-USUDA
closure phase Fig. 4. The residual fringe phases of the main carrier wave for 3 baselines and the closure phases. -250
-200
-150
-100
-50
0
50
100
07:00:00
07:01:00
07:02:00
Residual fringe phase [degree]
2003/5/27 [UT]
+/- 10Hz
100kHz
Fig. 3. The residual fringe phases of the main carrier wave for USD-KSM
baseline. The RMS of the closure phases is 3 degrees for the period
of 100 minutes when the integration time of the residual
fringe phases are 5.2 seconds. This result suggests that the
correlation by the software method has been carried out suc-
cessfully, and the intrinsic error of the residual fringe phase,
which is caused by the thermal noise of the ground systems
or the model of the software, is 3 degrees. Furthermore, the
residual fringe phase of each baseline varies with various
periods from several tens of seconds through several tens of
minutes as shown in Fig. 4. To clarify these fluctuations,
the Allan standard deviation (ASD) of the residual fringe
phases were calculated for each baseline and are shown in
Fig. 5. From Fig. 5, the ASD decreased at the rate of 1/τ
(τ is the averaging time) until τ was less than 10 seconds
for USD-KSM and 30 seconds for KSM-MZS and MZS-
USD. Consequently, the short-term variation of the resid-
ual fringe phase would be explained by the thermal noise
of the ground systems. 3.2
Result of correlation Two range tones were correlated by the same way as the
main carrier wave to carry out the group delay analysis. In contrast to the main carrier wave, we could detect the
residual fringe phase of the range tones only for the USD-
KSM baseline because their SNR was less than that of the 1045 F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 10-15
10-14
10-13
10-12
10-11
10-10
1
10
100
Allan standard deviation
Averaging time τ [second]
USUDA-KASHIMA
KASHIMA-MIZUSAWA
MIZUSAWA-USUDA
Fig. 5. The Allan standard deviations of residual fringe phases of the main
carrier wave for 3 baselines. and this result showed that the group delay is obtained with-
out cycle ambiguity of about 2 micro seconds, which is the
inverse of the frequency intervals of the three carrier waves. On the contrary, the RMS of the differences between the
geometric delays is 13 nsec. The tropospheric and the iono-
spheric fluctuations were at the order of a few nsec during
the observation period, so most of the error of the group
delay could be caused by the thermal noise in the ground
system. The SNR of the two range tones are almost half of
that of the main carrier wave, which is 19 for 40 seconds in-
tegration in average. The error of the group delay expected
from the SNR of the range tone is 12 nsec and is in con-
sistency with the RMS of the differences of the geometric
delays. The baseline length is about 200 km for USD-KSM
baseline, the precision of the angular distance of Nozomi is
3710 mas. The distance between Nozomi and the ground
station is 6 × 106 km in this observation, so the estimated
position error of Nozomi is 117 km. Moreover, it could be
expected that the accuracy of the angular distance and the
position of Nozomi would be improved to 46 mas and 1.4
km respectively, if the SNR of the range tones are as large
as the main carrier wave and the frequency intervals are 20
MHz. Fig. 5. The Allan standard deviations of residual fringe phases of the main
carrier wave for 3 baselines. main carrier wave. Moreover, the transmission of Nozomi
in ranging mode was divided into 2 modes, A and B. 4.
Discussion As mentioned in the previous section, we can continu-
ously track the residual fringe phase of the main carrier
wave for 100 minutes and obtain the group delay of the
three carrier waves without cycle ambiguity. These results
confirm the validity of the narrow bandwidth hardware and
software VLBI systems. In this section, we suppose the fea-
sibility of the VRAD mission of SELENE from the result of
Nozomi considering the C/N of each observation. 3.2.3
Estimation of group delay
Before analyzing
the group delay, the phase difference of the separate chan-
nels obtained from the phase calibrator signals has to be
removed from the residual fringe phase as follows, g
The three carrier waves in S-band whose frequency inter-
vals are 6 MHz and 75 MHz will be received to obtain the
precise group delay on differential VLBI observation of two
sub-satellites in VRAD. In order to obtain the group delay
without the cycle ambiguity, the phase error of the residual
fringe phases of these carrier waves are required to be less
than 10 degrees between the switching period of 120 sec-
onds. In the case of the main carrier wave of Nozomi for
the baseline of USD-KSM, the C/N is 6 and the RMS of the
residual fringe phases of every 1 PP of 1.3 seconds during
120 seconds is 8 degrees. In contrast, the specification of
the C/N of the carrier waves in VRAD is 3.5, and the phase
error is expected to be 14 degrees for 1 PP of 1.3 second
in VRAD because the phase error would be proportional to
the inverse of the C/N. This phase error would be improved
by the square root of the integration period. By integrating
the residual fringe phases for 3 PP, the phase error would
be reduced to 6 degrees and the requirement of 10 degrees
in VRAD would be achieved. This result suggests that the
group delay of the three carrier waves would be obtained
without cycle ambiguity and the small acceleration of the
sub-satellite caused by the gravity field of the Moon will be
detected from the geometric delay. δφ′
i = δφi −(φref
pcal,i −φslv
pcal,i), (i = 1, 2, 3)
(6) (6) where δφi is the residual fringe phase of ith channel and
φref
pcal,i and φslv
pcal,i are the phase of the phase calibration
signal in ith channel, respectively. 4.
Discussion The residual group delay
of the signals is given by, δτgroup−delay =
δφ′
i+1 −δφ′
i
2π( fi+1 −fi)
(7) (7) where fi is the frequency of the carrier wave. The propaga-
tion delays of the troposphere and the ionosphere are also
corrected. The atmospheric delay is corrected by using the
tropospheric model (Davis et al., 1985) and the ionospheric
delay is corrected by using a regional ionosphere map (Ping
et al., 2002). After these corrections, the geometric delays of the sig-
nals from Nozomi are obtained in every 100 seconds by
the group delay analysis. These derived geometric delays
well accorded with the geometric delay determined by the
range and Doppler measurements, and the differences be-
tween these geometric delays are shown in Fig. 7. The av-
erage of these differences are about 2 nano seconds (nsec) 5. 3.2
Result of correlation In the
mode A, the ambiguity tones were added to the downlink
signal and decreased the SNR of the range tones. So the
residual fringe phases of the range tones were not obtained
for this period of 60 seconds as shown in Fig. 6. On the
other hand, the ambiguity tones were not added in the mode
B and the residual fringe phases of the range tones were
obtained in this period of 40 seconds in B of Fig. 6. The
averaged SNR of two range tones in the mode B is 19 for
40 seconds integration. Therefore the group delay analysis
could only be carried out during the mode B. 5.
Conclusion We carried out a VLBI observation of Nozomi. In this
observation, we recorded three carrier wave signals by us- F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1046 -200
-100
0
100
200
300
07:00:00
07:02:00
07:04:00
07:06:00
07:08:00
07:10:00
Residual fringe phase [degree]
2003/5/27 [UT]
B: 40sec. A: 60sec. main carrier
range tone 1
range tone 2
Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. -200
-100
0
100
200
300
07:00:00
07:02:00
07:04:00
07:06:00
07:08:00
07:10:00
Residual fringe phase [degree]
2003/5/27 [UT]
B: 40sec. A: 60sec. main carrier
range tone 1
range tone 2
Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. -40
-20
0
20
40
07:00:00
07:30:00
08:00:00
08:30:00
O-C of geometric delay [nsec]
2003/5/27 [UT]
Fig. 7. The difference between the geometric delays in this VLBI obser-
vation and those calculated from the orbital motion estimated from the
range and Doppler measurements. -40
-20
0
20
40
07:00:00
07:30:00
08:00:00
08:30:00
O-C of geometric delay [nsec]
2003/5/27 [UT] phase error would be less than 10 degrees for 3.9 seconds
integration, which is the requirement of VRAD. It could
be expected that we can detect the regional gravity field
of the Moon precisely by using this system. Furthermore,
in addition to the range and Doppler measurements, VLBI
observation by this system has a capability of precise three-
dimensional positioning of an s/c. Acknowledgments. We would like to thank all the staffs of
Kashima space communication research center of NICT, Usuda
deep space center of JAXA and Mizusawa observation center of
National Astronomical Observatory for their helps in VLBI obser-
vations. Acknowledgments. We would like to thank all the staffs of
Kashima space communication research center of NICT, Usuda
deep space center of JAXA and Mizusawa observation center of
National Astronomical Observatory for their helps in VLBI obser-
vations. References Antreasian, P. G., D. T. Baird, J. S. Border, P. D. Burkhart, E. J. Graat,
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Odyssey Orbit Determination During Interplanetary Cruise, AIAA/AAS
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https://openalex.org/W3143530413 | https://www.nasemore.com/wp-content/uploads/2021/03/5_M_Petkovic_M_Zubcic_M_Krcum_I_Pavic.pdf | English | null | Wind Assisted Ship PropulsionTechnologies – Can they Help in Emissions Reduction? | Naše more | 2,021 | cc-by | 6,878 | Summary According to International Maritime Organization, emissions coming from global
shipping are expected to increase 50% to 250% by the year 2050. This concern led
to the introduction of various regulations that aims to encourage ship owners and
builders to explore innovative renewable technologies. The main focus of this article
is on wind-assisted ship propulsion technologies, as a complement to ship propulsion,
such as rigid sail, soft sail, wing sail, kite, and Flettner rotor. These technologies are
not widely accepted because ship owners have doubts due to the lack of real-life
results and their implementation and effi ciency greatly depends on ship design and
purpose. This article shows the progress in the fi eld of wind-assisted ship propulsion
in the last 15 years which proved the concept as they have the potential to reduce
fuel consumption, thus emissions, by double digits. The conclusion is drawn, from
fuel savings percentages, that rotor and soft sails technologies have great potential
in the future of the shipping industry. Wind Assisted Ship PropulsionTechnologies – Can they Help
in Emissions Reduction?
Tehnologije propulzije broda s pomoću vjetra – mogu li one
pomoći u smanjenju emisija? Marko Zubčić
University of Split
Faculty of Maritime studies
Department for Marine electrical
engineering and IT
E-mail: mzubcic@pfst.hr Marko Zubčić
University of Split
Faculty of Maritime studies
Department for Marine electrical
engineering and IT
E-mail: mzubcic@pfst.hr Miro Petković
University of Split
Faculty of Maritime studies
Department for Marine electrical
engineering and IT
E-mail: mpetkovic@pfst.hr Maja Krčum
University of Split
Faculty of Maritime studies
Department for Marine electrical
engineering and IT
E-mail: mkrcum@pfst.hr Ivan Pavić
University of Split
Faculty of Maritime studies
Department for Marine electrical
engineering and IT
E-mail: ipavic@pfst.hr DOI 10.17818/NM/2021/2.6
UDK 629.5.037:626.74
Review / Pregledni rad
Paper accepted / Rukopis primljen: 4. 9. 2020. Sažetak KLJUČNE RIJEČI
WASP
kruto jedro
krilno jedro
rotorsko jedro
kajt
Flettner rotor Prema Međunarodnoj pomorskoj organizaciji, očekuje se da će se emisije koje stvara
pomorska industrija na globalnoj razini povećati između 50% i 250% do 2050. Ova
svijest dovela je do uvođenja različitih propisa koji imaju cilj ohrabriti brodovlasnike i
brodograditelje te istraživati inovativne obnovljive tehnologije. Glavni je fokus ovoga
članka na tehnologijama propulzije broda s pomoću vjetra kao dopuna propulziji
broda kao što su: kruta jedra, mekana jedra, krilna jedra, kajt i Flettner rotor. Ove
tehnologije nisu općenito prihvaćene jer brodovlasnici imaju sumnje zbog nedostatka
stvarnih pouzdanih rezultata te njihova implementacija i djelotvornost uvelike ovise o
dizajnu namjeni broda. Ovaj članak pokazuje napredak u području propulzije broda
s pomoću vjetra u posljednjih 15 godina koji potvrđuje tu zamisao jer ima potencijal
smanjiti potrošnju goriva, a time i emisije na dvoznamenkasti broj. Izvodi se zaključak
na temelju postotaka uštede da rotorske i tehnologije mekanih jedara imaju velik
potencijal u budućnosti brodarske industrije. 1. INTRODUCTION / Uvod Energy Effi ciency Design Index (EEDI) which states that all newly
built ships, from 2013 and onwards, have to follow EEDI sets of
mandatory carbon dioxide emissions reduction targets. Also,
to ensure future production of more effi cient ships, reduction
targets are tightened every fi ve years up until 2030. Reports
[4], [5] submitted to the IMO Marine Environment Protection
Committee (MEPC) pointed that the EEDI is only encouraging
“mainstream” innovation. Proving that there has been no uptake
of innovative measures that yield signifi cant savings, which are
necessary to keep shipping’s CO2 emissions in line. To decrease
carbon dioxide emissions and improve energy effi ciency in
shipping activities, utilization of renewable energy solutions
and technologies is considered a necessary direction. According
to [6] EEDI is calculated: Energy Effi ciency Design Index (EEDI) which states that all newly
built ships, from 2013 and onwards, have to follow EEDI sets of
mandatory carbon dioxide emissions reduction targets. Also,
to ensure future production of more effi cient ships, reduction
targets are tightened every fi ve years up until 2030. Reports
[4], [5] submitted to the IMO Marine Environment Protection
Committee (MEPC) pointed that the EEDI is only encouraging
“mainstream” innovation. Proving that there has been no uptake
of innovative measures that yield signifi cant savings, which are
necessary to keep shipping’s CO2 emissions in line. To decrease
carbon dioxide emissions and improve energy effi ciency in
shipping activities, utilization of renewable energy solutions
and technologies is considered a necessary direction. According
to [6] EEDI is calculated: Global shipping transport demand is increasing around 4% per
year, while the world’s trade carried by sea reached over 90%
[1]. Shipping is the most energy-effi cient mode of transport
which is probably the reason why the sector has got away
with ignoring the carbon dioxide emissions problem. In 2014,
a greenhouse gas study presented by International Maritime
Organization (IMO) [1], carbon dioxide emissions coming from
global shipping are expected to increase 50% to 250% by the
year 2050. IMO concluded that this rapid increase of emissions
proves the need for energy effi ciency regulations, and made
them eff ective by January 2013 [2]. The regulation requires all
5000 GT ships and above to record fuel and oil consumption
and report them. As of March 2018, MARPOL Annex VI sets of
regulations [3], became mandatory. Also, IMO introduced the 102 M. (1) where: – CO2 emission factor based on type of fuel used by given
engine – cubic capacity correction factor (for chemical tankers, LNG
carriers and RoPax) – correction factor to compensate deadweight losses
through cargo-related equipment like cranes – capacity adjustment factor for any technical/regulatory
limitation on capacity – coeff icient indicating the decrease in ship speed due to
weather and environmental conditions – correction factor for ship-specific design elements correction factor for ship specific design elements
– availability factor of individual energy eff iciency
technologies. If we influence Peff(i), the main engine power requirement
will be reduced, thus the overall EEDI value will be decreased. Wind energy has great potential and advantage since its
availability is continuous at the open sea when comparing
to the other renewable solutions [7] and can offer significant
savings on existing ships [8]. For example, in [9] seasonal
forecasting of winds, waves, and currents in the North
Pacific were analyzed, with the conclusion that the western
North Pacific is the most predictable region and therefore
seasonal forecast data could be used for vessel routing and
confirms the potential application of some wind-assisted
technology. According to [10] wind assisted ship propulsion
(WASP) technologies have the potential to decrease fuel
consumption, thus emissions, by double digits. This leads
to the conclusion that this renewable technology will play
important role in the future of the shipping industry. Fuel
savings, that can be achieved, depending on the design of
the ship (rig and hull), the operating speed, and the wind
speeds and directions experienced [10]. Also, it is noted that
of the available wind assist technologies, kites and Flettner
rotors have received the most attention concerning to
helping reduce the fuel consumption and emissions from
larger commercial ships. where: – ship speed at reference conditions
– deadweight tonnage (DWT) rating for bulk ship
and tankers; gross tonnage for passenger ships Rigid sails are a mature technology with low uncertainties on
costs and with simple architecture with no huge motor. But,
we must keep in mind that the aerodynamic effi ciencies on the
vessels are limited by the tip speed ratio. Racing sailboats or
foiling catamarans, in specifi c situations, can sail faster than
the wind and achieve tip speed ratios above one, allowing
their sails to obtain a higher propulsion effi ciency [11]. Also,
the author noted when the ship is loaded with all the needs for
her serving purpose and cargo, the effi ciency is reduced by the
lack of ability to achieve the same tip speed ratios. – individual power of main engines – combined installed power of auxiliary engines – power of individual shaft motors divided by the
effi ciency of shaft generators – auxiliary engine power reduction due to individual
technologies for electrical energy effi ciency – main engine power reduction due to individual
technologies for mechanical energy effi ciency – fuel use per unit of engine power In paper [12] power profi le for a rigid sail is proposed
which could assist with modeling potential fuel savings and
emission reductions. Strengths, weaknesses, opportunities,
and threats (SWOT) analysis was conducted for rigid sail
technology by [13]. The analysis recognized that strengths are
lower fuel consumption, emission reduction, lower operating
costs, improved vessel stability, propulsion in emergencies,
and less volume for fuel bunkering. Weaknesses are safety for
the crew, additional operational cost, initial cost, interference
with cargo operations, increased weight of the ship, additional
training, and workload for the crew. Opportunities are the
implementation of IMO regulations, higher fuel costs which
make this approach economically viable, marketing regarding
brand presentation, slow steaming. Threats are shipping
industry suspicion, lower fuel cost, alternative or new fuels,
route changing, thus placing the ship in the conditions that
make rigid sail unfavorable and overall complex structure
(hardware and software solutions). 1. INTRODUCTION / Uvod Petković et al: Wind Assisted Ship PropulsionTechnologies... 2.2. Soft sails / Mekana jedral Soft sails are fl exible sails similar to traditional sails characterized
by very diff erent innovative features and are automated to a
great extent i.e. duplex rigs, freestanding square rigs, rotating
masts etc. Some of the innovative technologies are Pinta-
Rig, DynaRig, Delta wingsail and Fastrigs. DynaRig became a
popular soft sail technology mainly because of its easy to use
characteristics and self-sustainability. The main characteristic
is the mast, which is lightly guyed and rotatable, making
maneuvres of DynaRig safe and secured. When comparing
to the wing sail, its lift coeffi cients are lower, but by utilizing
the larger surface areas greater lift forces are achieved [14]. It is noted that when sailing upwind effi ciency of this type of
sail decreases. In [15] a coastal sailing vessel (3000 DWT) is
proposed, aiming to have zero carbon emissions by utilizing
the DynaRig soft sail system. By using this technology total
required thrust was reduced by 61%. In [16], a sailing Mult- 103 “Naše more” 68(2)/2021., pp. 102-109 Figure 1 Cargo Vessel “Eco liner”
Slika 1. Teretni brod „Ecoliner“
Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Figure 1 Cargo Vessel “Eco liner”
Slika 1. Teretni brod „Ecoliner“ Figure 1 Cargo Vessel “Eco liner”
Slika 1. Teretni brod „Ecoliner“
Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Slika 1. Teretni brod „Ecoliner“
Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Figure 1 Illustration of forces acting on wing sail; FT – thrust
force, FH – drift force, FL – lift force,
FD – drag force, θ – the angle between apparent wind and
ship’s longitudinal line. Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna
sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut
između prividnog vjetra i longitudinalne linije broda
Source: Authors purpose Cargo Vessel “Eco liner” 8000 DWT was proposed. In
[17], the characteristics of the “Eco liner” has been compared
with similar-sized motorized ship under given estimated
time of arrival by using computational fl uid dynamic (CFD)
simulations and weather routing programs. At a cruise speed
of 12 knots, simulations showed fuel savings up to 35% and
approximately 22% fewer costs of operation. 2.2. Soft sails / Mekana jedral When compared
to a similar conventional ship, “Eco liner” has a 3% cost benefi t
after 10 years of operation if we consider capital costs and
depreciation. 2.3. Wing sails / Krilna jedrai The wing sail profi le and the thickness of the airfoil shape can
generate a strong lift eff ect and provide a strong propulsive
force while decreasing the induced drag that slows down the
ship [14].The operating principle of the wing sail is to maximize
the aerodynamic lift force by rotating to the optimum wind
angle of attack. By using mast which rotates 360˚, the wing
sail works in diff erent wind angles and even upwind. Figure 1
illustrates the geometrical relationship between forces acting
on the wing sail due to apparent wind. Figure 1 Illustration of forces acting on wing sail; FT – thrust
force, FH – drift force, FL – lift force,
FD – drag force, θ – the angle between apparent wind and
ship’s longitudinal line. Figure 1 Illustration of forces acting on wing sail; FT – thrust
force, FH – drift force, FL – lift force,
FD – drag force, θ – the angle between apparent wind and
ship’s longitudinal line. Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna
sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut
između prividnog vjetra i longitudinalne linije broda
Source: Authors According to [18] wing sail should be as small as possible
and therefore should apply high lift devices, also sails or their
skins should be reefable from the wing structure. In [19],
[20] a collapsible wing sail is proposed with double fl aps. Also, the best confi guration of parameters was investigated
and using a numerical simulation method the aerodynamic
performance of the new wing sail was analyzed. These papers
show that double-fl ap wing sails provide more thrust force
in comparison to arc sail, variable-chamber sail [21], and
NACA0021. Another case study [22] states that with wing
sail technology, on a route from Ras Tanura (Saudi Arabia) to
Yokohama (Japan), 2.6 % fuel savings can be achieved per trip. Four wing sails were considered in this case study. Numerical
analysis of aerodynamic performances was conducted by
[23] for a two-element wing sail. Also, it is stated that multi-
element wing sails are diffi cult to operate so there is a need to
thoroughly investigate the fl ow around the wing sail. The paper Slika 1. 2.3. Wing sails / Krilna jedrai Ilustracija sila koje djeluju na krilno jedro; Fr – porivna
sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut
između prividnog vjetra i longitudinalne linije broda
Source: Authors Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna
sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut
između prividnog vjetra i longitudinalne linije broda
Source: Authors investigates the infl uence of the construction parameters on
the lift and drag coeffi cients. The WindShip project [24] proposed a new rigid concept
of a wing sail, as a case study ship a Product Carrier 50000
DWT was selected. For the given wind direction and speed,
a program was developed to predict the ship’s speed, rudder
angles, and drift. Within areas with strong winds wing sail
technology achieved 10% fuel savings when compared to
a similar conventional Product Carrier. But, it is noted that 104 M. Petković et al: Wind Assisted Ship PropulsionTechnologies... Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force
Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja
Source: Authors Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force
Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force
Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja
Source: Authors Source: Authors Source: Authors carrier “Aghia Marina”). the manufacturer claims that 10 –
15 % fuel saving can be achieved and up to 2 MW of power
generation under favorable wind conditions [28]. In paper
[29], the power output of a kite on five potential trade routes
is estimated. It is calculated that towing kite can provide
between 127 and 461 kW of power generation resulting in 1
to 32 % of fuel savings, depending on the ship type. In [30],
an analytical model is used to evaluate the performance
of a towing kite as an auxiliary power source. 2.5. Rotor sails – Flettner rotor / Rotorska jedra –
Flettner rotor The rotor sails or Flettner rotor is a rotating cylinder
vertically installed on the deck, the rotation of the cylinder
is achieved by using an electrical motor. By utilizing the
Magnus effect it generates lift force which is perpendicular
to the apparent wind vector as shown in Figure 3 b). The
direction of the lift force vector depends on the rotational
direction of the cylinder. The first rotors were installed
on the ship named Backau in 1925. In 1926 it crossed the
Atlantic and anchored in the port of New York. The concept
was proven technically sound and plausible but was
abandoned because of the economical situation regarding
low oil prices [31]. In [8] it is claimed that rotor sails could
achieve up to 20% fuel savings for commercial cargo ships,
assuming three rotors were installed. The lift and drag
coefficient study for the 2D case was conducted by [32] and
it showed that rotor spin ratio has significant implications
for the flow control strategies. The influence of the Thom
disc on the lift and drag coefficient was studied by [33] and
is illustrated in Figure 3 a). 2.3. Wing sails / Krilna jedrai On a tanker
(50,000 DWT) with 320 m2 towing kite, themodel showed
up to 10% of fuel savings on a 10 m/s wind speed and up
to 50% savings at 15.6 m/s. The performance of towing
kites proves to be volatile [29], but they are a low emissions
solution that should be considered. during voyages with high average speeds, in a less windy
area, fuel savings could be marginal. Another concept of
wing sail was studied during the Wind Challenger project
[25] on the Bulk Carrier “UT Wind Challenger” 18000 DWT. The result was the development of the energy prediction
program which predicts operational performance, also on
the route Yokohama - Seattle simulation showed fuel savings
up to 22%. In another project [26], a wing sail concept for the KVLCCM
type hull is proposed. Under certain wind and ship speeds
computational fluid dynamics (CFD) simulation showed
the reduction of thrust, required by the main engine, for
approximately 10% with proposed wing sails. The variables
investigated in the paper are true wind speed, ship speed,
wing sail area, and aspect ratio. Maximum power reduction
in this study was achieved for the case were total wing sail
area and the height of the sails were kept constant while the
variable was the number of the sails. The reduction of 14 % is
achieved for 8 wing sails and a true wing angle of 80 °. 2.4. Kites / Kajtovi The operating principle of a kite is to tow the ship when
deployed off his bow and Figure 2 illustrates forces acting
on the towing kite. They operate at an altitude between 100 – 300 m to tame the power of the higher altitude winds. In paper [27] parameters are used, based on experimental
data, to create the point-mass model. A path following
strategy was designed so that the kite can follow an eight-
shaped trajectory using a simple proportional controller. The result of their simulation showed that a 15 m2 kite was
enough to tow a small fishing boat, also a 30 m2 kite was
enough to tow a zero greenhouse gas emissions vessel 30.5
meters long by 12.80 meters wide. Skysails is one of the prominent kite technology’s and
some ships have used or are using it (general Cargo ship
“Michael A.”, container/cargo ship “M/V Theseus”, Bulk 105 “Naše more” 68(2)/2021., pp. 102-109 Figure 3 a) Illustration of Magnus eff ect; FL –Lift force, Fd –Drag force, b) Illustration of Flettner rotor and Thom disc
Slika 3. a) Ilustracija Magnus efekta; FL – Sila podizanja, Fd – Sila povlačenja; b) ilustracija Flettner rotora i Thom diska
Authors Figure 3 a) Illustration of Magnus eff ect; FL –Lift force, Fd –Drag force, b) Illustration of Flettner rotor and Thom disc
Slika 3. a) Ilustracija Magnus efekta; FL – Sila podizanja, Fd – Sila povlačenja; b) ilustracija Flettner rotora i Thom diska
Authors Source: Authors Source: Authors In 2015 Ro-Ro Carrier “Estraden” (9700 DWT) was
retrofitted with rotors, 18 m in height and 3 m in diameter,
made by Norsepower [38]. Sea trials conducted on a route
between the Netherlands and the United Kingdom showed a
2.6% fuel saving with only one rotor, after installing second
rotor trials showed 6.1% fuel savings. Analytical evaluation of net generated power for different
values of rotation coefficient was performed by [34], net
generated power decreased as the coefficient of rotation
increased. Evaluation of the aerodynamic performance of
the Flettner rotor was done in [35] by using CFD simulations
which showed the importance of 3D simulations over 2D
simulations. While evaluating CFD simulation results, in [29]
a performance model for power saving simulation of Flettner
rotors is proposed. A cargo ship (5500 DWT) was used as
a case study, with three Flettner rotors (27m in height and
4m in diameter) installed. 2.4. Kites / Kajtovi The simulation showed a 50%
power reduction used by the main engine. In another study
[36], the authors followed the performance and handling
tests of the Panamax Bulk Carrier with installed Integrated
Greenwave MK1 Rotor. A scaled model of a 182 m Bulk carrier
with Flettner rotor installed, was used. The results of the
experimental tests were that Flettner rotor provided 50%
of nominal thrust during light wind conditions and 100%
during moderate winds. Currently, there are six ships with installed rotor
technology. All six are stated in the Table 1. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS /
Analiza rezultata WASP tehnologija Summary of results from WASP technology’s literature,
discussed in this paper, is presented in Table 2. Based on the literature, this paper presents that wing sail
technology can achieve fuel saving in the range of 2.6 – 22 %,
depending on the route, ship type, sail angle, number of sails. Soft sail, even though having a lower lift coefficient, can
achieve fuel saving up to 35 %. For DynaRig soft sail system,it
is reported that 61 % reduction of main engine power is
possible. Towing kite can provide 1- 32 % fuel savings. Simulations results show that for Flettner rotor technology
fuel savings up 50 % can be expected. From the results, it can
be seen that Flettner rotor and soft sail technologies have the
most potential. In 2010 the Cargo ship “Enercon E-ship” (10500 DWT) came
into operation with four rotors, 25m high and 4 m in diameter,
installed onboard [37]. On the voyage between Germany and
Portugal, fuel consumption was decreased by 23 %. Table 1 Ships in operation with installed Flettner rotor
Tablica 1. Brodovi koji djeluju s ugrađenim Flettner rotorom Ship
Type
Year of Built
No. of rotors
Rotor dimensions
(H x d) [m]
Fehn Pollux [39]
General Cargo
1996
1
18 x 3
Estraden [38]
Ro-Ro Cargo
1999
2
18 x 3
Maersk Pelican [40]
Crude Oil Tanker
2008
2
30 x 5
E-Ship 1 [37]
General Cargo
2010
4
25 x 4
Viking Grace [41]
Ro-Ro/Passenger
2013
1
24 x 4
Afros [42]
Bulk Carrier
2018
4
/
Source: Authors Source: Authors M. Petković et al: Wind Assisted Ship PropulsionTechnologies... Table 2 Summary of wind-assisted ship propulsion technology
Tablica 2. Sažetak tehnologija propulzije broda s pomoću vjetra Table 2 Summary of wind assisted ship propulsion technology
Tablica 2. Sažetak tehnologija propulzije broda s pomoću vjetra
WASP
tech. Ref. Methodology
Results
Real ship /
Simulation
Fuel
savings
Rigid
sails
[12]
Methodology (power profi le) is
developed by which key performance
values can be calculated and displayed
in a standardized format by using a
virtual wind tunnel. Power profi le will outline key performance
characteristics and allow comparisons to be made
between diff erent types of rigid sails. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS /
Analiza rezultata WASP tehnologija Simulation
[13]
SWOT analysis
Strengths, weaknesses, and opportunities are
emphasized for rigid sail technology
Simulation
Soft sails
[14]
Developed software to calculate fuel-
saving performance of three wind-
assisted ship propulsion technologies
– the Flettner rotor, the Soft sails -
DynaRig, and a wing sail
Comparison of DynaRig soft sail with Wing sail
showed lower lift coeffi cients of DynaRig, but
greater lift force can be achieved. Simulation
[15]
Performance of zero carbon emission
coastal sailing vessel is simulated
Simulation showed 61% reduction of required
thrust
Simulation
[17]
Using CFD simulations and weather routing
programs “Eco liner” has been compared
with similar-sized motorized ship
The simulation showed up to 35% fuel savings and
approximately 22% fewer costs of operation
Simulation
35%
Wing
sails
[19]
[20]
Using numerical simulations methods
aerodynamic performance of collapsible
wing sail was studied
Double fl ap wing sails provide more thrust force in
comparison to other wing sail technologies
Simulation
[22]
ANSYS is used to perform simulation-
based study
On a route from Ras Tanura to Yokohama, 2.6% fuel
savings can be achieved per trip
Simulation
2.6%
[23]
Numerical analysis of aerodynamic
performance for two-element wing sail
Infl uence of the construction parameters on the lift
and drag coeffi cients
Simulation
[24]
A new rigid concept of wing sail with
realistic simulations based on measured
and simulated performance
Rigid wing sail mounted on a case study ship of a
Product Carrier achieved 10% fuel savings when
compared to similar conventional Product Carrier
Real ship
10%
[25]
Development of energy prediction
program for Wind Challenger project on
the case study ship
The simulation showed fuel savings of up to 22%
on the route from Yokohama to Seattle
Simulation
22%
[26]
CFD simulation of a wing sail concept for
KVLCCM type hull
Under certain wind and ship speeds simulation
showed a reduction of required thrust, by the main
engine, for approximately 10%. Also, the reduction
of 14% is achieved for 8 wing sails and a true wing
angle of 80 degrees. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS /
Analiza rezultata WASP tehnologija Simulation
Kites
[27]
Based on experimental data parameters
are used to create a point mass model
The simulation showed that 30 m2 kite was enough
to tow zero carbon emission vessel 30.5 m long and
12.8 m wide
Real ship
[28]
Performance test of Skysails kite is
conducted on a general Cargo ship
10 - 15 % fuel savings and up to 2 MW of power
generation can be achieved under favorable wind
conditions
Real ship
10 – 15%
[29]
The numerical model of a kite on fi ve
potential trade routes
Towing kite can provide between 127 and 461
kW of power generation resulting 1 to 32% of fuel
savings
Real ship
1 – 32%
[30]
Analytical model for towing kite
performance evaluation
Tanker with 320 m2 towing kite, the model showed
10% of fuel savings on a 10 m/s wind speed and up
to 50% savings at 15.6 m/s
Simulation
10 – 50%
Rotor
sails
[8]
Techno-economic and environmental
analysis study
Authors claim that rotor sails could achieve up to
20% fuel savings
Simulation
20%
[32]
Using the fi nite element method the
fl ow past a rotating cylinder in 2D is
calculated
Rotor spin ratio has signifi cant implication for the
fl ow control strategies
Simulation
[33]
CFD simulation of spinning cylindrical
rotors for maritime propulsion
Infl uence of the Thom disc on the lift and drag
coeffi cient
Simulation
[34]
Analytical evaluation of net generated
power
Net generated power decreases as the rotation
coeffi cient increases
Simulation
[35]
Aerodynamic performance of Flettner
rotor by using CFD simulations
Importance of 3D simulations over 2D simulations
Simulation
[29]
A performance model for power saving
simulation of Flettner rotors
On a case study, Cargo ship simulation showed 50%
power reduction used by the main engine
Simulation
50%
[36]
Authors followed tests on a scaled
model of a 182 m Bulk carrier with
installed Flettner rotor
Experimental tests showed that Flettner rotor
provided 50% of nominal thrust during light wind
conditions and 100% during moderate winds
Simulation
50 – 100%
[37]
Experimental tests on the Cargo ship
“Enercon E-ship”
On the voyage between Germany and Portugal,
fuel consumption was decreased by 23%
Real ship
23%
[38]
Sea trials on Ro-Ro Carrier “Estraden”
retrofi tted with rotor sails
Sea trials showed 2.6% fuel savings with only one
rotor, after installing second rotor trials showed
6.1% fuel savings
Real ship
2.6 – 6.1% “Naše more” 68(2)/2021., pp. 4. CONCLUSION / Zaključak Wind technologies that directly contribute to ship’s propulsion,
were presented in this paper. This segment of renewable energy
sources is potentially of great meaning to a shipping industry
when considering the requirements from IMO for emissions
reduction. This conclusion is drawn from the percentages of
fuel savings achieved, thus reduction of CO2, NOx, SO , and
PM emissions. Due to diff erent construction designs, diff erent
WASP technologies contribute more or less to ship propulsion. The utilization of these technologies depends on the ship deck
construction, speed, and ship routing (weather situation along
the route). WASP technologies are not widely accepted because
ship owners have doubts due to the lack of real-life results
regarding fuel savings, for example, from 1999 till 2020 there
were only six commercial ships in the world fi tted with Flettner
rotors. The fact that simulations provide high fuel saving is the
motivation for the shipbuilders and owners to consider these
technologies as a measure for compliance with IMO emissions
regulations. Also, the implementation of fuel cells, solar energy,
and other energy-effi cient technologies should be considered
for emissions reduction for IMO regulations compliance and
these technologies will be scope in our future work. [15] Surplus, D. C. (2011). “B9 Ships: Sail and Virtual Bio-Methane Powered Coastal
Vessels”. LCS 2011 - International Conference on Technologies, Operations,
Logistics and Modelling for Low Carbon Shipping. [16] WASP (Ecoliner) - Dykstra Naval Architects, Dykstra Naval Architects (2019). Available
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hybrid shipping Hybrid shipping market opportunities Niche market”. Available at: http://www.nsrsail.eu/wp-content/uploads/2015/06/Factsheet-
Brochure_SAIL_2015.pdf [accessed 18/6/2020] [18] Kralj, D. M., Klarin, B. (2016).”Wing sails for hybrid propulsion of a ship”. J. Sustain. Dev. Energy, Water Environ. Syst., Vol. 4, No. 1, pp. 1-13. https://doi. org/10.13044/j.sdewes.2016.04.0001 [19] Li, D., Li, G., Dai, J., Li, P. (2017). “A new type of collapsible wing sail and its
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cascade hard sails and sail-equipped vessels”. Ocean Eng., Vol. 98, pp. 23-31. REFERENCES / Literatura Further technical and operational measures for enchancing the
energy effi ciency of international shipping, The Existing Shipping Fleet’s CO2
Effi ciency MEPC 68/INF24/REV1. [Online]. Available at: http://www.imo.org/. vA – apparent wind speed [m/s]fi cL – lift coeffi cient fi [6] Ren, H., Ding, Y., Sui, C. (2019). “Infl uence of EEDI (Energy Effi ciency Design
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Index) on Ship-Engine-Propeller Matching”. J. Mar. Sci. Eng., Vol. 7, No. 12, p. 425. https://doi.org/10.3390/jmse7120425 cD – drag coeffi cientfi cD – drag coeffi cientfi D
gfi
The effi ciency of these technologies is defi ned by their lift
and drag force ratio. Paper [44] reports that for towing kite
technology value of lift and drag ratio is from 3 to 8, depending
on relative power setting. Paper [43] reports that Skysail towing
kite has a lift to drag ratio of 5. For Flettner rotor lift to drag
ratio is a function of a spin ratio. In [45] author reported that
a lift to drag ratio depends on the ratio of the diameters of
Thom disc and spinning rotor. Lift to drag ratio is a non linear
function, for spin ratio interval from 0 to 2, its value increases
achieving maximum when the spin ratio is around 2. When the
value of spin ratio is from 2 to 8, a lift to drag ratio decreases. The maximum values of lift to drag ratio ranges from 2.5 to 6.5. In the study [46] authors reported nine lift to drag ratio curves
where each curve diff ers one from another in terms of shape
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value of 2.5, where another curve has a maximum value of 13.5. This shows the discrepancy in research data and proves the
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Analiza rezultata WASP tehnologija 102-109 All WASP technologies can be analytically described with lift
and drag force. These forces are mathematically expressed by
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FD – drag force [N]
ρ – air density [kg/m3]
A – projected area of the rotor [m2]
vA – apparent wind speed [m/s]
cL – lift coeffi cient
cD – drag coeffi cientfii FL – lift force [N]
FD – drag force [N]
ρ – air density [kg/m3]
A – projected area of the rotor [m2]
vA – apparent wind speed [m/s]
cL – lift coeffi cient
cD – drag coeffi cientfi [4] IMO (2014). EEDI Database - Review of Status of Technological Development
- MEPC 67-INF3 - Third IMO GHG Study 2014 - Final Report (Secretariat). [Online]. Available at: http://www.imo.org/. [4] IMO (2014). EEDI Database - Review of Status of Technological Development
- MEPC 67-INF3 - Third IMO GHG Study 2014 - Final Report (Secretariat). [Online]. Available at: http://www.imo.org/. [5] IMO (2015). Further technical and operational measures for enchancing the
energy effi ciency of international shipping, The Existing Shipping Fleet’s CO2
Effi ciency MEPC 68/INF24/REV1. [Online]. Available at: http://www.imo.org/. [5] IMO (2015). 4. CONCLUSION / Zaključak https://doi.org/10.1016/j.oceaneng.2015.02.005 [22] Ariffi n, N. I. B., Hannan, M. A. (2020). “Wingsail technology as a sustainable
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https://openalex.org/W2010358161 | https://ccforum.biomedcentral.com/counter/pdf/10.1186/cc12869 | English | null | The subxiphoid view cannot replace the apical view for transthoracic echocardiographic assessment of hemodynamic status | Critical care | 2,013 | cc-by | 6,370 | Abstract Introduction: This prospective study aimed to assess whether use of the subxiphoid acoustic window in
transthoracic echocardiography (TTE) can be an accurate alternative in the absence of an apical view to assess
hemodynamic parameters. Methods: This prospective study took place in a teaching hospital medical ICU. Over a 4-month period, TTE was
performed in patients admitted for more than 24 hours. Two operators rated the quality of parasternal, apical, and
subxiphoid acoustic windows as Excellent, Good, Acceptable, Poor, or No image. In the subpopulation presenting
adequate (rated as acceptable or higher) apical and subxiphoid views, we compared the left ventricular ejection
fraction (LVEF), the ratio between right and left ventricular end-diastolic areas (RVEDA/LVEDA), the ratio between
early and late mitral inflow on pulsed Doppler (E/A ratio), the aortic velocity time integral (Ao VTI), and the ratio
between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging (E/Ea ratio). Results: An adequate apical view was obtained in 80%, and an adequate subxiphoid view was obtained in 63% of
the 107 patients included. Only 5% of patients presented an adequate subxiphoid view without an adequate apical
view. In the subpopulation of patients with adequate apical and subxiphoid windows (n = 65), LVEF, E/A, and
RVEDA/LVEDA were comparable on both views, and were strongly correlated (r > 0.80) with acceptable biases and
precision. However, the Ao VTI and the E/Ea ratio were lower on the subxiphoid view than on the apical view (18
± 5 versus 16 ± 5 cm and 9.6 ± 4.6 versus 7.6 ± 4 cm, respectively, P = 0.001 for both). Conclusions: An adequate TTE subxiphoid window was obtained in fewer than two thirds of ICU patients. In
addition to the classic indication for the subxiphoid window to study the vena cava and pericardium, this view can
be used to study right and left ventricular morphology and function, but does not provide accurate hemodynamic
Doppler information. ICU echocardiographers should therefore record both apical and subxiphoid views to assess
comprehensively the cardiac function and hemodynamic status. subxiphoid. As recommended in guidelines, the appropri-
ate window corresponds to the Doppler mode with the
best alignment obtained between the ultrasound beam and
the direction of blood flow [5]. RESEARCH Open Access Open Access © 2013 Maizel et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. Abstract For that reason, most para-
meters recorded for hemodynamic assessment classically
require an apical window: left ventricular ejection fraction
(LVEF) [6,7], ratio between early and late mitral inflow (E/
A) [8], ratio between early mitral inflow and displacement
of the mitral annulus on tissue Doppler imaging (E/Ea) [8],
velocity time integral of aortic blood flow (Ao VTI) [9],
and the ratio between right (RVEDA) and left (LVEDA)
ventricular end-diastolic area [7]. However, many factors
in the ICU can interfere with apical image quality. More The subxiphoid view cannot replace the apical
view for transthoracic echocardiographic
assessment of hemodynamic status Julien Maizel1, Ahmed Salhi1, Christophe Tribouilloy2, Ziad A Massy1, Gabriel Choukroun1 and Michel Slama1* * Correspondence: slama.michel@chu-amiens.fr
1Medical Intensive Care Unit, Department of Nephrology, Amiens University
Medical Center, Amiens, France and INSERM U-1088, Jules Verne University
of Picardie, Amiens, France
Full list of author information is available at the end of the article Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Introduction Transthoracic echocardiography (TTE) has become the
leading noninvasive examination to assess the hemody-
namic status of patients hospitalized in intensive care units
(ICUs) [1-3]. It allows the physician to study noninvasively
the contractility, relaxation, and fluid responsiveness of the
two ventricles [4]. All parameters must be recorded in one
of the following three windows: parasternal, apical, or * Correspondence: slama.michel@chu-amiens.fr
1Medical Intensive Care Unit, Department of Nephrology, Amiens University
Medical Center, Amiens, France and INSERM U-1088, Jules Verne University
of Picardie, Amiens, France
Full list of author information is available at the end of the article Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Page 2 of 8 Page 2 of 8 sample cursor placed in the lateral mitral annulus, and aor-
tic blood flow was measured with the sample volume
placed at the aortic annulus. The size of the sample volume
was not modified between apical and subxiphoid views. specifically, in this setting, the lung interposition between
the probe and the heart, the presence of mechanical venti-
lation, the inability to position the patient in left-sided
decubitus, tachypnea, and the presence of bandages or
tubes on the chest can alter the quality of the images
obtained on apical and parasternal views. The two operators then blindly reviewed the quality of
the 2D images recorded with these windows offline on a
computer (General Electric Healthcare, Fairfield, CT,
USA), according to the following scoring system: Excellent
(visualization of the four chambers with complete endo-
cardial visualization of both ventricles); Good (visualiza-
tion of the two ventricles with complete endocardial
visualization of both ventricles); Acceptable (visualization
of both ventricles, but short segments of endocardium are
not correctly visualized); Poor (the endocardium cannot
be visualized in most portions of the ventricles); and No
image (no visualization of the ventricles). An adequate
acoustic window was defined by an acceptable, good, or
excellent score. Each physician separately scored the video
recording of the three windows (parasternal, apical, and
subxiphoid) and compared their results. When both scores
were identical, the final score was accepted. When the two
scores were different, the physicians jointly visualized the
video, discussed their points of view, and reached a con-
sensus to establish a final score. To complete the examination in this setting, the echo-
cardiographer may perform transesophageal echocardio-
graphy. However, transesophageal echocardiography is
more invasive and can be difficult to perform, especially
in nonintubated ICU patients. Introduction In this setting, use of the
transthoracic subxiphoid view can be an attractive alter-
native to transesophageal echocardiography for less-
experienced operators who may be reluctant to perform
an invasive examination. The subcostal view is classically
used to study respiratory variations of the inferior vena
cava and the presence of pericardial effusion. This view
can provide additional hemodynamic parameters, such
as LVEF, mitral or aortic flows, and RV/LV areas. Although the subxiphoid view does not provide the
same alignment as the apical view, it is not known to
what degree this different alignment affects the results
of the hemodynamic examination. To address this issue, we tried to determine the accuracy
of the subxiphoid window to record various echocardio-
graphic parameters usually recorded on the apical view for
hemodynamic assessment. In the subpopulation of patients with adequate apical and
subxiphoid windows (scored excellent, good, or accepta-
ble), LVEF (according to the Monoplane Simpson method)
and RVEDA/LVEDA ratio were measured on both the
apical and subxiphoid 2D cine-loops. The mitral peak
E velocity (E), peak A velocity (A), E/A ratio, Ao VTI, and
E/Ea ratio were measured on Doppler images in the apical
and subxiphoid windows. All data were the average of
three end-expiratory measurements (excluding outliers). In
the presence of an outlier, an additional assessment was
recorded. In the subxiphoid window, LVEF and RVEDA/
LVEDA were recorded on a longitudinal four-chamber
view visualizing both right and left ventricles in their lar-
gest dimensions. On a modified four-chamber view, the
operator tried to obtain the best alignment between flow
and the Doppler axis by obtaining the highest maximum
Doppler velocity to record mitral and aortic flows on the
subxiphoid view. Materials and methods
Patients In accordance with French legislation, the local institu-
tional review board (CPP Nord-Ouest II, Amiens Univer-
sity Hospital, France) approved the study protocol, and all
patients or their relatives gave their informed consent. This single-center prospective study was performed in an
eight-bed teaching hospital medical ICU (Amiens, France). Over a 4-month period, all patients admitted to the ICU
were included in the study, except when one of the two
experienced echocardiographers (JM and AS) was absent
and except for patients admitted to the unit for less than
24 hours. Patient characteristics were recorded. Demographic data Patient characteristics are presented in Table 1. Supra-
ventricular arrhythmia (atrial fibrillation and atrial
flutter) was reported in 23 (21%) patients. The admission
diagnoses were shock in 35%, respiratory distress in 23%,
acute renal failure in 10%, cardiac arrest in 5%, severe
sepsis in 4%, deliberate drug overdose in 5%, scheduled
postoperative surveillance in 5%, and other (seizures,
pancreatitis, ketoacidosis) in 13%. A higher mean number of the five parameters (LVEF,
Ao VTI, E/A, E/Ea, and RVEDA/LVEDA) was obtained on
the apical view than on the subxiphoid view (3.7 ± 1.9 and
2.9 ± 2.2, respectively; P = 0.001). When considered sepa-
rately, each parameter was recorded significantly more
frequently on the apical view than on the subxiphoid view
(Table 2). The subpopulation of 65 patients with adequate apical
and subxiphoid windows were not significantly different
from the overall population, except for the proportion of
acceptable apical windows (27% versus 21%; P = 0.04 for
the overall population and subpopulation, respectively). The various parameters obtained on each of these two
views were compared in this group of 65 patients (Table 3). No significant difference was observed for the parameters
based on the two-dimensional mode: LVEF, RVEDA,
LVEDA, and the RVEDA/LVEDA ratio. In the Doppler
mode, Ao VTI, E, A, Ea, and E/Ea ratio were significantly
decreased on the subxiphoid view, suggesting inadequate
alignment between the cursor and blood flow. However,
E and A velocities on the subcostal view were underesti-
mated in the same proportion, so the E/A ratio was equiva-
lent to that observed on the apical view. Table 1 Patient characteristics of the overall population
Overall population
N = 107
Age (years)
63 ± 16
Men, n (%)
59 (55)
SAPS II
49 ± 20
BMI, kg/m2
28 ± 8
COPD, n (%)
26 (24)
Mechanical ventilation, n (%)
VC
PSV
PEEP, cm H2O
48 (45)
40 (37)
8 (7)
3.4 ± 1.7
MAP, mm Hg
79 ± 17
HR, bpm
97 ± 23
Arrhythmia, n (%)
23 (21)
Catecholamines, n (%)
36 (34)
Tubes, bandages, n (%)
Chest
Abdomen
10 (9)
6 (6)
4 (4) Table 1 Patient characteristics of the overall population Similar differences were observed when only patients
with a history of COPD or mechanically ventilated patients
were considered (data not shown). A strong correlation was observed between apical and
subxiphoid values for all parameters (Figure 1). The
Bland-Altman graphs are presented in Figure 1. Measurements The mean number of adequate acoustic windows per
patient was 2.2 ± 0.9. An adequate parasternal view was
obtained in 69% of patients; an adequate apical view was
obtained in 86% of patients; and an adequate subxiphoid
view was obtained in 66% of patients. The proportion of
adequate views was significantly higher for the apical
window than for the subxiphoid window for the overall
population and the subpopulation of mechanically venti-
lated patients and was close to significant in COPD
patients (Table 2). Three adequate views were obtained
in 45% of patients; two adequate views were obtained in
37%; only one adequate view was obtained in 10%; and
no adequate window was obtained in 8% of patients. An
adequate subxiphoid view but no adequate apical view
was obtained in only 5% of patients. The proportion of
adequate subxiphoid windows was not affected by
mechanical ventilation (67% versus 66%; P = 0.9 with or
without mechanical ventilation, respectively), the mode of
ventilation (67% versus 62%; P = 0.9 in VC or PSV mode,
respectively), the level of PEEP (67% versus 73%; P = 0.9,
PEEP <5 and PEEP ≥5 cm H2O, respectively), or a history
of COPD (58% versus 69%; P = 0.4 COPD versus absence
of COPD, respectively). The inter- and intraobserver reproducibilities were deter-
mined for each parameter (LVEF, E/A, E/Ea, RVEDA/
LVEDA, and Ao VTI) in both the apical and subxiphoid
windows. All intraobserver variabilities were <5%, and
interobserver variabilities were <9%. Statistical analysis was performed by using MedCalc ver-
sion 12.0.4.0 (MedCalc Software, Mariakerke, Belgium). The limit of significance was set at ≤0.05. BMI, body mass index; COPD, chronic obstructive pulmonary disease; HR,
heart rate; MAP, mean arterial pressure; PEEP, positive end-expiratory pressure;
PSV, pressure-support ventilation; SAPSII, simplified acute physiology score II;
VC, volume controlled. Statistics Transthoracic echocardiography was performed during the
first 2 days after admission in all patients by one of the two
operators (JM or AS) by using a Vivid i (General Electrics
Healthcare Fairfield, CT, USA) equipped with a 3-MHz
probe. Parasternal (long and short axis), apical four-cham-
ber, and subxiphoid four-chamber views were obtained
successively in 2D mode, and a cine-loop was stored for
offline analysis. In the apical and subxiphoid windows,
pulsed Doppler mitral inflow was recorded with the sample
cursor placed at the mitral valve tips; early diastolic velocity
(Ea) was determined from Doppler tissue imaging with the All variables are expressed as mean ± 1 SD or proportions. The normal distribution was tested with a Kolmogorov-
Smirnov test. Quantitative variables were compared by
using a Student t test, and proportions were compared
with a c2 test. Pearson correlation coefficient and Bland-Altman analy-
sis were used to assess the adequacy of the various para-
meters obtained in the subxiphoid and apical windows. This analysis was performed in the subpopulation of
patients in whom apical and subxiphoid windows were Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Page 3 of 8 Page 3 of 8 scored as excellent, good, or acceptable (n = 65). The bias
and limit of agreement (LOA) around the bias were given
by the Bland-Altman representation. However, no consen-
sus has been reached concerning the acceptable LOA to
confirm validation of the subcostal view. To define an
acceptable LOA, Cecconi et al. [10] proposed assessing the
precision of the reference technique (in this case, the apical
view) and the tested technique (the subxiphoid view). We
prospectively defined the validation criteria for the various
parameters studied on the subxiphoid view: to be accepta-
ble, the parameter on the subxiphoid view had to be accu-
rate (bias <10%) and precise (a lower percentage precision
value than on the apical view). Demographic data The per-
centage bias, percentage error, and precisions of the apical BMI, body mass index; COPD, chronic obstructive pulmonary disease; HR,
heart rate; MAP, mean arterial pressure; PEEP, positive end-expiratory pressure;
PSV, pressure-support ventilation; SAPSII, simplified acute physiology score II;
VC, volume controlled. Page 4 of 8 Page 4 of 8 Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid
windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid
windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid
windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid
windows in the overall population (n = 107)
Apical
Subxiphoid
P
Number of patients with adequate apical or subxiphoid acoustic window, n (%)
Overall population (n = 107)
Mechanically ventilated patients (n = 48)
COPD population (n = 26)
92 (86)
38 (78)
21 (81)
71 (66)
32 (67)
15 (58)
0.009
0.002
0.1
Quality of the window
A Excellent
B Good
C Acceptable
D Poor
E No image
27 (25)
36 (34)
29 (27)
11 (10)
4 (4)
19 (18)
36 (34)
16 (15)
21 (20)
15 (14)
0.7
0.3
0.9
0.06
0.2
LVEF, n (%)
80 (75)
67 (63)
0.001
E/A, n (%)
71 (66)
46 (43)
0.001
E/Ea, n (%)
85 (79)
66 (62)
0.001
Ao VTI, n (%)
83 (78)
66 (62)
0.001
RVEDA/LVEDA, n (%)
79 (74)
67 (63)
0.001
Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the
mitral annulus on tissue Doppler imaging; LVEF, left ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area. of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the
pler imaging; LVEF, left ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area. and subxiphoid views are presented in Table 4 for each
parameter. Demographic data All parameters presented a better precision
(lower percentage value) on the subxiphoid view than on
the apical view, but two parameters (Ao VTI and E/Ea)
presented a bias >10% (12% ± 16 and 22% ± 28, respec-
tively) and therefore did not meet the a priori defined
criteria. patients did not have an adequate apical view, but had an
adequate subxiphoid view. These results emphasize the
good feasibility of the apical view in TTE, even in venti-
lated or COPD patients. This study also shows that the
subxiphoid view is a reliable view to study the right- and
left-ventricular morphology and function on two-dimen-
sional echocardiography, but not in Doppler mode. The
subxiphoid view should be used to explore only the vena
cava, pericardium, and the morphology of the left or right
ventricles. Semiquantitative evaluation of the diagnostic accuracy of
the subxiphoid view was determined for the three para-
meters selected (LVEF, E/A, and RVEDA/LVEDA) by
identifying several previously published criteria obtained
on the apical view (Figure 2). The useful window most frequently obtained in our
population was the apical window (86%), followed by the
parasternal window (66%), and finally the subxiphoid
window (49%), as already reported [11-13]. Only 5% of
the patients of our population presented an inadequate
apical view and an adequate subxiphoid view. Moreover,
a greater number of parameters were recorded on the
apical view than on the subxiphoid view. Altogether,
these results emphasize the better feasibility of the apical
view compared with the subxiphoid view in TTE. Discussion In this study, the apical view was the view most frequently
obtained (86%), and only a small proportion (5%) of Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51)
Apical window
Subxiphoid window
P value
LVEF, %
54 ± 16
55 ± 14
0.9
Ao VTI, cm
18 ± 5
16 ± 5
0.001
E, cm/sec
80 ± 25
59 ± 24
0.001
A, cm/sec
75 ± 32
55 ± 29
0.001
E/A
1.2 ± 0.9
1.1 ± 0.5
0.3
Ea, cm/sec
9.5 ± 3.7
8.8 ± 2.8
0.009
E/Ea
9.6 ± 4.6
7.6 ± 4
0.001
RVEDA, cm2
13 ± 6
13 ± 6
0.9
LVEDA, cm2
26 ± 8
27 ± 8
0.3
RVEDA/LVEDA
0.5 ± 0.19
0.49 ± 0.18
0.2
Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early
and late mitral inflow; E/Ea, ratio between early mitral inflow and
displacement of the mitral annulus on tissue Doppler imaging; LVEF, left
ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left
ventricular end-diastolic area. Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51) Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51) The proportion of mechanically ventilated patients in
our population was 45%, which is lower than the propor-
tion usually reported in ICU [14]. However, in our study,
TTE was performed within the first 2 days after admission
of the patients and mostly at the time of admission. We
do not believe that a higher proportion of mechanically
ventilated patients would have modified our conclusions,
as the proportion of adequate views was significantly
higher for the apical view than for the subxiphoid view
in the population of mechanically ventilated patients
(Table 2). The subxiphoid view is an essential element of echocar-
diography in an ICU, particularly to analyze the inferior
vena cava (for example, size and collapsibility) and pericar-
dium (for example, pericardial effusion). According to our Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Page 5 of 8 Figure 1 Regression plot and Bland-Altman analysis between apical and subxiphoid views for the various parameters in the
subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between
early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; RVEDA/
LVEDA, ratio between right and left ventricular end-diastolic area. Figure 1 Regression plot and Bland-Altman analysis between apical and subxiphoid views for the various parameters in the
subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between
early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; RVEDA/
LVEDA, ratio between right and left ventricular end-diastolic area. results, only parameters recorded in two-dimensional
mode (LVEF and RVEDA/LVEDA) can be recorded on
the subxiphoid window without any bias. The bias of E/A
was almost nil, but this ratio alone does not constitute a
reliable parameter to analyze LV filling pressure in this
setting of critically ill patients [15]. The fairly large limits
of agreement in the Bland-Altman representations for
LVEF, E/A, and RVEDA/LVEDA can also be an argument
in favor of the use of a semiquantitative approach for
these parameters. approach: preserved or altered LVEF, or normal or
dilated right ventricle [16,17]. results, only parameters recorded in two-dimensional
mode (LVEF and RVEDA/LVEDA) can be recorded on
the subxiphoid window without any bias. CV, coefficient of variation; CE, coefficient of error. Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51) The bias of E/A
was almost nil, but this ratio alone does not constitute a
reliable parameter to analyze LV filling pressure in this
setting of critically ill patients [15]. The fairly large limits
of agreement in the Bland-Altman representations for
LVEF, E/A, and RVEDA/LVEDA can also be an argument
in favor of the use of a semiquantitative approach for
these parameters. The discrepancy between apical and subxiphoid values
for E, A, E/Ea, and Ao VTI can be explained by the angle
between the Doppler axis and blood flow or myocardial
movement in the various acoustic windows. With the
Doppler mode, red blood cell velocity (or myocardial tis-
sue movement on tissue Doppler) depends on the cosine
of the angle between the axis of the Doppler beam and
blood flow (myocardial tissue movement): the smaller the
angle, the higher the velocity [18]. On the apical view, the
heart is examined in the longitudinal (anteroposterior)
axis, ensuring perfect alignment between the Doppler Figure 2 demonstrates the low rate of misclassified
patients. Use of the subxiphoid window to analyze ven-
tricular morphology therefore allows a point-of-care Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on the reference apical
view
Mean
apical
CV
apical
CE
apical
Precision of
apical
Mean
subxiphoid
Bias (± SD)
Bias (% of the apical
value)
Percentage
error
Precision of
subxiphoid
LVEF
54% ± 16
29.6
17.1
34%
55% ± 14
-0.1 ± 8.6
-1.5% ± 17
32%
12%
Ao VTI
18 cm ±
5
29.1
16.8
34%
16 cm ± 5
2.0 ± 2.8
12% ± 16
31%
13%
E/A
1.2 ± 0.9
75.7
43.7
87%
1.1 ± 0.5
0.03 ± 0.2
5% ± 16
33%
81%
E/Ea
9.6 ± 4.6
47.5
27.4
55%
7.6 ± 4
1.9 ± 2.4
22% ± 28
50%
23%
RVEDA/
LVEDA
0.5 ± 0.19
37.5
21.6
43%
0.49 ± 0.18
0.01 ± 0.1
3% ± 22
40%
16%
CV, coefficient of variation; CE, coefficient of error. Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on the reference apical
view analysis of the various parameters obtained on the subxiphoid view and on the reference apical Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on th
i Maizel et al. Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51) Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Page 6 of 8 Figure 2 Accuracy of subxiphoid view for classifying various hemodynamic parameters according to the apical view in the
subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; E/A, ratio between early and late mitral inflow; RVEDA/LVEDA, ratio
between right and left ventricular end-diastolic area). Figure 2 Accuracy of subxiphoid view for classifying various hemodynamic parameters according to the apical view in the
subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; E/A, ratio between early and late mitral inflow; RVEDA/LVEDA, ratio
between right and left ventricular end-diastolic area). This study presents several limitations. The lower veloci-
ties obtained on the subxiphoid view are due to the poor
alignment between the Doppler axis and blood flow. Some
echocardiography devices apply a correction of this angle
by aligning the Doppler beam with blood flow, but this
angle correction was not tested in this study. However,
accurate determination of the appropriate angle correction
for velocity is difficult, essentially because this angle can
be measured only in a two-dimensional plane, which
therefore disregards the angle in the third dimension of
the heart. Moreover, angle correction would not be suffi-
cient to correct the velocity of Ea, as the observed decrease
is not exclusively due to poor alignment, but also because
this view measures a different relaxation property of the
myocardium: radial instead of longitudinal. Not all hemo-
dynamic parameters were evaluated by TTE in this study. Right ventricular function was not extensively analyzed,
apart from RVEDA/LVEDA (an important parameter of
biventricular interaction). However, the misalignment
observed in Doppler mode would also be expected to
affect measurement of the tricuspid proto-systolic S-wave
velocity on tissue Doppler, tricuspid annular plane systolic
excursion in M mode (TAPSE), or pulmonary artery pres-
sure. We also did not study the variation of aortic blood
flow during passive leg raising or mechanical ventilation to
predict fluid responsiveness, as this would have required a
strictly selected population [19]. Although the position of beam and blood flow through the mitral or aortic rings
and maximum velocities. On the subxiphoid view, the
heart is viewed in a different axis (inferoanterior). Conse-
quently, on this view, the alignment between the Doppler
beam and aortic flow is not perfect, and the velocity
reported by the echocardiographer will be underestimated. Conclusions 2. Vieillard-Baron A, Slama M, Cholley B, Janvier G, Vignon P:
Echocardiography in the intensive care unit: from evolution to
revolution? Intensive Care Med 2008, 34:243-249. 2. Vieillard-Baron A, Slama M, Cholley B, Janvier G, Vignon P:
Echocardiography in the intensive care unit: from evolution to
revolution? Intensive Care Med 2008, 34:243-249. 3. Mayo PH, Beaulieu Y, Doelken P, Feller-Kopman D, Harrod C, Kaplan A,
Oropello J, Vieillard-Baron A, Axler O, Lichtenstein D, Maury E, Slama M,
Vignon P: American College of Chest Physicians/La Société de
Réanimation de Langue Française statement on competence in critical
care ultrasonography. Chest 2009, 135:1050-1060. 4. Beaulieu Y: Bedside echocardiography in the assessment of the critically
ill. Crit Care Med 2007, 35:S235-S249. 5. Sahn DJ: Real-time two-dimensional Doppler echocardiographic flow
mapping. Circulation 1985, 71:849-853. 6. Schiller NB, Shah PM, Crawford M, DeMaria A, Devereux R,
Feigenbaum H, Gutgesell H, Reichek N, Sahn D, Schnittger I:
Recommendations for quantitation of the left ventricle by two-
dimensional echocardiography: American Society of Echocardiography
Committee on Standards, Subcommittee on Quantitation of
Two-Dimensional Echocardiograms. J Am Soc Echocardiogr 1989,
2:358-367. Echocardiography comprises a combination of various
acoustic windows. The subxiphoid view is already estab-
lished as an essential part of echocardiography in the ICU
to explore the inferior vena cava and pericardium. The
results of this study also emphasize that the subxiphoid
view cannot replace the apical view to perform complete
hemodynamic assessment. In the absence of an apical
view, the subxiphoid view can provide only partial infor-
mation based on analysis of two-dimensional images. To
obtain a complete hemodynamic examination, echocardio-
graphers should therefore record both apical and subxi-
phoid views or use another monitoring device, such as
transesophageal echocardiography. 3. Mayo PH, Beaulieu Y, Doelken P, Feller-Kopman D, Harrod C, Kaplan A,
Oropello J, Vieillard-Baron A, Axler O, Lichtenstein D, Maury E, Slama M,
Vignon P: American College of Chest Physicians/La Société de
Réanimation de Langue Française statement on competence in critical
care ultrasonography. Chest 2009, 135:1050-1060. 5. Sahn DJ: Real-time two-dimensional Doppler echocardiographic flow
mapping. Circulation 1985, 71:849-853. 6. Schiller NB, Shah PM, Crawford M, DeMaria A, Devereux R,
Feigenbaum H, Gutgesell H, Reichek N, Sahn D, Schnittger I:
Recommendations for quantitation of the left ventricle by two-
dimensional echocardiography: American Society of Echocardiography
Committee on Standards, Subcommittee on Quantitation of
Two-Dimensional Echocardiograms. J Am Soc Echocardiogr 1989,
2:358-367. 7. References 1. Expert Round Table on Ultrasound in ICU: International expert statement
on training standards for critical care ultrasonography. Intensive Care Med
2011, 37:1077-1083. 1. Expert Round Table on Ultrasound in ICU: International expert statement
on training standards for critical care ultrasonography. Intensive Care Med
2011, 37:1077-1083. 1. Expert Round Table on Ultrasound in ICU: International expert statement
on training standards for critical care ultrasonography. Intensive Care Med
2011, 37:1077-1083. Conclusions Lang RM, Bierig M, Devereux RB, Flachskampf FA, Foster E, Pellikka PA,
Picard MH, Roman MJ, Seward J, Shanewise J, Solomon S, Spencer KT, St
John Sutton M, Stewart W, European Association of Echocardiography,
European Society of Cardiology: Recommendations for chamber
quantification. Eur J Echocardiogr 2006, 7:79-108. Received: 4 March 2013 Revised: 14 May 2013
Accepted: 3 September 2013 Published: 3 September 2013 Received: 4 March 2013 Revised: 14 May 2013
Accepted: 3 September 2013 Published: 3 September 2013 the heart and consequently our findings should not differ
according to the reason for admission, it would be inter-
esting to confirm our conclusions in a specific population
of acute circulatory failure patients. Competing interests
The authors declare that they have no competing interests. p
g
The authors declare that they have no competing interests. Key messages • The apical view appears to be more accurate and
more feasible than the subxiphoid window, even in
mechanically ventilated or COPD patients. • The apical view appears to be more accurate and
more feasible than the subxiphoid window, even in
mechanically ventilated or COPD patients. 8. Nagueh SF, Appleton CP, Gillebert TC, Marino PN, Oh JK, Smiseth OA,
Waggoner AD, Flachskampf FA, Pellikka PA, Evangelista A:
Recommendations for the evaluation of left ventricular diastolic function
by echocardiography. J Am Soc Echocardiogr 2009, 22:107-133. • The E/Ea ratio and Ao VTI appear to be signifi-
cantly underestimated on the subxiphoid view and
therefore should not be recorded. 9. Quinones MA, Otto CM, Stoddard M, Waggoner A, Zoghbi WA:
Recommendations for quantification of Doppler echocardiography: a
report from the Doppler Quantification Task Force of the Nomenclature
and Standards Committee of the American Society of Echocardiography. J Am Soc Echocardiogr 2002, 15:167-184. 9. Quinones MA, Otto CM, Stoddard M, Waggoner A, Zoghbi WA:
Recommendations for quantification of Doppler echocardiography: a
report from the Doppler Quantification Task Force of the Nomenclature
and Standards Committee of the American Society of Echocardiography. J Am Soc Echocardiogr 2002, 15:167-184. • In addition to its ability to explore the vena cava
and pericardium, the subxiphoid view can provide
information based on morphologic analysis of the
ventricles in two-dimensional mode. g
10. Cecconi M, Rhodes A, Poloniecki J, Della Rocca G, Grounds RM: Bench-to-
bedside review: the importance of the precision of the reference
technique in method comparison studies: with specific reference to the
measurement of cardiac output. Crit Care 2009, 13:201. g
10. Cecconi M, Rhodes A, Poloniecki J, Della Rocca G, Grounds RM: Bench-to-
bedside review: the importance of the precision of the reference
technique in method comparison studies: with specific reference to the
measurement of cardiac output. Crit Care 2009, 13:201. Authors’ contributions 15. Feissel M, Maizel J, Robles G, Badie J, Faller JP, Slama M: Clinical relevance
of echocardiography in acute severe dyspnea. J Am Soc Echocardiogr
2009, 22:1159-1164. 15. Feissel M, Maizel J, Robles G, Badie J, Faller JP, Slama M: Clinical relevance
of echocardiography in acute severe dyspnea. J Am Soc Echocardiogr
2009, 22:1159-1164. JM and AS contributed to the acquisition and analysis of data and drafting
the manuscript JM and AS contributed to the acquisition and analysis of data and drafting
the manuscript JM and MS contributed to the conception and design of the study. CT, ZM,
GC, and MS were involved in interpretation of data, critically revising the
manuscript, and giving final approval. All authors read and approved the
final manuscript. 16. Labovitz AJ, Noble VE, Bierig M, Goldstein SA, Jones R, Kort S, Porter TR,
Spencer KT, Tayal VS, Wei K: Focused cardiac ultrasound in the emergent
setting: a consensus statement of the American Society of
Echocardiography and American College of Emergency Physicians. J Am Soc Echocardiogr 2010, 23:1225-1230. 16. Labovitz AJ, Noble VE, Bierig M, Goldstein SA, Jones R, Kort S, Porter TR,
Spencer KT, Tayal VS, Wei K: Focused cardiac ultrasound in the emergent
setting: a consensus statement of the American Society of
Echocardiography and American College of Emergency Physicians. J Am Soc Echocardiogr 2010, 23:1225-1230. Abbreviations
l Ao VTI: velocity time integral of aortic blood flow; BMI: body mass index; CE:
coefficient of error; COPD: chronic obstructive pulmonary disease; CV:
coefficient of variation; E/A: ratio between early and late mitral inflow on
pulsed Doppler; E/Ea: ratio between early mitral inflow and displacement of
the mitral annulus on tissue Doppler imaging; HR: heart rate; ICU: intensive
care unit; LOA: limit of agreement; LVEDA: left ventricular end-diastolic area;
LVEF: left ventricular ejection fraction; MAP: mean arterial pressure; PEEP:
positive end-expiratory pressure; PSV: pressure support ventilation; RVEDA:
right ventricular end-diastolic area; SAPS2: simplified acute physiologic score
2; TTE: transthoracic echocardiography; VC: volume controlled. 11. Vignon P, Chastagner C, François B, Martaillé J-FF, Normand S, Bonnivard M,
Gastinne H: Diagnostic ability of hand-held echocardiography in
ventilated critically ill patients. Crit Care 2003, 7:R84-R91. 12. Vignon P, Frank MBJ, Lesage J, Mücke F, François B, Normand S,
Bonnivard M, Clavel M, Gastinne H: Hand-held echocardiography with
Doppler capability for the assessment of critically-ill patients: is it
reliable? Intensive Care Med 2004, 30:718-723. 13. Jensen MB, Sloth E, Larsen KM, Schmidt MB: Transthoracic
echocardiography for cardiopulmonary monitoring in intensive care. Eur J Anaesthesiol 2004, 21:700-707. 13. Jensen MB, Sloth E, Larsen KM, Schmidt MB: Transthoracic
echocardiography for cardiopulmonary monitoring in intensive care. Eur J Anaesthesiol 2004, 21:700-707. 14. Vincent JL, Sakr Y, Sprung CL, Ranieri VM, Reinhart K, Gerlach H, Moreno R,
Carlet J, Le Gall JR, Payen D, Sepsis Occurrence in Acutely Ill Patients
Investigators: Sepsis in European intensive care units: results of the SOAP
study. Crit Care Med 2006, 34:344-353. Table 3 Echocardiographic measurements in apical and
subxiphoid windows in the subpopulation of 65 patients
(except for A and E/A; n = 51) Interestingly, the E/A ratio is not modified on the subxi-
phoid view, as the E and A waves are both decreased to a
similar degree. The velocity of the mitral annulus (Ea) is
measured in tissue Doppler mode. On the apical view, the
Doppler beam is aligned with the longitudinal movement
of the mitral annulus, but the subxiphoid view measures
the radial movement of the annulus, accounting for the
lower Ea velocity obtained in this window. It is noteworthy
that the E/Ea and Ao VTI were also underestimated in
patients with a history of COPD and in mechanically ven-
tilated patients, two situations theoretically associated with
a vertical heart axis that could have resulted in better
alignment on the subxiphoid view. An adequate apical view could not be obtained in the
present study in fewer than 15% of cases, whereas use of
the subxiphoid view was incomplete, as Doppler analysis
appears to be unreliable. Therefore, in the unusual situa-
tion of absence of an apical window, the use of another
monitoring device should be considered (particularly in
intubated patients, in whom transesophageal echocardio-
graphy can usually be performed). Page 7 of 8 Page 7 of 8 Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 Authors’ details
1 17. Arntfield RT, Millington SJ: Point of care cardiac ultrasound applications in
the emergency department and intensive care unit: a review. Curr Cardiol Rev 2012, 8:98-108. 17. Arntfield RT, Millington SJ: Point of care cardiac ultrasound applications in
the emergency department and intensive care unit: a review. Curr Cardiol Rev 2012, 8:98-108. 1Medical Intensive Care Unit, Department of Nephrology, Amiens University
Medical Center, Amiens, France and INSERM U-1088, Jules Verne University
of Picardie, Amiens, France. 2Department of Cardiology, Amiens University
Medical Center, Amiens, France and INSERM U-1088, Jules Verne University
of Picardie, Amiens, France. 18. Nelson TR, Pretorius DH: The Doppler signal: where does it come from
and what does itmean? AJR Am J Roentgenol 1988, 151:439-447. Page 8 of 8 Page 8 of 8 Maizel et al. Critical Care 2013, 17:R186
http://ccforum.com/content/17/5/R186 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid
therapy. Ann Intensive Care 2011, 1:1. doi:10.1186/cc12869
Cite this article as: Maizel et al.: The subxiphoid view cannot replace
the apical view for transthoracic echocardiographic assessment of
hemodynamic status. Critical Care 2013 17:R186. 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid
therapy. Ann Intensive Care 2011, 1:1. 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid
therapy. Ann Intensive Care 2011, 1:1. doi:10.1186/cc12869
Cite this article as: Maizel et al.: The subxiphoid view cannot replace
the apical view for transthoracic echocardiographic assessment of
hemodynamic status. Critical Care 2013 17:R186. Submit your next manuscript to BioMed Central
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https://openalex.org/W2135913935 | https://journals.iucr.org/e/issues/2005/09/00/lh6485/lh6485.pdf | English | null | 1,2:3,4-Di-<i>O</i>-isopropylidene-α-<scp>D</scp>-tagatofuranose | Acta crystallographica. Section E | 2,005 | cc-by | 3,371 | Received 3 August 2005
Accepted 5 August 2005
Online 12 August 2005 organic papers organic papers Acta Crystallographica Section E
Structure Reports
Online
ISSN 1600-5368 David J. Watkin,a* Andreas F. G.
Glawar,a Raquel Soengas,b
Ulla P. Skytte,c Mark R.
Wormald,d Raymond A. Dwekd
and George W. J. Fleetb aDepartment of Chemical Crystallography,
Chemical Research Laboratory, Oxford
University, Mansfield Road, Oxford OX1 3TA,
England, bDepartment of Organic Chemistry,
Chemical Research Laboratory, Oxford
University, Mansfield Road, Oxford OX1 3TA,
England, cArla Foods Ingredients, Viby J,
DK-8260 Denmark, and dGlycobiology Institute,
Department of Biochemistry, Oxford University,
South Parks Road, Oxford OX1 3QU, England 1,2:3,4-Di-O-isopropylidene-a-D-tagatofuranose Acta Crystallographica Section E
Structure Reports
Online
ISSN 1600-5368 The crystal structure
of diacetone
tagatose, C12H20O6,
establishes the stereochemistry of the anomeric spiroacetal
as 1,2:3,4-di-O-isopropylidene--d-tagatofuranose. Molecules
are
linked
by
O—H O
hydrogen
bonds
[O O
=
2.862 (2) A˚ ] to form chains running parallel to the b axis. David J. Watkin,a* Andreas F. G. Glawar,a Raquel Soengas,b
Ulla P. Skytte,c Mark R. Wormald,d Raymond A. Dwekd
and George W. J. Fleetb Acta Cryst. (2005). E61, o2891–o2893 doi:10.1107/S1600536805025092 Comment Carbohydrates provide a rich source of chirons (Lichtenthaler
& Peters, 2004). d-Tagatose, (1), is the first example for more
than 50 years of a sugar that has changed its status from rare
($5,000 per lb) to common ($2.5 per lb). The driving force for
the production of large quantities of hitherto scarce carbo-
hydrates is their potential as enhanced dietary targets. d-Tagatose is a healthy sweetener prepared cheaply from
galactose (Beadle et al., 1992). Its use as a dietary substitute in
soft drinks and ready-to-eat cereals (Skytte, 2002) is rapidly
increasing. So far, there has been little exploitation of tagatose
as a chiral building block, although recently the easy
preparation of branched sugar lactones by the Kiliani cyano-
hydrin reaction on d-tagatose has been reported (Soengas,
Izumori et al., 2005); the structures of the diacetonide products
could only be firmly established by X-ray crystallographic
analysis (Harding et al., 2005; Shallard-Brown et al., 2004). For
a sugar to be used as a chiral starting material in organic
synthesis, it must not only be cheap but also efficiently
protected (Bols, 1996). Correspondence e-mail:
david.watkin@chem.ox.ac.uk Correspondence e-mail:
david.watkin@chem.ox.ac.uk Correspondence e-mail:
david.watkin@chem.ox.ac.uk Key indicators
Single-crystal X-ray study
T = 190 K
Mean (C–C) = 0.002 A˚
R factor = 0.036
wR factor = 0.087
Data-to-parameter ratio = 13.7 Key indicators For details of how these key indicators were
automatically derived from the article, see
http://journals.iucr.org/e. Acta Cryst. (2005). E61, o2891–o2893
# 2005 International Union of Crystallography
Printed in Great Britain – all rights reserved The first reports of the protection of tagatose, (1), with
acetone (Reichstein & Bosshard, 1934; Barnett & Reichstein,
1937) gave no indication of the chemistry at the anomeric
position of the diacetonide, (3). Otherwise, compound (3) has
only been prepared by lengthy synthesis from d-fructose
(Cubero et al., 1988); the enantiomer of (3) was derived from a
multi-step procedure from l-sorbose (Furneaux et al., 1993). No previous publication has provided any evidence for the
anomeric configuration of the diacetonide, (3). In recent
studies, treatment of tagatose, (1), which exists in both its
crystalline form and in solution in the pyranose form, (2), with
acetone produces high yields of crystalline (3) (Soengas,
Wormald et al., 2005). The present report of the crystal # 2005 International Union of Crystallography
Printed in Great Britain – all rights reserved # 2005 International Union of Crystallography
Printed in Great Britain – all rights reserved Watkin et al. C12H20O6
o2891 doi:10.1107/S1600536805025092 Acta Cryst. (2005). E61, o2891–o2893 organic papers Figure 1
A view of the title compound, with displacement ellipsoids drawn at the
50% probability level. H atoms (except for the hydroxyl atom H15) have
been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. structure of (3) unequivocally establishes the anomeric
configuration of the diacetonide, (3), as the -form. The crystal structure of (3) consists of O—H O hydrogen-
bonded chains running parallel to the b axis (Table 1 and
Fig. 2). There are no other short intermolecular contacts. Atoms C17 and C18 refined to have very anisotropic displa-
cement parameters. A difference electron-density map phased
on all the structure except for atoms C17 and C18 showed only
a single elongated peak at these sites, indicating that the
anisotropic displacement parameter model would be appro-
priate. The large anisotropic displacement parameters for
these atoms are due to disorder of these atoms arising from
out-of-plane displacements of atoms in the adjacent ring, and
in particular of O15. A single-temperature experiment cannot
resolve static from dynamic disorder. Figure 1 Figure 1
A view of the title compound, with displacement ellipsoids drawn at the
50% probability level. H atoms (except for the hydroxyl atom H15) have
been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. Figure 1
A view of the title compound, with displacement ellipsoids drawn at the
50% probability level. H atoms (except for the hydroxyl atom H15) have
been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. The title material (Soengas, Wormald et al., 2005) was crystallized
from petroleum ether (333–353 K). Crystal data
C12H20O6
Mr = 260.29
Orthorhombic, P212121
a = 5.8241 (1) A˚
b = 8.4972 (2) A˚
c = 27.1899 (7) A˚
V = 1345.59 (5) A˚ 3
Z = 4
Dx = 1.285 Mg m3
Mo K radiation
Cell parameters from 1961
reflections
= 5–30
= 0.10 mm1
T = 190 K
Prism, colourless
0.60 0.20 0.20 mm
Data collection
Nonius KappaCCD area-detector
diffractometer
! scans
Absorption correction: multi-scan
(DENZO/SCALEPACK;
Otwinowski & Minor, 1997)
Tmin = 0.84, Tmax = 0.98
7561 measured reflections
2239 independent reflections
1980 reflections with I > 2(I)
Rint = 0.027
max = 30.0
h = 8 ! 8
k = 11 ! 11
l = 37 ! 37
Refinement
Refinement on F 2
R[F 2 > 2(F 2)] = 0.036
wR(F 2) = 0.087
S = 0.97
2239 reflections
163 parameters
H-atom parameters constrained
w = 1/[2(F 2) + ( 0.04P)2
+ 0.29P]
where P = (max(Fo
2,0) + 2Fc
2)/3
(/)max < 0.001
max = 0.31 e A˚ 3
min = 0.18 e A˚ 3
Table 1
Hydrogen-bond geometry (A˚ , ). D—H A
D—H
H A
D A
D—H A
O7—H15 O15i
0.81
2.06
2.862 (2)
167
Symmetry code: (i) x; y þ 1; z. In the absence of significant anomalous scattering, Friedel pairs
were merged and the absolute configuration was assigned from
known chiral centres. The relatively large ratio of minimum to
maximum corrections applied in the multi-scan process (1:1.16) is due
to the prismatic shape of the crystal. Figure 1 The H atoms were all located in
a difference map, but those attached to C atoms were repositioned Crystal data
C12H20O6
Mr = 260.29
Orthorhombic, P212121
a = 5.8241 (1) A˚
b = 8.4972 (2) A˚
c = 27.1899 (7) A˚
V = 1345.59 (5) A˚ 3
Z = 4
Dx = 1.285 Mg m3
Mo K radiation
Cell parameters from 1961
reflections
= 5–30
= 0.10 mm1
T = 190 K
Prism, colourless
0.60 0.20 0.20 mm
Data collection
Nonius KappaCCD area-detector
diffractometer
! scans
Absorption correction: multi-scan
(DENZO/SCALEPACK;
Otwinowski & Minor, 1997)
Tmin = 0.84, Tmax = 0.98
7561 measured reflections
2239 independent reflections
1980 reflections with I > 2(I)
Rint = 0.027
max = 30.0
h = 8 ! 8
k = 11 ! 11
l = 37 ! 37
Refinement
Refinement on F 2
R[F 2 > 2(F 2)] = 0.036
wR(F 2) = 0.087
S = 0.97
2239 reflections
163 parameters
H-atom parameters constrained
w = 1/[2(F 2) + ( 0.04P)2
+ 0.29P]
where P = (max(Fo
2,0) + 2Fc
2)
(/)max < 0.001
max = 0.31 e A˚ 3
min = 0.18 e A˚ 3 Figure 2
A diagram showing a projection along the a axis of the title compound,
with hydrogen bonds indicated as dotted lines. Mo K radiation
Cell parameters from 1961
reflections
= 5–30
= 0.10 mm1
T = 190 K
Prism, colourless
0.60 0.20 0.20 mm Figure 2 Figure 2 Figure 2
A diagram showing a projection along the a axis of the title compound,
with hydrogen bonds indicated as dotted lines. geometrically. The H atoms were initially refined with soft restraints
on their bond lengths and angles to regularize their geometry (C—H
distances in the range 0.93–0.98 A˚ and O—H distances of 0.82 A˚ ) and
displacement parameters [Uiso(H) in the range 1.2–1.5 times Ueq of
the parent atom], after which they were refined with riding
constraints. Experimental Figure 1
A i
f organic papers Lichtenthaler, F. W. & Peters, S. (2004). C. R. Chim. 7, 65–90. Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands. Table 1 Data collection: COLLECT (Nonius, 2001); cell refinement:
DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduc-
tion: DENZO/SCALEPACK; program(s) used to solve structure:
SIR92 (Altomare et al., 1994); program(s) used to refine structure:
CRYSTALS
(Betteridge
et
al.,
2003);
molecular
graphics:
CAMERON (Watkin et al., 1996); software used to prepare material
for publication: CRYSTALS D—H A
D—H
H A
D A
D—H A
O7—H15 O15i
0.81
2.06
2.862 (2)
167
Symmetry code: (i) x; y þ 1; z. In the absence of significant anomalous scattering, Friedel pairs
were merged and the absolute configuration was assigned from
known chiral centres. The relatively large ratio of minimum to
maximum corrections applied in the multi-scan process (1:1.16) is due
to the prismatic shape of the crystal. The H atoms were all located in
a difference map, but those attached to C atoms were repositioned Financial support (RS) provided by the Xunta de Galicia is
gratefully acknowledged. Acta Cryst. (2005). E61, o2891–o2893 o2892
Watkin et al. C12H20O6 Acta Cryst. (2005). E61, o2891–o2893 References Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276,
Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C.,
Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. (
)
pp
y
Barnett, T. & Reichstein, T. (1937). Helv. Chim. Acta, 20, 1529–1536. Reichstein, T. & Bosshard, W. (1934). Helv. Chim. Acta, 17, 753–
761. (
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Beadle, J. R., Saunders, J. P. & Wajda, T. J. (1992). US Patent 5078796. Shallard-Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. Shallard-Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. & Fleet G W J (2004) Acta Cryst E60 o2163 o2164 Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, C. K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Shallard Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. & Fleet, G. W. J. (2004). Acta Cryst. E60, o2163–o2164. ,
(
)
y
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Soengas, R., Izumori, K., Simone, M. I., Watkin, D. J., Skytte, U. P., Soetaert, W. (
)
pp
y
Bols, M. (1996). Carbohydrate Building Blocks. New York: John Wiley & Sons. Soengas, R., Izumori, K., Simone, M. I., Watkin, D. J., Skytte, U & Fleet, G. W. J. (2005). Tetrahedron Lett. 46, 5755–5759. Cubero, I., Lopez-Espinosa, M. T. P. & Osorio, P. L. T. (1988). An. Quim. 84,
340–343. Soengas, R., Wormald, M. R., Dwek, R. A., Izumori, K., Watkin, D. J., Skytte
U P & Fl
G W J (2005) I
i Soengas, R., Wormald, M. R., Dwek, R. A., Izumori, K., Watkin, D. J., Skytte,
U. P. & Fleet, G. W. J. (2005). In preparation. Furneaux, R. H., Tyler, P. C. & Whitehouse, L. A. (1993). Tetrahedron Lett. 34,
3609–3612. Skytte, U. P. (2002). Cereal Foods World, 47, 224-227. Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical
Crystallography Laboratory, University of Oxford, England. Harding, C. C., Watkin, D. J., Cowley, A. R., Soengas, R., Skytte, U. P. & Fleet,
G. W. J. (2005). Acta Cryst. E61, o250–o252. Crystallography Laboratory, University of Oxford, England. Watkin et al. C12H20O6
o2893 Acta Cryst. (2005). E61, o2891–o2893 supporting information Acta Cryst. (2005). E61, o2891–o2893 sup-1
Acta Cryst. (2005). E61, o2891–o2893 supporting information C4
0.8065 (3)
0.94288 (17)
0.61795 (5)
0.0256
O5
0.95355 (19)
0.80726 (12)
0.62382 (4)
0.0237
C6
0.9294 (4)
1.08802 (18)
0.63558 (6)
0.0348
O7
1.1138 (3)
1.12609 (14)
0.60326 (5)
0.0445
O8
0.6151 (2)
0.94136 (13)
0.69726 (4)
0.0291
C9
0.5377 (3)
0.81064 (19)
0.72565 (5)
0.0249
O10
0.6022 (2)
0.67635 (12)
0.69686 (4)
0.0308
C11
0.2794 (3)
0.8147 (2)
0.73296 (6)
0.0324
C12
0.6658 (3)
0.8066 (2)
0.77381 (6)
0.0339
O13
0.7586 (2)
0.63541 (13)
0.57085 (4)
0.0278
C14
0.9287 (3)
0.52851 (19)
0.55314 (6)
0.0331
O15
1.0252 (3)
0.45663 (14)
0.59641 (4)
0.0413
C16
0.9356 (3)
0.52887 (17)
0.63902 (6)
0.0284
C17
1.1201 (4)
0.6157 (3)
0.52718 (8)
0.0539
C18
0.8104 (6)
0.4066 (3)
0.52222 (10)
0.0721
H21
0.4514
0.6744
0.6302
0.0359*
H31
0.4509
0.9496
0.6316
0.0365*
H41
0.7674
0.9559
0.5835
0.0352*
H61
0.8183
1.1751
0.6360
0.0488*
H62
0.9859
1.0683
0.6693
0.0490*
H111
0.2308
0.7218
0.7514
0.0568*
H112
0.2002
0.8174
0.7024
0.0569*
H113
0.2387
0.9082
0.7525
0.0565*
H121
0.6235
0.7138
0.7913
0.0598*
H122
0.8263
0.8083
0.7675
0.0608*
H123
0.6238
0.8987
0.7933
0.0594*
H161
0.8265
0.4586
0.6557
0.0409*
H162
1.0590
0.5539
0.6614
0.0421*
H181
0.9248
0.3339
0.5111
0.1291*
H182
0.7341
0.4578
0.4946
0.1288*
H183
0.6983
0.3525
0.5434
0.1289*
H15
1.1118
1.2217
0.6016
0.0793*
H171
1.2372
0.5416
0.5168
0.0958*
H172
1.0592
0.6686
0.4986
0.0958*
H173
1.1836
0.6950
0.5500
0.0968* sup-2
Acta Cryst. (2005). supporting information Acta Cryst. (2005). E61, o2891–o2893 [https://doi.org/10.1107/S1600536805025092]
1,2:3,4-Di-O-isopropylidene-α-D-tagatofuranose F(000) = 560
Dx = 1.285 Mg m−3
Mo Kα radiation, λ = 0.71073 Å
Cell parameters from 1961 reflections
θ = 5–30°
µ = 0.10 mm−1
T = 190 K
Prism, colourless
0.60 × 0.20 × 0.20 mm Primary atom site location: structure-invariant
direct methods
Hydrogen site location: inferred from
neighbouring sites
H-atom parameters constrained
w = 1/[σ2(F2) + ( 0.04P)2 + 0.29P]
where P = (max(Fo2,0) + 2Fc2)/3
(Δ/σ)max < 0.001
Δρmax = 0.31 e Å−3
Δρmin = −0.18 e Å−3 Primary atom site location: structure-invariant sup-1
Acta Cryst. (2005). E61, o2891–o2893
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x
y
z
Uiso*/Ueq
C1
0.8104 (3)
0.67374 (17)
0.62049 (5)
0.0221
C2
0.5871 (3)
0.71970 (17)
0.64639 (5)
0.0253
C3
0.5892 (3)
0.90127 (17)
0.64648 (5)
0.0264 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) supporting information Acta Cryst. (2005). E61, o2891–o2893 supporting information E61, o2891–o2893
C4
0.8065 (3)
0.94288 (17)
0.61795 (5)
0.0256
O5
0.95355 (19)
0.80726 (12)
0.62382 (4)
0.0237
C6
0.9294 (4)
1.08802 (18)
0.63558 (6)
0.0348
O7
1.1138 (3)
1.12609 (14)
0.60326 (5)
0.0445
O8
0.6151 (2)
0.94136 (13)
0.69726 (4)
0.0291
C9
0.5377 (3)
0.81064 (19)
0.72565 (5)
0.0249
O10
0.6022 (2)
0.67635 (12)
0.69686 (4)
0.0308
C11
0.2794 (3)
0.8147 (2)
0.73296 (6)
0.0324
C12
0.6658 (3)
0.8066 (2)
0.77381 (6)
0.0339
O13
0.7586 (2)
0.63541 (13)
0.57085 (4)
0.0278
C14
0.9287 (3)
0.52851 (19)
0.55314 (6)
0.0331
O15
1.0252 (3)
0.45663 (14)
0.59641 (4)
0.0413
C16
0.9356 (3)
0.52887 (17)
0.63902 (6)
0.0284
C17
1.1201 (4)
0.6157 (3)
0.52718 (8)
0.0539
C18
0.8104 (6)
0.4066 (3)
0.52222 (10)
0.0721
H21
0.4514
0.6744
0.6302
0.0359*
H31
0.4509
0.9496
0.6316
0.0365*
H41
0.7674
0.9559
0.5835
0.0352*
H61
0.8183
1.1751
0.6360
0.0488*
H62
0.9859
1.0683
0.6693
0.0490*
H111
0.2308
0.7218
0.7514
0.0568*
H112
0.2002
0.8174
0.7024
0.0569*
H113
0.2387
0.9082
0.7525
0.0565*
H121
0.6235
0.7138
0.7913
0.0598*
H122
0.8263
0.8083
0.7675
0.0608*
H123
0.6238
0.8987
0.7933
0.0594*
H161
0.8265
0.4586
0.6557
0.0409*
H162
1.0590
0.5539
0.6614
0.0421*
H181
0.9248
0.3339
0.5111
0.1291*
H182
0.7341
0.4578
0.4946
0.1288*
H183
0.6983
0.3525
0.5434
0.1289*
H15
1.1118
1.2217
0.6016
0.0793*
H171
1.2372
0.5416
0.5168
0.0958*
H172
1.0592
0.6686
0.4986
0.0958*
H173
1.1836
0.6950
0.5500
0.0968*
Atomic displacement parameters (Å2)
U11
U22
U33
U12
U13
U23
C1
0.0280 (7)
0.0193 (6)
0.0190 (6)
0.0001 (6)
−0.0002 (6)
−0.0015 (5)
C2
0.0276 (7)
0.0233 (6)
0.0250 (6)
−0.0002 (6)
0.0016 (7)
−0.0024 (5)
C3
0.0303 (8)
0.0236 (7)
0.0252 (6)
0.0064 (7)
−0.0007 (7)
−0.0004 (5)
C4
0.0340 (8)
0.0193 (6)
0.0236 (6)
0.0055 (7)
0.0010 (7)
0.0023 (5)
O5
0.0268 (5)
0.0165 (4)
0.0279 (5)
0.0014 (5)
−0.0001 (4)
−0.0005 (4)
C6
0.0465 (11)
0.0196 (6)
0.0382 (8)
−0.0008 (8)
0.0129 (9)
0.0003 (6)
O7
0.0510 (8)
0.0227 (5)
0.0599 (8)
0.0018 (6)
0.0241 (7)
0.0059 (6)
O8
0.0398 (6)
0.0226 (5)
0.0248 (5)
−0.0013 (5)
0.0066 (5)
−0.0033 (4)
C9
0.0265 (7)
0.0238 (6)
0.0243 (6)
0.0003 (7)
0.0029 (6)
−0.0024 (6) Acta Cryst. (2005). supporting information E61, o2891–o2893 sup-2 supporting information
O10
0.0449 (7)
0.0229 (5)
0.0245 (5)
0.0028 (6)
0.0091 (5)
−0.0001 (4)
C11
0.0260 (8)
0.0407 (9)
0.0305 (7)
−0.0009 (8)
0.0016 (6)
−0.0045 (7)
C12
0.0273 (7)
0.0457 (9)
0.0286 (7)
−0.0001 (8)
−0.0010 (6)
0.0004 (7)
O13
0.0340 (6)
0.0280 (5)
0.0214 (5)
0.0051 (5)
−0.0024 (5)
−0.0055 (4)
C14
0.0438 (10)
0.0302 (8)
0.0252 (7)
0.0105 (8)
0.0017 (7)
−0.0039 (6)
O15
0.0630 (9)
0.0325 (6)
0.0284 (5)
0.0227 (7)
0.0122 (6)
0.0056 (5)
C16
0.0400 (9)
0.0198 (6)
0.0252 (6)
0.0057 (7)
−0.0009 (7)
−0.0003 (5)
C17
0.0534 (12)
0.0664 (14)
0.0420 (10)
0.0165 (12)
0.0199 (10)
0.0190 (10)
C18
0.0824 (19)
0.0585 (14)
0.0755 (16)
0.0166 (15)
−0.0150 (15)
−0.0442 (13)
Geometric parameters (Å, º)
C1—C2
1.530 (2)
C9—C12
1.507 (2)
C1—O5
1.4108 (18)
C11—H111
0.978
C1—O13
1.4209 (16)
C11—H112
0.951
C1—C16
1.517 (2)
C11—H113
0.985
C2—C3
1.543 (2)
C12—H121
0.953
C2—O10
1.4235 (18)
C12—H122
0.950
C2—H21
0.983
C12—H123
0.977
C3—C4
1.526 (2)
O13—C14
1.428 (2)
C3—O8
1.4302 (18)
C14—O15
1.4399 (19)
C3—H31
0.990
C14—C17
1.513 (3)
C4—O5
1.4448 (18)
C14—C18
1.501 (3)
C4—C6
1.505 (2)
O15—C16
1.4110 (19)
C4—H41
0.969
C16—H161
0.983
C6—O7
1.425 (2)
C16—H162
0.966
C6—H61
0.983
C17—H171
0.970
C6—H62
0.989
C17—H172
0.964
O7—H15
0.814
C17—H173
0.988
O8—C9
1.4256 (19)
C18—H181
0.957
C9—O10
1.4339 (18)
C18—H182
0.975
C9—C11
1.518 (2)
C18—H183
0.984
C2—C1—O5
105.52 (11)
C9—O10—C2
107.71 (11)
C2—C1—O13
108.37 (13)
C9—C11—H111
109.6
O5—C1—O13
111.77 (11)
C9—C11—H112
111.5
C2—C1—C16
117.58 (13)
H111—C11—H112
109.2
O5—C1—C16
110.31 (13)
C9—C11—H113
109.1
O13—C1—C16
103.39 (11)
H111—C11—H113
107.7
C1—C2—C3
104.43 (14)
H112—C11—H113
109.6
C1—C2—O10
108.97 (13)
C9—C12—H121
109.0
C3—C2—O10
104.88 (12)
C9—C12—H122
109.2
C1—C2—H21
112.1
H121—C12—H122
111.0
C3—C2—H21
113.5
C9—C12—H123
109.2
O10—C2—H21
112.4
H121—C12—H123
109.1
C2—C3—C4
103.75 (14)
H122—C12—H123
109.4
C2—C3—O8
103.92 (12)
C1—O13—C14
108.59 (12)
C4—C3—O8
110.39 (14)
O13—C14—O15
105.38 (11) O10
0.0449 (7)
0.0229 (5)
0.0245 (5)
0.0028 (6)
0.0091 (5)
−0.0001 (4)
C11
0.0260 (8)
0.0407 (9)
0.0305 (7)
−0.0009 (8)
0.0016 (6)
−0.0045 (7)
C12
0.0273 (7)
0.0457 (9)
0.0286 (7)
−0.0001 (8)
−0.0010 (6)
0.0004 (7)
O13
0.0340 (6)
0.0280 (5)
0.0214 (5)
0.0051 (5)
−0.0024 (5)
−0.0055 (4)
C14
0.0438 (10)
0.0302 (8)
0.0252 (7)
0.0105 (8)
0.0017 (7)
−0.0039 (6)
O15
0.0630 (9)
0.0325 (6)
0.0284 (5)
0.0227 (7)
0.0122 (6)
0.0056 (5)
C16
0.0400 (9)
0.0198 (6)
0.0252 (6)
0.0057 (7)
−0.0009 (7)
−0.0003 (5)
C17
0.0534 (12)
0.0664 (14)
0.0420 (10)
0.0165 (12)
0.0199 (10)
0.0190 (10)
C18
0.0824 (19)
0.0585 (14)
0.0755 (16)
0.0166 (15)
−0.0150 (15)
−0.0442 (13) sup-3 Acta Cryst. Acta Cryst. (2005). E61, o2891–o2893 supporting information (2005). E61, o2891–o2893 supporting information C2—C3—H31
114.1
O13—C14—C17
110.92 (14)
C4—C3—H31
111.7
O15—C14—C17
107.53 (16)
O8—C3—H31
112.4
O13—C14—C18
108.04 (17)
C3—C4—O5
104.52 (11)
O15—C14—C18
110.12 (17)
C3—C4—C6
115.00 (13)
C17—C14—C18
114.48 (19)
O5—C4—C6
109.66 (14)
C14—O15—C16
110.00 (12)
C3—C4—H41
108.8
C1—C16—O15
104.95 (12)
O5—C4—H41
109.7
C1—C16—H161
109.6
C6—C4—H41
109.0
O15—C16—H161
110.7
C4—O5—C1
106.49 (11)
C1—C16—H162
112.9
C4—C6—O7
110.38 (13)
O15—C16—H162
109.8
C4—C6—H61
107.9
H161—C16—H162
108.9
O7—C6—H61
109.4
C14—C17—H171
109.6
C4—C6—H62
108.4
C14—C17—H172
109.4
O7—C6—H62
111.1
H171—C17—H172
109.1
H61—C6—H62
109.6
C14—C17—H173
108.5
C6—O7—H15
104.5
H171—C17—H173
111.2
C3—O8—C9
107.69 (11)
H172—C17—H173
109.0
O8—C9—O10
103.99 (10)
C14—C18—H181
107.6
O8—C9—C11
111.48 (15)
C14—C18—H182
109.4
O10—C9—C11
110.43 (15)
H181—C18—H182
111.3
O8—C9—C12
109.38 (13)
C14—C18—H183
107.4
O10—C9—C12
109.06 (14)
H181—C18—H183
110.2
C11—C9—C12
112.17 (13)
H182—C18—H183
110.9
Hydrogen-bond geometry (Å, º)
D—H···A
D—H
H···A
D···A
D—H···A
O7—H15···O15i
0.81
2.06
2.862 (2)
167
Symmetry code: (i) x, y+1, z. sup-4 sup-4 Acta Cryst. (2005). E61, o2891–o2893 |
https://openalex.org/W2963158600 | https://www.swsc-journal.org/10.1051/swsc/2018004/pdf | English | null | The NWRA Classification Infrastructure: description and extension to the Discriminant Analysis Flare Forecasting System (DAFFS) | Journal of space weather and space climate | 2,018 | cc-by | 18,062 | The NWRA Classification Infrastructure: description and
extension to the Discriminant Analysis Flare Forecasting System
(DAFFS) NorthWest Research Associates, Boulder Office, 3380 Mitchell Ln., Boulder, CO 80301, USA Abstract – A classification infrastructure built upon Discriminant Analysis (DA) has been developed at
NorthWest Research Associates for examining the statistical differences between samples of two known
populations. Originating to examine the physical differences between flare-quiet and flare-imminent solar
active regions, we describe herein some details of the infrastructure including: parametrization of large
datasets, schemes for handling “null” and “bad” data in multi-parameter analysis, application of non-
parametric multi-dimensional DA, an extension through Bayes’ theorem to probabilistic classification, and
methods invoked for evaluating classifier success. The classifier infrastructure is applicable to a wide range
of scientific questions in solar physics. We demonstrate its application to the question of distinguishing flare-
imminent from flare-quiet solar active regions, updating results from the original publications that were
based on different data and much smaller sample sizes. Finally, as a demonstration of “Research to
Operations” efforts in the space-weather forecasting context, we present the Discriminant Analysis Flare
Forecasting System (DAFFS), a near-real-time operationally-running solar flare forecasting tool that was
developed from the research-directed infrastructure. Keywords: Sun / statistical analysis / flares / prediction / Discriminant Analysis / Bayes Empirical event-based forecasting is an application of
statistical classifiers to historical samples drawn from two
known populations: those that did and those that did not
produce the event in question. For statistical classification
methods, there are essentially four steps: (1) defining the event
in question and hence the populations to be sampled, (2)
sample acquisition (data acquisition), with attention to bias that
may be imposed to the samples of the populations, and
parametrization of the data in such a way as to be testable by
the classifier, (3) applying the classifier with appropriate
safeguards against undue influence from outlier data and
statistical flukes, (4) evaluate the classification by way of
validation metrics or similar measures. Finally, (5) the results
are available for scientific understanding or operational
forecasting. *Corresponding author: leka@nwra.com This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Available online at:
www.swsc-journal.org Available online at:
www.swsc-journal.org va ab e o
e a :
www.swsc-journal.org Developing New Space Weather Tools: Transitioning fundamental science to operational prediction systems J. Space Weather Space Clim. 2018, 8, A25
© K.D. Leka et al., Published by EDP Sciences 2018
https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25
© K.D. Leka et al., Published by EDP Sciences 2018
https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25
© K.D. Leka et al., Published by EDP Sciences 2018
https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25
© K.D. Leka et al., Published by EDP Sciences 2018
https://doi.org/10.1051/swsc/2018004 pen Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/license
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1 Introduction The prospect of forecasting rare events such as solar flares
is a daunting one, especially in situations where the exact
trigger mechanism or threshold for instability is not yet known. Still, due to their impact on the space weather environment, the
forecasting of solar flares enjoys some prominence of priority
due to the combination of the speed-of-light impact due to X-ray
emission, their association with high-energy particle enhance-
ments, and their correspondence to coronal mass ejections. ,
p
j
Early empirical efforts to forecast solar flares focused on
the white-light morphology of their host active regions
(Sawyer et al., 1986). Different classes of active region (based
on size and sunspot-group characteristics) were observed to
produce flares at different rates, and applying Poisson statistics
resulted in probabilistic forecasts for flares (McIntosh, 1990;
Bornmann & Shaw, 1994). This approach forms the basis for
many forecasts published today, including those from the US
National Oceanic and Atmospheric Administration (NOAA)/
Space Weather Prediction Center (SWPC) (Sawyer et al.,
1986; Gallagher et al., 2002; Murray et al., 2017; Steenburgh &
Balch, 2017). We describe herein a classifier infrastructure that has been
developed at NorthWest Research Associates (NWRA) based
on Non-Parametric Discriminant Analysis (NPDA). Discrimi-
nant Analysis (DA) is a tool that has been used for a variety of
scientific investigations (Solovyev et al., 1994; Filella et al.,
1995; Jombart et al., 2010); it is particularly useful for the
analysis of statistically-significant samples of what are
believed to be two distinct populations, asking how well are
the populations separable in parameter space? While the K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 1. Avery generalized flow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and the
diamond is output. ow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and t Fig. 1. Avery generalized flow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and the
diamond is output. instruments (the Solar Optical Telescope, Tsuneta et al., 2008,
and the EUV Imaging Spectrograph, Culhane et al., 2007). instruments (the Solar Optical Telescope, Tsuneta et al., 2008,
and the EUV Imaging Spectrograph, Culhane et al., 2007). 2.1 Posing the question A classifier attempts to separate samples from known
populations in the context of the parameter space constructed
by variables which describe some physical aspect of the system
in question. As such, the questions posed must be constructed
in such a way as to be addressable with a statistical classifier. Classifiers can, for example, answer “are these three things
uniquely associated with an event?” but cannot answer, “does
this thing cause that event to occur?” The crux of posing an
appropriate question rests on the event definition. In Section 3, we present a detailed example of NCI in use,
specifically NWRA’s ongoing research regarding flare-immi-
nent active regions. Following the steps above, this includes a
description of the event definitions (Sect. 3.1), data sources and
parametrization modules (Sect. 3.2) including parametrization
of temporal evolution (Sect. 3.2.8), classifier application
examples (Sect. 3.3) and evaluation results (Sect. 3.4). We
discuss the results of this updated flare-imminence research in
Section 3.5. 1 Introduction NWRA Classification Infrastructure (NCI) has been used for
topics including detecting solar emerging flux regions (Leka
et al., 2013; Barnes et al., 2014), and filament eruptions
(Barnes et al., 2017), it developed from a series of works which
examined the question, “what is the difference between a flare-
imminent and flare-quiet solar active region?” (Leka & Barnes,
2003b; Barnes & Leka, 2006; Leka & Barnes, 2007; Welsch
et al., 2009; Komm et al., 2011). To understand a physical phenomena and guide relevant
modeling efforts, it is frequently important to identify what
features are unique or predisposed to an event. NCI is a tool
for doing that. We describe NCI here in general terms, guided
by the steps outlined above (a general flow-chart is provided
in Fig. 1). We describe in Section 2 the NCI research-focused
infrastructure, with which new questions, new data, param-
eters, approaches, etc. are developed and evaluated. We
discuss framing the question and event definition consider-
ations (Sect. 2.1), data analysis and parametrization (Sect. 2.2),
the various flavors of DA employed (Sect. 2.3) and the
extension to probabilistic classification by way of Bayes’
theorem (Sect. 2.3.3), evaluation tools (Sect. 2.4), and a
discussion of interpreting the results and selecting good
parameter combinations (Sect. 2.5). 2.2 Data and parametrization Statistical classifiers attempt to separate samples drawn
from different populations within parameter space. The
samples are thus representations of the physical state of the
systems in question. For
image-based
or
otherwise
spatially
distributed
variables, NCI derives both extensive and intensive parame-
ters, meaning those that do and do not depend on the size of the
feature in question, respectively (see Leka & Barnes, 2003a, b,
2007; Welsch et al., 2009). The spatially distributed variables
(i.e., “x”) are parametrized by the first four moments: mean x,
standard deviation s(x), skew &(x), and kurtosis k(x), often
weighted by some relevant quantity, plus spatial summations
as appropriate. The lower order moments capture the typical
properties of the target image, while the higher-order moments
capture the presence of small-scale features. The image data
themselves can be highly processed derived physical quantities
which have a 2-dimensional extent: in the case of imaging
spectroscopy, for example, an image of equivalent widths is
appropriate. For helioseismology, the image may be phase-
shifts or inferred vorticity maps (Komm et al., 2011; Barnes
et al., 2014). Linear DA has the advantage of being able to consider
large numbers of variables simultaneously even for small
sample sizes. If the variables are uncorrelated and in
standardized form, the magnitude of each variable’s coefficient
in the discriminant function gives its relative predictive power
(e.g., Klecka, 1980). If variables are correlated then their
predictive power will be shared. In practice diminishing
returns are usually found beyond at most 10 parameters, likely
due to correlations among variables in the solar contexts tested
thus far (Leka & Barnes, 2003b, 2007; Komm et al., 2011). The
disadvantage to linear DA is that it assumes a functional form
for the probability distribution which may not be valid, and for
most parameters considered here is likely invalid. Thus linear
DA is best suited to problems for which only small samples are
available, and in which large numbers of variables are needed
to make accurate classifications. NCI is routinely used to analyze time-series data. The
approach taken thus far is to fit time-series data with an
appropriate model and then use the retrieved coefficients or
model fits as parametrizations. 2.1.1 Event definitions Flare forecasting research tools are becoming somewhat
common (Gallagher et al., 2002; Wheatland, 2005; Georgoulis
& Rust, 2007; Colak & Qahwaji, 2009; Bloomfield et al., 2012;
Bobra & Couvidat, 2015) and their performance an active
subject of evaluation (e.g., Barnes & Leka, 2008; Bloomfield
et al., 2012; Falconer et al., 2014; Barnes et al., 2016). As a
demonstration of Research-to-Operation efforts in the space
weather forecasting context, we finally describe here the
details of the Discriminant Analysis Flare Forecasting System
(DAFFS, Sect. 4), a Near-Real-Time (NRT) operationally-
designed forecasting tool which grew from the NCI. DAFFS
was recently implemented under a Phase-II Small Business
Innovative Research (SBIR) project through the NOAA/
SWPC, as an answer to “Delivering a Solar Flare Forecast
Model that Improves Flare Forecast (Timing and Magnitude)
Accuracy by 25%.” (topic NOAA 2013-1 9.4.3W). It is
presently in use to aid target selection for the Hinode mission
(Kosugi et al., 2007), specifically its limited field-of-view The event definition is simply the categorical description
of an “event” and the countering “non-event”. In solar
physics, event definitions have included whether (or not) a
solar active region emerged (Barnes et al., 2014), or whether a
filament produced a coronal mass ejection (Barnes et al.,
2017). A widespread application has been regarding the
occurrence (or not) of a solar flare within the context of
photospheric magnetic field measurements (Leka & Barnes,
2003b, 2007), plasma velocity (Welsch et al., 2009) and
helioseismology-derived parametrizations (Komm et al.,
2011). An event definition can be any such description, the more
refined and specific the better. It must uniquely assign data
points to one of the two populations (event/non-event) against
which the ability to distinguish the populations may be
judged. j
g
By default, the NCI events are defined in a true forecasting
sense, with an upcoming interval during which the timing of an Page 2 of 23 Page 2 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 2.2 Data and parametrization In the case of the evolution of
photospheric magnetic field over the course of a few hours, for
example, a first-order function is fit to the image-derived
parameters, then the slope and intercept at a designated future
time are considered as two input parameters. 2.3 Discriminant Analysis event is unknown. However, NCI is designed for flexibility for
scientific investigations. With the construction of suitable
event definitions and event lists, NCI an also be invoked in an
super-posed epoch analysis mode (“SPE”; Leka et al., 2013;
Barnes et al., 2014) for which the event time is known and
analysis is carried out relative to that reference time (Mason &
Hoeksema, 2010; Reinard et al., 2010; Bobra & Couvidat,
2015). Discriminant Analysis (DA) (Kendall et al., 1983) is the
classifier employed here: DA is a statistical approach to
classify new measurements as belonging to one of two
populations based on characterizing the Probability Density
Functions (PDF) from known examples. In brief, DA divides
parameter space into two regions based on where the
probability density of one population exceeds the other. Key
to success is estimating the PDFs well. There are two general
approaches to estimating PDFs: parametric, in which the
functional form of the distribution is assumed, and non-
parametric, in which it is estimated directly from the data. Both
options are available in the NCI. For scientific investigations the emphasis could be on
understanding the physical differences between populations. Such a study could use either balanced sample sizes of the
populations in question or invoke equal prior probabilities for
the two populations, in order to highlight distinguishing
characteristics (Leka et al., 2013). This is in contrast to a
forecasting system where unequal sample sizes are the norm,
and one must incorporate the prior probabilities into the
analysis. 2.3.1 Parametric density estimation When each variable is assumed to have a Gaussian
distribution, with the same variance for each population, the
discriminant boundary is a linear function of the variables. This is quite a strong assumption, and one which is known to
be routinely violated for many solar physics relevant para-
metrizations; in practice, for some topics, the results have been
found to not depend strongly on the assumption (Leka &
Barnes, 2007), especially for rarer events. 2.3.2 Non-parametric density estimation In nonparametric DA (NPDA), no assumption is made
about
the
distribution
of
any
parameter. Instead,
the
distributions are estimated directly from the data. This negates
the need for making assumptions, but requires large sample
sizes to accurately estimate the distributions, especially when
considering the shape of the tails of the distribution, and
especially when considering multiple variables simultaneously
(see Table 4.2 in Silverman, 1986). As such, NPDA can only
reasonably be used for combinations of small numbers of
variables. Within NCI, NPDA is generally employed with at
most 2-variable combinations. p
p
The classifier employed here works best with continuous
variables, although it can handle discrete values. As discussed
below (Sect. 2.3), correlated parameters do not add useful
information. Sample size matters. Sufficient data allows for robust
estimates of the classifier performance, as demonstrated by
the resulting error bars on the validation metrics (see Sect. 2.4.1). Small sample sizes are especially problematic for
multi-variable analysis. While each situation is different,
samples significantly fewer than 100 data points in any
one population are challenging. Sample sizes may be
unbalanced. The NCI NPDA code presently estimates the probability
density using a kernel method with the Epanechnikov kernel; a
single smoothing parameter is set based on its optimum value
for a normal distribution (Silverman, 1986). This works well
for distributions which are not too far from a normal
distribution, but does not accurately represent long tails of Page 3 of 23 Page 3 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 distributions without very large sample sizes. Using a single
smoothing parameter has a tendency to undersmooth the tails
of a distribution when the peak of the distribution is
appropriately smoothed, or to oversmooth the peak if the
tails are appropriately smoothed. This is a particularly
important effect when multiple variables are considered, as
the volume of space occupied by the tails (where key parameter
differences can lie) grows rapidly with the number of variables,
and thus the difference between the density of observations
near the peak and in the tails becomes even more pronounced. To counteract this, the NCI works with the logarithm of
positive definite variables with a large skew (or the logarithm
of the absolute value of negative definite variables with a large
negative skew). 2.4.1 Metrics The success of the classification exercise is judged
quantitatively using metrics that are standard in classification
and forecast validation (Woodcock, 1976; Jolliffe & Stephen-
son, 2003; Bloomfield et al., 2012; Barnes et al., 2016). We
focus on the following: the Peirce skill score, also known as the
True Skill Statistic, or Hanssen and Kuipers discriminant
(H&KSS) and the Appleman skill score (ApSS) for categorical
forecasts, and the Brier Skill Score (BSS) for probability
forecasts. The Rate Correct (RC) is included for completeness. The full derivations and descriptions can be found in the cited
references; of note here are the critical functions of each: the
H&KSS measures the discrimination between the Probability
of Detection and the False Alarm Rate, the ApSS measures the
skill against the climatological forecast, and the BSS evaluates
the performance of probabilistic forecasts against observed
occurrence. All are normalized such that 1.0 is the highest
possible score and 0.0 represents no separation/no skill relative
to the appropriate reference. p
y
pp
Since it is impractical to apply NPDA to large numbers of
variables simultaneously, it is often helpful to consider the
performance of all possible permutations of small numbers of
variables to determine which ones are best able to classify the
data (see Sect. 2.5). Combining correlated variables does not
substantially improve the performance of NPDA over each
variable used alone. 2.4.2 Removing bias To make unbiased estimates of the performance of the
tested parameters, the NCI system uses cross-validation (Hills,
1966). In cross-validation, one data point is removed from the
sample of size n, and the remaining n 1 data points are used
to make a probabilistic forecast about or to classify the
removed point. This process is then repeated for all n data
points and the elements of the standard classification table can
be filled in (True Positive, False Positive, False
Negative and True Negative). Essentially, this approach
minimizes the influence of outliers classifying themselves, and 2.3.4 Missing data The BSS is itself a summary of Reliability plots which
graphically display systematic under- and over-forecasting
through the comparison of the predicted probabilities to
observed frequency (see Barnes et al., 2016, for a discussion). In NCI missing data (e.g., due to outages) is differentiated
from “well-measured null values” such as the length of a
strongly-sheared magnetic polarity inversion line in a unipolar
region (with no such line). Neither of these categories of data
are ignored or removed; instead, they are assigned the
climatology derived for all other datapoints with the same
missing-data assignment. For multiple-parameter analysis, the
climatology is determined by those regions which have the
same combination of data flags (good, null, bad/missing). In
this manner, as much information as is possible (for example if
one parameter is good but the other is missing) can be used in
the classification. 2.3.2 Non-parametric density estimation NPDA is thus best suited to problems for
which large samples are available, and for cases in which only
a small numbers of variables are needed to make accurate
classifications. With sufficiently large sample sizes, even the
tails of a distribution will be well captured by this approach. validation metrics but estimating their uncertainty, identifying
and removing bias, and accounting for statistical flukes. Challenges to this and other statistical methods include: small
and/or unbalanced sample sizes, bias in the samples, and undue
influence from outlier data. However, with the use of
appropriate metrics and error estimates, these challenges are
not insurmountable to achieving valuable understanding. 2.3.3 Extension to probabilistic forecasts To predict the probability of a data point belonging to a
given population, rather than a categorical (yes/no) classifica-
tion, Bayes’ theorem
is invoked (Barnes et al., 2007). The
probability that a measurement x belongs to population j is
given by: pp
p
The categorical skill scores require a probability threshold
(Pth) above which an event is classified (or forecast) to occur. By default NCI uses Pth = 0.5, which effectively optimizes the
ApSS because the errors of both types are treated equally. As
discussed by Bloomfield et al. (2012); Barnes et al. (2016) the
optimal H&KSS occurs when Pth ≈R, R being the event rate. The Relative Operating Characteristic (ROC) curve tracks
performance of the H&KSS as a function of varying Pth; the
Gini coefficient G1 (or ROC Skill Score; Jolliffe &
Stephenson, 2003) then quantifies the ROC curve: G1 = 2 *
A 1.0 where A is the area under the ROC curve, and again
G1 = 1.0 denotes a perfect score. Given the sensitivity of the
H&KSS to this Pth, which is to some level a function of
customer priority between False Alarms and Misses, we report
the Gini coefficient as a concise summary of the behavior of
this metric. PjðxÞ ¼
qj f jðxÞ
q1 f 1ðxÞ þ q2 f 2ðxÞ ;
ð1Þ ð1Þ where qj is the prior probability of belonging to population
j, f jðxÞ is the PDF for population j, and (for the flare study)
j = 2 refers to the flaring population, while j = 1 refers to the
flare-quiet population. This expression is valid for any well
behaved probability density function f. 2.5.1 Identifying multiple well-performing parameters A bootstrap method is used to account for random errors
(Efron & Gong, 1983), employing 100 draws by default. The
draws are performed randomly across all data (meaning the
sample sizes in each draw are equal to the sample sizes of the
two populations for the data), with points selected randomly
with replacement (each sampled point is not removed from the
drawn-upon sample, it may be drawn again). The resulting skill
scores are computed for each draw, and the uncertainties are
estimated by the standard deviation of the draws’ scores. To choose the best-performing single variable, NPDA is
performed on all available data including cross-validation and
100-draw bootstrap as outlined above. The single variables
with the highest values of the skill score of interest are selected
for 1-variable results. Bootstrap draws with no samples in one
or all populations (possible for small sample sizes) have a flag
assigned for the skill scores, to either include in later
computation or to ignore. Small samples will generally result in large uncertainties. For the examples given in Section 3.4, with a sample size of
events of 40 (for Xþ1) the typical uncertainty in a skill score is
0.06–0.10, while with a sample of events of 2636 (for Cþ1),
the typical uncertainy is 0.01. In both cases, the sample size of
non-events is more than a factor of 10 larger than the sample
size of events, so the dominant source of the uncertainty is the
density estimates for the events. We developed a practical approach to evaluate multi-
variable combinations which likely captures the best-perform-
ing 2-variable combinations, although it remains a possibility
that a well-performing combination is missed. We first compute
the skill scores for all possible 2-variable combinations without
a bootstrap and using a simplified form of cross-validation in
which the contribution from the removed point is subtracted
from the density estimate, but the full density estimate is not
recomputed with an updated value of the smoothing parameter. Six variables which appear in almost every combination of the
top performing combinations are selected. Those are then
paired with each of the others available with the full cross-
validation and bootstrap draws applied, and the results are
sorted on the skill score of choice. There are generally
parameters or parameter combinations which perform similarly
within the uncertainties (Leka & Barnes, 2003b). This is
especially true for classes having larger sample sizes. 2.5 What was learned? Having identified the best-performing parameters (or
parameter combinations) and their discriminating power one
is then poised to physically interpret the results in the context of
the posed question. Conversely, if there are no results which
indicate skill, then none of the parameters tested are able to
successfully distinguish the populations in parameter space, and
are essentially irrelevant to the question posed. Identifying the
well-performing parameters also serves as a method for
selecting those to be used for successful operational forecasting. After the four steps above, the final one allows for analysis
of what are the physically important parameters for the
physical question at hand, i.e. “what variables provide the most
insight into the physical processes at play in the context of the
posed question?” Alternatively, in the operational context,
determining the best performing parameters is tantamount to
producing a good forecast. For many of the scientific questions addressed and
addressable in NCI, hundreds of parameters calculated from
the data are considered, which leads to millions of available
parameter combinations. In practice only 1- or 2-variable
combinations are most appropriate for use, especially with
NPDA, where sample-size requirements increase very quickly
with the number of variables considered simultaneously. However, with so many parameters under consideration,
statistical flukes will occur: variables or variable combinations
may seem to perform well (or poorly) when in fact they do not,
upon testing further with larger sample size. As noted 2.5.1 Identifying multiple well-performing parameters The point
of reporting multiple parameter-combination (classification,
forecast) results is not an ensemble result but a guard against
statistical flukes (see below). 2.4.4 Accounting for statistical flukes With a large number of parameters being tested, even with
cross-validation and bootstrap error estimates, statistical flukes
can occur such that a parameter appears to work well when it in
fact does not. The best remedy for this is sample size, although
the Sun does not always cooperate. As described in Barnes et al. (2014), a Monte Carlo
experiment can be used to check that the outcome is not simply
a result of random chance: two random samples with sizes
equal to the sample sizes of the two samples are drawn from the
same normal distribution to represent one variable with no
power to distinguish the two populations. This is repeated for a
large number of variables, and the same analysis is performed
on these random variables as on the actual parameters being
studied. In this manner, it can be determined what statistical
outliers in the skill scores may be expected given no difference
in the two underlying populations (see Sect. 3.4). Different event definitions (Sect. 2.1.1) will lead to
different top-performing parameters or parameter combina-
tions. Similarly, optimizing the results according to different
skill scores will result in different parameters being chosen
(Barnes et al., 2016). In practice, however, while there may be
a slight re-ordering of the results, we find that the same
parameters (or very closely related parameters, such as total
magnetic flux vs. total negative magnetic flux) are routinely
within the top few percent of the results. 2.4 Evaluation Evaluating the results of a classification exercise is a multi-
faceted task that includes not just the calculation of the Page 4 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 is a particularly important process when working with small
sample sizes. previously, multi-parameter combinations formed from corre-
lated variables do not add discriminating power (Leka &
Barnes, 2007). 3 NCI and empirical research into the
causes of solar flares As mentioned above, NCI originated from early research
into the statistical differences between flare-imminent and
flare-quiet time intervals (Leka & Barnes, 2003b; Barnes &
Leka, 2006; Leka & Barnes, 2007). The research has continued Page 5 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 will have an extended large-value tail compared to single ARs. Second, most HARP numbers are assigned to regions which do
not have a corresponding NOAA number. Such regions are
plentiful, are predominantly small (often consisting solely of
plage), and hence the parameters (both extensive and
intensive) will have distributions which are more densely
populated at lower values than AR-based distributions. Table 1. Event definitions. Label
Minimum
threshold
(nomenclature)
Minimum
threshold
(W m2)
Latency
(h)
Validity
period
(h)
Region/full
disk
C þ 1
C1.0
≥106
2.2
24
R, FD†
M þ 1
M1.0
≥105
2.2
24
R, FD
X þ 1
X1.0
≥104
2.2
24
R, FD
C þ 2† C1.0
≥106
26.2
24
R, FD
M þ 2
M1.0
≥105
26.2
24
R†, FD
X þ 2
X1.0
≥104
26.2
24
R†, FD
C þ 3† C1.0
≥106
50.2
24
R, FD
M þ 3
M1.0
≥105
50.2
24
R†, FD
X þ 3
X1.0
≥104
50.2
24
R†, FD
†
Not included in NOAA’s forecasts but included here for
completeness. Table 1. Event definitions. p p
The full-disk forecasts are created by combining the flaring
probabilities of the regions: PFD ¼ 1:0 ∏
AR
ð1:0 PARÞ;
ð2Þ ð2Þ where PAR are the flaring probabilities of each active region
and PFD is the resulting full-disk flaring probability. Of note,
combining probabilities in this manner assumes independent
events; this assumption may not hold during times of high solar
activity when numerous magnetically interconnected regions
are present on the solar disk (Schrijver & Higgins, 2015). The
NCI can thus provide full-disk forecasts but those are usually
less useful for research purposes and more appropriate for the
operational tool (see Sect. 4). where PAR are the flaring probabilities of each active region
and PFD is the resulting full-disk flaring probability. Of note,
combining probabilities in this manner assumes independent
events; this assumption may not hold during times of high solar
activity when numerous magnetically interconnected regions
are present on the solar disk (Schrijver & Higgins, 2015). 3.2 Data sources and parametrization Early NWRA NCI-based research examined the question
of differences in flare-imminent vs. flare-quiet active regions
(Leka & Barnes, 2003a, b; Barnes & Leka, 2006; Leka &
Barnes, 2007) using a substantial database of time-series
photospheric vector magnetic field data from the U. Hawai‘i
Imaging Vector Magnetograph (Mickey et al., 1996; LaBonte
et al., 1999; LaBonte, 2004; Leka et al., 2012). Additional
studies (Barnes et al., 2016) used line-of-sight photospheric
magnetic
field
data
from
the
Solar
and
Heliospheric
Observatory/Michelson Doppler Imager (SoHO/MDI Scherrer
et al., 1995). Current NWRA research and performance
baselines use new data sources, as described here. 3 NCI and empirical research into the
causes of solar flares The
NCI can thus provide full-disk forecasts but those are usually
less useful for research purposes and more appropriate for the
operational tool (see Sect. 4). †
Not included in NOAA’s forecasts but included here for
completeness. with new data sources and parameters; as such, NCI has proven
useful as a testbed infrastructure for this research topic. Here
we demonstrate NCI with this specific flare-related topic, and
thus provide an update of the state of NWRA’s research from
earlier publications. 3.1 Event definitions For the NCI research on flare-imminent active regions, we
adopted a “forecast” model for event definitions, and essentially
match the forecasts issued by NOAA, as summarized in Table 1
based on events as illustrated in Figure 2. The thresholds are defined by the peak Soft X-ray flux as
reported by NOAA/SWPC, based on the 1–8 Å Soft X-ray
detector on the Geostationary Observing Earth Satellite
(GOES) platform at the time of the event. It should be noted
that in the application of DA to flaring active regions as defined
in this manner, a continuous variable (the Soft X-ray emission)
defines the categorical event definition required by DA by
means of a fairly arbitrary threshold. Additionally, defining an
event by its peak Soft X-ray emission captures only a limited
measure of flare-associated energetic output. To characterize the state of the active regions and their
likelihood to flare, we perform parametric analysis on the data
sets described above. The goal is to reduce the ([x, y, t]) vector
magnetic field time series plus the flaring history of each active
region into a series of parameters suitable for statistical
analysis. The parametrization packages which are now well-
established or are under active research are fairly modular; the
results from each are often merged after the parameters are
calculated, for classifier analysis. g
p
We included a 2.2 h delay needed for all data processing
(including initial Solar Dynamics Observatory/Helioseismic
and Magnetic Imager (SDO/HMI) data-reduction at Stanford)
between data acquisition time and forecast issuance time,
although for research based on the definitive time series, this is
effectively moot. In other words, when relying upon the
definitive data, the last dataset used is from 21:48 TAI for a
forecast (classification) issued at 00:00 UT. The Soft X-Ray
(SXR) events considered to match the forecast validity periods,
are taken from that issuance time. 3.2.2 Data: SDO/HMI photospheric vector magnetic field
data The present NCI research extends earlier work naturally by
relying upon time-series of vector magnetic field data from the
Helioseismic and Magnetic Imager from the Solar Dynamics
Observatory (Pesnell, 2008; Scherrer et al., 2012; Schou et al.,
2012; Centeno et al., 2014; Hoeksema et al., 2014). NWRA
became
an
SDO
remote
SUMS/DRMS
(Storage
Unit
Management System/Data Record Management System) site
early in the mission, as NWRA's “ME0” disambiguation code
is used for the pipeline data reduction (Leka et al., 2009;
Hoeksema et al., 2014) and easy access to the data was needed
for pipeline-code implementation. NWRA maintains local
copy of the definitive hourly HMI data through the remote-
SUMS system and automated updates of the metadata DRMS
database. Definitive data are transferred roughly monthly using
the JSOC Mirroring Daemon1. The hourly HARP-based sub-areas are extracted, coal-
igned, and gathered together as custom in-house Flexible
Image Transport System (FITS) files. The filename describes
the start time, length of time-series, cadence, and HARP
number, and is unique; as such it forms the basis for cross
referencing throughout NCI. The hmi.Bharp_720s and hmi. sharp_720s series (both linked to hmi.MEharp_720s)
provide disambiguated extracted HARP-area vector field data
cut-outs. Following earlier studies (Leka & Barnes, 2003a,b, 2007),
the image-plane coordinate system is used by default, with
transformations to heliographic components performed using
point-by-point observing angle component computation and a
propagation of uncertainties based on the uncertainties from the
inversion as included in the hmi.ME_720s_fd10 series. The
multi-point approach avoids significant errors arising from a
planar assumption in the (not infrequent) case that a HARP
extends over a significant portion of a visible half-hemisphere. A potential field whose normal component matches the input
normal component boundary is computed using a Cartesian
Fourier-component method; a guard ring which is a factor of 2
larger than the input boundary size is invoked in order to reduce
artifacts which can arise with a boundary occurring on, or too
near, strong-field areas. An estimate of the 1s uncertainty in
the potential-field components is computed using the computed
components themselves: within active pixels, those that are
brighter than the mean less the mean absolute deviation of the
continuum intensity are used to compute histograms of that
component’s field strengths. The field strength where 68% of
the area under the histogram curve is achieved is denoted that
component’s 1s uncertainty level. 3.2.1 Data: NOAA-generated Soft X-ray event lists NWRA gathers the event lists of solar flares as defined by
NOAA/SWPC; the information required includes the start
time, peak time, peak flux and associated NOAA-numbered
active region source (Fig. 2). These are acquired from the
NOAA archives through ftp.swpc.noaa.gov/pub/warehouse
and from the NRT updating lists at http://services.swpc.noaa. gov/text/solar-geophysical-event-reports.txt
Additionally,
NWRA subscribes to the NOAA External Space Weather
Data Store (E-SWDS) NRT space weather data access system,
where events are recorded with minimal delay. We do not
attempt to perform any of the analysis by which to
independently determine start time, peak flux, or location. The region-by-region forecasts are based on the HMI
active region patches (‘HARPs’ Bobra et al., 2014; Hoeksema
et al., 2014, see Sect. 3.2.2) rather than strictly on NOAA
Active Regions (ARs). This approach has two consequences if
the results are compared to strictly NOAA AR-based methods:
first, there are many HARPs which contain more than one
NOAA region. As such, the distributions of parameters (in
particular extensive parameters such as total magnetic flux) Page 6 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å
channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional
demonstrations below). Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å
channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional
demonstrations below). Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å
channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional
demonstrations below). In particular, flares for which NOAA does not provide an
associated active region, as occurs for a fraction of smaller
flares and a few larger flares, are not included in the NCI
analysis by default. calibrations that are scheduled at some of the :00 times, we
focus on the :48 data. No data are used that have a quality flag
different from zero. 3.2.1 Data: NOAA-generated Soft X-ray event lists As described in Section 3.2.8, data
covering 6 h inclusive (7 time periods) provide input for short-
term temporal-evolution parameters. By default the NCI
classification mimics a midnight-issued forecast, thus hourly
data from 15:48 to 21:48 are targeted. For definitive data, there
is no constraint regarding the HMI data reduction pipeline
timing requirements. 1 See http://vso.tuc.noao.edu/VSO/w/index.php/Main_Page. 3.2.3 Data: photospheric line-of-sight magnetic field data 3.2.3 Data: photospheric line-of-sight magnetic field data 3.2.4 Other data sources Photospheric line-of-sight magnetic field data is used in
some NCI research on solar flare productivity. The SoHO/MDI
mission provided a significant data set, used in one of the first
systematic forecasting comparison efforts (Barnes et al.,
2016). Presently, the National Solar Observatories (NSO)
Global Oscillations Network Group (“GONG”; Hill et al.,
2003), in particular the line-of-sight magnetograms, is an
ingested dataset for analysis by NCI tools. The GONG data is
used in the NRT forecasting system in the event that the vector
field data are unavailable (see Sect. 4.1). The GONG data do
have the advantage of lengthy coverage, which increases the
statistical significance of the training results. For research purposes, the NCI has been used for
investigations using helioseismology and coronal emission
as related to emerging magnetic flux (Leka et al., 2013; Barnes
et al., 2014) as well as flaring. The data sources for these
investigations have been or will be described in detail in the
relevant publications. 3.2.2 Data: SDO/HMI photospheric vector magnetic field
data The analysis of the vector
field data extends to viewing angle u ≈80 from disk center. g
For the flare-targeted research with NCI the definitive data
series are used; we do not generally employ the cylindrical
equal-area reprojected data. The hmi.Mharp_720s series,
including the bitmap which flags active-pixel “blobs” (see
Fig. 3 and Table 8; Hoeksema et al., 2014) is used to identify
theHARPsthatareextractedfromthefull-diskMilne-Eddington
inversion data series hmi.ME_720s_fd10, including uncertain-
ties from the inversion (Centeno et al., 2014). The hmi.B_720s
series provides the pipeline disambiguation results and their
confidence (Hoeksema et al., 2014). Additionally, we optionally
extract the same HARP sub-areas from the continuum images in
hmi.Ic_720sandtheline-of-sightmagnetogramsinhmi.M_720s. Anexample HARP and active-pixel map isshown in Figure3 for
the region associated with the flares demonstrated in Figure 2. g
g
To keep the data volume and analysis tenable, an hourly
cadence is generally used; to avoid problems from daily Page 7 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 3. An image of NOAA AR 11283 at 2011.09.07 21:48 TAI as an SDO/HARP #833), showing the vertical component of the magnetic field
Bz from SDO/HMI (red/positive, blue/negative contours at ±100 Mx cm2); axes are in arcsec, and green/yellow contours indicate the vertical
current density Jz at ±50, 100 m Am2. The HARP “active pixel” area is outlined in grey. Fig. 3. An image of NOAA AR 11283 at 2011.09.07 21:48 TAI as an SDO/HARP #833), showing the vertical component of the magnetic field
Bz from SDO/HMI (red/positive, blue/negative contours at ±100 Mx cm2); axes are in arcsec, and green/yellow contours indicate the vertical
current density Jz at ±50, 100 m Am2. The HARP “active pixel” area is outlined in grey. 3.2.5 Parametrization: prior flare history Future solar energetic events often follow previous
activity, with a somewhat predictable distribution in size
and frequency (Wheatland, 2005). As such it is not surprising
that “flare persistence” can be a good indicator of future
activity (Falconer et al., 2012); in fact, it forms one of the
primary
predictors
used
for
NOAA/SWPC
operational
forecasts (Sawyer et al., 1986). Data from all available GONG stations are acquired for a
target time from the NSO near-real-time GONG website, and
assessed. The best is chosen based on metrics (moments of
spatial gradients) which quantify the seeing quality with a
normalization to account for slightly differing plate scales
between the sites. From this module, the parametrization of prior flaring
activity provides event probabilities based on peak Soft X-ray
output over the prior 6, 12, and 24 h, including the change in
flaring output between those intervals. This “Prior Peak Flux”
(PFF) parametrization essentially follows Abramenko (2005): GONG-based active-region patches are extracted accord-
ing to the NOAA E-SWDS AR data, with a bounding-box
generally reflecting the size of the region (latitude, longitude,
and area), then adjusted for solar rotation to the target time of
the acquired data. FL ¼
X
indexC þ 10 indexM þ 100 indexX;
ð3Þ FL ¼
X
indexC þ 10 indexM þ 100 indexX;
ð3Þ FL ¼
X
indexC þ 10 indexM þ 100 indexX;
ð3Þ ð3Þ q
In general when Blos is employed for analysis, an estimate
of Bz is derived using a potential field which matches the
observed Blos, following Leka et al. (2017). Note that this
differs from assuming that Blos ≈Bz. From this potential field,
a radial field estimation, Bpot
z , is retrieved to be used for the
input. The advantage of this treatment of a Blos boundary is
twofold, as discussed in Leka et al. (2017): the magnetic field
strengths better approximate the radial field strengths and the
apparent magnetic polarity inversion lines that are in fact
caused only by viewing angle are removed or significantly
mitigated. As such, for line-of-sight sources as with vector
data sources, the magnetic field analysis functions fully to
u ≈80. where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES
1–8 Å detectors. Example categories include: where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES
1–8 Å detectors. 3.2.6 Parametrization: photospheric magnetic field The parametrization of the photospheric magnetic field
essentially follows Leka & Barnes (2003a and b); Barnes et al. (2007). The goal is to identify signatures of magnetic field
complexity, to estimate energy storage, and identify non-
potential structures and magnetic twist – in the context that
regions showing evidence of minimal available magnetic
energy, minimal energy storage, low complexity and nearly-
potential (current-free) fields are much less likely to flare, and
vice versa. As described in Barnes et al. (2007), the
photospheric parameters in many ways quantify the character-
istics which are used for the sunspot-group classifications such
as
the
McIntosh
(McIntosh,
1990)
(modified
Zurich)
nomenclature. The variables, described in detail in Leka &
Barnes (2003a), fall into nine broad categories: )
For each quantity, the parametrization only includes
“active pixels” within the full HARP box. For all magnetic
field data, we include only those pixels with signal/noise ratio
S/N > 4 by default (the S/N threshold is a definable parameter). Masks are created using these criteria, but which are then
eroded and dilated using a 2 2 shape operator in order to
avoid single-pixel inclusions. For quantities that, for example,
require spatial derivatives, the derivatives are taken on the full
sub-area, then the appropriate computation (moment analysis,
totals, etc.) include only those pixels that meet the selection
criteria. Separate but analogous masks are created to identify
the magnetic neutral lines, using similar thresholds and
boundary-smoothing approaches. (
)
g
– the magnetic field vector component magnitudes, Bz and Bh;
– the inclination angle of the fields, g ¼ tan1ðBz=BhÞ; – the magnetic field vector component magnitudes, Bz and Bh;
h i
li
i
l
f h fild
1ðB =B Þ – the inclination angle of the fields, g ¼ tan1ðBz=BhÞ; g
g
ð
=
Þ
– the horizontal spatial gradients of the magnetic fields, | ∇h
B|, | ∇h Bz|, | ∇h Bh|; |, |
h
z|, |
h
h|;
– the vertical current density, Jz ∼(∂By/∂x ∂Bx/∂y); – the force-free parameter, a ∼Jz/Bz; – the vertical portion of the current helicity density, hc ∼JzBz;
1 – the shear angle from potential, C ¼ cos1ðBp⋅Bo=BpBoÞ; ð
=
Þ
– the
photospheric
excess
magnetic
energy
density,
re ¼ ðBp BoÞ2=8p; – the magnetic flux near strong-gradient magnetic neutral
lines, ℛnwra. As described above, moment analysis and extensive
parameters are used to describe the spatially distributed
variables. 3.2.5 Parametrization: prior flare history Example categories include: where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES
1–8 Å detectors. Example categories include: – the total peak flux of the target active region in the 12 h
prior to the forecast; – the total peak flux from the time the region was first
identified prior to the forecast; p
– the number of flares produced by a target active region in
the prior 12 h compared to the prior 24 h. There is no additional statistical sophistication in these
parametrizations of flaring history. While the comparisons and
summations are performed for the prior 6, 12, and 24 h Page 8 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Barnes
et
al.,
2016). Only
strong-flare
regions
were
considered. intervals, there has not yet been any systematic testing of
whether these terrestrially-defined periods are optimal (Leka &
Barnes, 2017). The approach taken here is to calculate a quantity ℛnwra
which
more
closely
represents
the
physically
relevant
boundary properties: as such, the vertical component of the
field Bz is used rather than Blos; the threshold is based on the
noise in the Bz component (and thus varies), and all steps which
depend on distances or sizes use an appropriate physical
distance in 106 m as computed according to pixel size and
observing angle (and thus the number of pixels used will vary
with observing angle). Of note, there is no attempt to identify
only a single or primary strong-gradient neutral line, and
depending on sizes and thresholds chosen, numerous small
strong-gradient neutral lines may be identified (Fig. 4). The
resulting magnitudes of ℛnwra differ from Schrijver (2007), in
part due to the new implementation but also due to the different
data source, although the general behavior is very similar (see
discussion in Barnes et al., 2016). 3.2.7 Parametrization: magnetic charge topology Most solar energetic events are believed to ultimately
originate in the corona, where the magnetic field generally
dominates the plasma and the climate is more conducive to the
storage and subsequent rapid release of energy via magnetic
reconnection. A corona with a very complex magnetic
topology is one which should more readily allow magnetic
reconnection to initiate, and hence an eruptive event to begin. The Magnetic Charge Topology model describes the coronal
topology and its evolution, using as a boundary time-series
maps of the photospheric radial field Bz. Concentrations of
magnetic flux in an active region are represented by point
sources (Fig. 5, top). A gradient-based tessellation scheme,
supplemented by the partitioning of a reference time-averaged
magnetogram, is used to track each magnetic concentration
with time (Barnes et al., 2005). The coronal magnetic field is
modeled as the potential field of the point sources, from which
a unique magnetic connectivity matrix is derived (Fig. 5,
bottom). While arguably inappropriate for very complex active
regions, using a potential field is fast (significantly faster than
non-linear
force-free
extrapolations),
physics-based
(see
discussion in Barnes & Leka, 2008), and arguably captures ℛnwra ¼
X
f ℬð∇hℬz ± ÞdA;
ð4Þ ð4Þ where ℬ(∇h Bz ±) identifies polarity-inversion lines and f is a
Gaussian convolution function. Schrijver (2007) identified
magnetic neutral lines using polarity-specific bitmaps con-
structed using SoHO/MDI (Domingo et al., 1995; Scherrer
et al., 1995) Blos magnetograms, including only areas that
exceeded a fixed 150 Mx cm2 threshold, and dilating the
bitmaps with a 6'' 6'' kernel; overlapping regions were thus
identified as strong-gradient magnetic neutral lines. A new
bitmap with the neutral lines thus identified was convolved
with a Gaussian of FWHM Dsep = 15 Mm (fixed at 10 MDI
pixels) to obtain a weighting map which, when multiplied by
the |Blos| magnetogram and summed (assuming a fixed areal
coverage of 2.2 1016 cm2 per pixel), resulted in ℛ. In
Schrijver (2007), regions were only considered within 45 of
disk center, with the assumption Blos ≈Br, and viewing-angle
impacts on pixel-sampled area, etc, were negligible (see also where ℬ(∇h Bz ±) identifies polarity-inversion lines and f is a
Gaussian convolution function. 3.2.6 Parametrization: photospheric magnetic field The magnetic character of an active region is thus
reduced to approximately 150 variables. In the event that the
Blos data are used, only parameters that do not rely on the
horizontal component of the field are calculated. where Bp is the computed potential field referred to in
Section 3.2.2. All quantities are based on physically-
meaningful helioplanar components that include or are
weighted by the deprojected pixel area, as approrpiate. The last category follows Schrijver (2007), who developed
a parameter to characterize current-carrying emerging flux
systems which manifest as magnetic neutral lines displaying
strong spatial gradients: 3.3 Discriminant Analysis As discussed in Barnes & Leka (2008), fij is essentially
indistinguishable from the “effective connected magnetic
field” Beff ¼ cij=jxi xjj2 (Georgoulis & Rust, 2007) with the
primary distinguishing features being the square of the
distance and more importantly, a physics-based potential field
forming the basis of the connectivity matrix for the MCT
parameters. A quantity f2, which uses the potential-field based
connectivity in the expression for Beff, is included in the NCI. All forecasting methods include a statistical analysis
or machine learning in order to produce a forecast from
the observational input. Ranging from the simple (a
correlation, e.g. Falconer et al., 2011) to quite complex
(a Cascade Correlation Neural Network (e.g., Ahmed et al.,
2013)), the basic goal is the same: use a description of past
event behavior in the context of past data, to predict future
events given new data. DA as a general statistical characteri-
zation was first applied to solar flare forecasting in an early
attempt to quantify improvements which could be made
through multi-parameter analysis (Sawyer et al., 1986). 3.2.7 Parametrization: magnetic charge topology The MCT variables used in the NCI analysis (see Barnes &
Leka, 2006) focus on categories describing the distribution of: – the number and separation of magnetic sources S; – the number and separation of magnetic sources S; p
g
– the flux assigned to each source, |Fi|; – the magnetostatic energy EB ¼
1
ð2pÞ2
P
i<j
FiFj
jxixjj; – the magnetostatic energy EB ¼
1
ð2pÞ2
P
i<j
FiFj
jxixjj; – the characteristics of the connectivity matrix cij describing
the flux connecting source i to source j; – the characteristics of the connectivity matrix cij describing
the flux connecting source i to source j; – the characteristics of the connectivity matrix cij describing
the flux connecting source i to source j; The HMI magnetic field data incur a temporal variation as a
function of the orbital velocity of the SDO spacecraft, as
described in Hoeksema et al. (2014). Although efforts are
underway to mitigate the impact (Schuck et al., 2016), for the
moment, any analysis based on temporal variation of the
magnetic field must accommodate these variations. In the case
of DAFFS the “dt” parameters are all calculated using the same
part of the orbit, and as such will present a bias in the
magnitude of parameters calculated for all samples, but will
not preferentially select one population over another. Forecasts
or classifications which target a different time and use data
from a different time of day (undergoing a different part of the
daily orbit) are considered separately. – the flux in each connection weighted by inverse distance
between connected sources, ’ij ¼
cij
jxixjj; j
jj
– the angle between the north/south axis and the line segment
between connected sources, jij ¼ tan1 xjxi
yjyi
h
i
for cij ≠0; j
yj
yi
h
i
– the distribution of the number of connections from each
source Ci. The basic analysis calculates almost 50 parameters based
on the above-mentioned characteristics. Of note, due to
computational requirements the magnetic null-finding (as was
described in Barnes et al., 2005) is not routinely performed for
large datasets. 3.2.7 Parametrization: magnetic charge topology Schrijver (2007) identified
magnetic neutral lines using polarity-specific bitmaps con-
structed using SoHO/MDI (Domingo et al., 1995; Scherrer
et al., 1995) Blos magnetograms, including only areas that
exceeded a fixed 150 Mx cm2 threshold, and dilating the
bitmaps with a 6'' 6'' kernel; overlapping regions were thus
identified as strong-gradient magnetic neutral lines. A new
bitmap with the neutral lines thus identified was convolved
with a Gaussian of FWHM Dsep = 15 Mm (fixed at 10 MDI
pixels) to obtain a weighting map which, when multiplied by
the |Blos| magnetogram and summed (assuming a fixed areal
coverage of 2.2 1016 cm2 per pixel), resulted in ℛ. In
Schrijver (2007), regions were only considered within 45 of
disk center, with the assumption Blos ≈Br, and viewing-angle
impacts on pixel-sampled area, etc, were negligible (see also Page 9 of 23 Page 9 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 4. The vertical magnetic field strength (white/black being positive/negative, scaled to 500 G) of HARP 833 i.e. NOAA AR 11283 (cf. Fig. 3), showing regions identified as strong-gradient magnetic neutral lines for which the ℛnwra parameter is calculated (green boxes) with the
0.68-level contour of the Gaussian-convolved bitmap indicated (purple contours). Similar masks are used for the “magnetic neutral line”-related
parametrizations. Fig. 4. The vertical magnetic field strength (white/black being positive/negative, scaled to 500 G) of HARP 833 i.e. NOAA AR 11283 (cf. Fig. 3), showing regions identified as strong-gradient magnetic neutral lines for which the ℛnwra parameter is calculated (green boxes) with the
0.68-level contour of the Gaussian-convolved bitmap indicated (purple contours). Similar masks are used for the “magnetic neutral line”-related
parametrizations. the key features of coronal complexity associated with event-
productive solar active regions (Régnier, 2012). parametrizations discussed in the prior sections. For the
photospheric magnetic field parameters and the coronal
topology parameters, a linear function is fit to the parameters
computed at each of the seven times acquired. The slope and
intercept at the forecast issuance time are used (Fig. 6) as two
separate parameters. The intercept is used instead of the mean
(or similar) of the times considered, in order to account for
latency between data acquisition, analysis time, and the
forecast issuance time. 3.2.8 Static vs. temporal variation The NCI as implemented for research on flare-imminent
active regions is designed to include the recent evolution of the Page 10 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 tration of Magnetic Charge Topology analysis, characterizing the coronal magnetic topology of NOAA AR
:48:00 TAI. Top: magnetogram showing the vertical field (greyscale), the partitions (contours), and the locatio
ositive and negative). Areas outside of the active-pixel bitmap (cf. Fig. 3) are set to zero. Bottom: same a
howing the connectivity matrix (blue lines) with dark/thick lines indicating more flux in the connection than Fig. 5. Demonstration of Magnetic Charge Topology analysis, characterizing the coronal magnetic topology of NOAA AR 11283 (Fig. 3),
2011.09.07 at 21:48:00 TAI. Top: magnetogram showing the vertical field (greyscale), the partitions (contours), and the locations of the sources
(þ and for positive and negative). Areas outside of the active-pixel bitmap (cf. Fig. 3) are set to zero. Bottom: same as top panel, but
schematically showing the connectivity matrix (blue lines) with dark/thick lines indicating more flux in the connection than light/thin lines. 3.3.1 NCI flare research error estimation The bootstrap method described above (Sect. 2.4.3) is
performed randomly on each HARP for region forecasts;
uncertainties for the full disk probabilities are calculated by
performing the bootstrap on daily ensembles. The resulting
skill scores are computed for each draw, and their uncertainties
are calculated by the standard deviation of the draws. 3.3.2 Accounting for statistical flukes The NCI research into flare productivity generally uses
NPDA (Sect. 2.3). Examples of 1-variable and 2-variable
results are shown in Figure 7, for one event definition
(Sect. 3.1). The issues raised regarding small tail sample sizes
are readily apparent in the graphic for the 2-variable sample
results. As mentioned above, a Monte-Carlo approach can be used
to estimate how likely any of the reported scores would be by
statistical fluke, given the sample sizes and number of
parameters considered. Using the flare-probability parameters
described above and the HMI-data sample sizes, we estimate
there would be <1% chance of a resulting BSS > 0.001/0.002/
0.003 by chance alone for single variable NPDA for C1.0þ/
M1.0þ/X1.0þ flares, respectively. 3.4 NCI flare research: evaluation We present first some representative results using the
“research-based” modules for flare-imminent classification Page 11 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 of 6 h intervals (7 samples) of time-series parameters from the magnetic field analysis of NOAA AR 11283 for three t
the evolution of the total magnetic flux, the evolution of the proxy of the free magnetic energy; evolution of the
ear in the vicinity of the magnetic neutral line; Bottom: the evoluton of the log of the ℛparameter. The times relative t
own, in these cases the three intervals end just before the X1.8 flare on 2011.09.07, just before the X2.1 flare on 201
eriod of 2011.09.7, respectively. That is, this would be an example invoking a super-posed epoch analysis whereas in
e forecast issuance time would likely be a particular time of day. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 6. Plots of 6 h intervals (7 samples) of time-series parameters from the magnetic field analysis of NOAA AR 11283 for three time intervals. From Top: the evolution of the total magnetic flux, the evolution of the proxy of the free magnetic energy; evolution of the area of strong
magnetic shear in the vicinity of the magnetic neutral line; Bottom: the evoluton of the log of the ℛparameter. The times relative to the issuance
times are shown, in these cases the three intervals end just before the X1.8 flare on 2011.09.07, just before the X2.1 flare on 2011.09.06, and a
flare-quiet period of 2011.09.7, respectively. That is, this would be an example invoking a super-posed epoch analysis whereas in a forecasting
approach the forecast issuance time would likely be a particular time of day. at the time of this writing2). This provides almost 30 000
HARP-days (individual HARPs acquired on separate single
days). and NCI; this includes the magnetic parameters, the topological
parameters, the prior flare parameters, and the temporal
behavior of each as appropriate (Table 2). We focus on region
forecasts, as that is most appropriate for research purposes. 3.4 NCI flare research: evaluation This report serves at some level as an update to earlier
publications (Barnes et al., 2007; Leka & Barnes, 2007), now
with updated data and a significantly larger sample size: data
covering the full SDO mission for “definitive” vector magnetic
field HARPs are used 2010 May 01–2017 June 30 (as available For Table 2, a selection of performance results are shown,
specifying the parameter combination used, and some relevant
metrics. NCI by default uses Pth = 0.5, and the “well-
performing” combinations are generally selected by high
BSS as probabilistic forecasts are the most widespread in
operational settings and a preferred metric for NOAA/SWPC Page 12 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 7. Examples of non-parametric Discriminant Analysis for one variable (total “excess” photospheric energy, see Leka & Barnes, 2003a)
and two variables (same, plus the standard deviation of the horizontal gradients of the horizontal component of the magnetic field, ibid.) for the
C1.0þ, 24 h event definition. For both, event/non-event NPDA estimates are shown in red/black respectively, and the 50% probability threshold
is shown in blue. Fig. 7. Examples of non-parametric Discriminant Analysis for one variable (total “excess” photospheric energy, see Leka & Barnes, 2003a)
and two variables (same, plus the standard deviation of the horizontal gradients of the horizontal component of the magnetic field, ibid.) for the
C1.0þ, 24 h event definition. For both, event/non-event NPDA estimates are shown in red/black respectively, and the 50% probability threshold
is shown in blue. Table 2. Representative NCI research-mode region-by-region flare classification performance metrics. Region-by-region, 2010.05.01–2017.05.31
Event def. 3.4 NCI flare research: evaluation Event rate
Parameter(s)
RC
BSS
ApSS
Optimal H&KSS
C þ 1
0.0879
’tot, s (∇h Bz)
0.937 ± 0.005
0.40 ± 0.01
0.28 ± 0.01
0.68 ± 0.01
M þ 1
0.0145
Ee, s(|hc|)
0.987 ± 0.001
0.26 ± 0.02
0.14 ± 0.03
0.76 ± 0.02
X þ 1
0.0013
Ih
tot, ℱ(cNL > 45°)
0.9988 ± 0.0003
0.12 ± 0.06
0.12 ± 0.07
0.74 ± 0.07
C þ 2
0.0837
’tot, s (∇h Bz)
0.936 ± 0.007
0.35 ± 0.01
0.23 ± 0.01
0.64 ± 0.01
M þ 2
0.0134
Ee, s(|hc|)
0.990 ± 0.001
0.22 ± 0.02
0.11 ± 0.03
0.69 ± 0.02
X þ 2
0.0013
FL24, sðCNL;WÞ
0.9988 ± 0.0002
0.13 ± 0.06
0.12 ± 0.06
0.69 ± 0.07
C þ 3
0.0767
’tot, log(ℛnwra)
0.938 ± 0.007
0.31 ± 0.01
0.19 ± 0.01
0.60 ± 0.01
M þ 3
0.0124
Ih
tot, re
0.9884 ± 0.0008
0.15 ± 0.02
0.07 ± 0.02
0.66 ± 0.02
X þ 3
0.0011
log(ℛnwra), ðrij; cÞ
0.9989 ± 0.0002
0.11 ± 0.06
0.08 ± 0.06
0.63 ± 0.10
Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which indicates the fraction of magnetic
neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) for a prior 24 h interval. Table 2. Representative NCI research-mode region-by-region flare classification performance metrics. Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which in
neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which indicates the fraction of magnetic
neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) for a prior 24 h interval. H&KSS which is found by stepping through Pth values, with
cross-validation but without bootstrap (leading to some
expected discrepancies with Table 2), and the Gini coefficient. Of note is a degradation, but not a substantial one, between
increasing latencies. H&KSS which is found by stepping through Pth values, with
cross-validation but without bootstrap (leading to some
expected discrepancies with Table 2), and the Gini coefficient. 3.4 NCI flare research: evaluation Of note is a degradation, but not a substantial one, between
increasing latencies. evaluation. This threshold is used for the quoted RC and ApSS. The “Optimal H&KSS” is the H&KSS for which Pth = Event
Rate, which is not necessarily the highest H&KSS but is
generally very close, especially once error bars are considered
(Bloomfield et al., 2012; Barnes et al., 2016). The full
contingency tables are not presented here, since their entries
are sensitive to Pth, but all information needed to construct
them for any chosen Pth is provided. 2 The NCI demonstration results shown here include parameters from
HMI “mode-L” data starting from 2016.04 that were discovered to
include alignment errors. As of this manuscript’s acceptence, the
affected data are being reprocessed by the HMI team but the task has
not yet completed. Substantive quantitative differences are present
between parameters generated from the initially released model-L
data and examples of reprocessed data. Especially impacted are
parameters that rely on the horizontal component of the field. What is
presented here are the results given the data available. In
Figure
8
the
Relative
(or
Receiver)
Operating
Characteristic Curves (ROC) are shown for the entries in
Table 2. As described in Section 2.4.1, a perfect Gini
coefficient or ROC Skill Score results in G1 = 1.0, manifest by
an ROC curve consisting of three points: [0,0], [0,1], and [1,1]. The discontinuities are caused at small probability levels due to
many regions being assigned the same probability (specifical-
ly, the value of climatology). We also indicate the maximum Page 13 of 23 Page 13 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 8. Relative (or Receiver) Operating Characteristic Curve for NCI research on flaring vs. flare-quiet active regions, using a forecasting
context as described in the text. Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 hr) for
effectively 0 h, 24 h, and 48 h latencies (left:right), region-by-region “forecasts” using the parameter combinations for each event definition listed
in Table 2. Also noted on each plot are the maximum H&KSS (TSS) achieved, the probability threshold Pth used for that maximum TSS score,
and the Gini coefficient for the relevant curve. Fig. 8. Relative (or Receiver) Operating Characteristic Curve for NCI research on flaring vs. flare-quiet active regions, using a forecasting
context as described in the text. 3.4 NCI flare research: evaluation Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 hr) for
effectively 0 h, 24 h, and 48 h latencies (left:right), region-by-region “forecasts” using the parameter combinations for each event definition listed
in Table 2. Also noted on each plot are the maximum H&KSS (TSS) achieved, the probability threshold Pth used for that maximum TSS score,
and the Gini coefficient for the relevant curve. 4 The DAFFS Near-Real-Time (NRT) flare
forecasting tool – a measure of size (e.g. Ftot, Itot); – a measure of energy storage and non-potential magnetic
field (e.g. log(ℛnwra), ℱ(CNL > 45)); – a measure of energy storage and non-potential magnetic
field (e.g. log(ℛnwra), ℱ(CNL > 45)); The NCI infrastructure recently bifurcated to include a
near-real-time operational flare forecasting tool. The DAFFS
is the result of a NOAA SBIR Phase-II contract to NWRA. To
achieve a truly operational forecasting tool, many aspects that
originated from the NCI were redesigned for automated stand-
alone performance (no “human in the loop”), with operational
redundancy. In short, the DAFFS cron scripts use the
prescribed forecast issuance time as the basis for their
schedules, with drivers of all needed modules written in
Python. There are a few key differences from the research-
based NCI approach above, including some design features
not yet implemented due to limited resources, and we
describe those below. A generalized flow-chart for DAFFS is
provided in Figure 9. ( g
g(
)
(
))
– a measure of magnetic complexity (e.g. fij, k(Bz)). Often a parameter based on the temporal evolution is
included, however within the error bars there are always
combinations without temporal evolution which perform
similarly. Using two-parameter NPDA, we generally find
dozens of parameter combinations that perform similarly
within the error bars. When looking at some of the better-
performing combinations, we find a gradual decrease in
performance for probabilistic forecasts with respect to latency,
and a substantial decrease in performance with increasing
event magnitude. g
These results are consistent with both our earlier results
(Leka & Barnes, 2003b; Barnes et al., 2005; Barnes et al.,
2007; Leka & Barnes, 2007) and with the present state of the
literature (e.g., Falconer et al., 2014; Al-Ghraibah et al., 2015;
Bobra & Couvidat, 2015; Murray et al., 2017; Nishizuka et al.,
2017), but should not be compared directly due to different
event definitions, testing intervals, and validation methodolo-
gies (cf. Barnes et al., 2016). 3.5 Flare research: results rarely require that the boundary field to provide distinguish-
ing differences of magnetic complexity in addition to a
sheared polarity inversion line (although see Kusano et al.,
2012). In general, we find that the top-performing parameter pairs
routinely include (but are not exclusive to) the following
parameters categories (in no particular order): – a measure of recent flare activity (e.g. FL12 or FL24); 4.1 NRT data sources The choice of target time (Table 3) is in part
due to GONG data being published “on the fours”, and (similar
to HMI NRT data) the time by which the data would be reliably
made available. All matching gzipped FITS files are down-
loaded for evaluation (see Sect. 3.2.3), and the image with the
best seeing is then used. The target times for data sources were chosen according to
when the target data products typically become available for
transfer (Table 3). The master time was chosen to be 6 min
(0.1 h) prior to forecast time, to give the forecast code sufficient
time to complete by the forecast issuance time. By referring all
of the data acquisition and processing time to a master time
(and specifically a master time which is on the same day as the
data acquisition), and setting the relative times through
keywords, flexibility is afforded for setting different forecast
issuance times. Timing tests were performed for each aspect of the
pipeline, from data retrieval and staging to producing a
forecast and making it live, to come up with a task schedule
(implemented via cron) for smooth and automatic operation as
well as automated failure handling. In the case of HMI, if the
target time is not available, adjacent times are searched as
described in Table 3. The HMI NRT data are generally
processed and available for transfer within 90 min of the
observation time, but delays are not unusual (see Fig. 10). If no
HMI sources can be found after a certain amount of time, the
forecast is presently issued based on evaluating NOAA-
provided flare history parameters (see Sect. 3.2.5). GONG data
are intended to serve as a backup for HMI as a fully parallel
system. Fig. 10. Histogram of processing delay distributions (elapsed time in
between data acquisition and its availability for transfer) for six fairly
random weeks between 2014 and 2015 (colored lines) and the
distribution for all points (black). While there is a tail to delays greater
than 90 min, the majority of data are available within that time. then the target is moved back and forth in time by the HMI
vector field cadence (12 min) up to one hour prior and
including up to 48 min later – beyond which it is deemed to be
missing data (see Table 4). 4.1 NRT data sources The first difference is the source of the vector magnetic
field data. For the research system the HMI “definitive” series
are used, but for the operational forecasts, the HMI NRT data
are used. Specifically the hmi.ME_720s_fd10_nrt full-disk
vector field data are retrieved, along with the NRT HARP
information from the hmi.Mharp_720s_nrt series and the
disambiguation results from the hmi.Bharp_720s_nrt series. The expected latency for the HMI NRT data processing and
retrieval was investigated (Fig. 10), and the estimates for
expected delays are such that the latest target data practicable
are slightly more than 2 h prior to forecast issuance time; this
imposes a latency by default, as summarized in Table 3. If the
target data are unavailable due to processing or transfer delays, The lack of a few well-identified parameters which
definitively distinguish the two defined populations highlights
the challenge of using statistical empirical relationships to
investigate the fundamental physics of flares. Flares occur in
regions which are large and magnetically complex, and
preferentially in regions which have flared previously. The
latter point is consistent with flare models based on Self
Organized Criticality (Lu & Hamilton, 1991; Strugarek et al.,
2014). However, one can also view some of the empirical
results as guidance for modeling efforts, which (thus far) Page 14 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 9. A very generalized flow chart for the DAFFS system, outlining training to determine best-performing parameter pairs at the top, whose
results impact the daily near-real-time operation, in the bottom flow chart. Circles generally indicate input, squares are processes, and diamonds
are output. Fig. 9. A very generalized flow chart for the DAFFS system, outlining training to determine best-performing parameter pairs at the top, whose
results impact the daily near-real-time operation, in the bottom flow chart. Circles generally indicate input, squares are processes, and diamonds
are output. Fig. 10. Histogram of processing delay distributions (elapsed time in
between data acquisition and its availability for transfer) for six fairly
random weeks between 2014 and 2015 (colored lines) and the
distribution for all points (black). While there is a tail to delays greater
than 90 min, the majority of data are available within that time. are performed via Python script to find all sources (magneto-
gram images from all GONG sites) that exist for a given day
and targeted time. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Training occurs over a set period of time, generally
using as much NRT data as are available, e.g., over the full
HMI NRT-data availability period of 2012.10.01 through a
“recent” month. The top-performing parameter pairs are then
used for forecasts, separate pairs for each event definition. The
NPDA estimates of the distributions are re-computed on-the-
fly, against which new data are compared and thus for which
flare probabilities are computed. Additionally, the NRT HARP definitions themselves are
generated in near-real-time, and do not have the benefit of size
or identity consistency over a disk-passage as is the case for the
definitive HARP series (Fig. 11). This difference actually
precludes exact region-by-region comparisons between the
research NCI results and NRT DAFFS results, although
comparisons are possible via full-disk forecasts. Training occurs separately for permutations of param-
eters based on those available: e.g., SDO/HMI þ NOAA/
SXR
events,
NOAA/SXR
events
by
themselves,
and
eventually GONG þ NOAA/SXR events. For the larger
events, single-variable DA and linear DA were considered
as well as multi-parameter NPDA, because of the often
improved performance by these simpler approaches for
small sample sizes, however they are not presently used. The parameters presently used (as of this writing) are listed
in Table 5; these are the parameters used for the results
reported
here. The
exact
parameter
combinations
are
determined by the training interval used (indicated), and
may
change
upon retraining the system,
although as
mentioned above there are common parameter “families”
that routinely appear in the top-performing results. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Table 3. DAFFS Near-Real-Time data target timing. Table 3. DAFFS Near-Real-Time data target timing. Table 3. DAFFS Near-Real-Time data target timing. As relevant for a “midnight” forecast:
Time
Data source
Keyword
21:48:00
HMI/MAG target time = Master 2.1 h
DAFFS_HMI_LATENCY
22:30:00
NOAA GOES/PFF target time = Master 1.4 h
DAFFS_PFF_LATENCY
22:54:00
GONG/LOS_MAG target time = Master 1.0 h
DAFFS_GONG_LATENCY
23:54:00
Master time
–
00:00:00
Forecast time = Master þ 0.1 h
DAFFS_TFORECAST_LATENCY Table 4. DAFFS Data acquisition and processing timeline. As relevant for a “midnight” forecast:
Time
Task
23:34
Retrieve GONG NRT data, targeting 22:54. 23:36
Retrieve data from HMI magnetogram series (hmi.M_720s_nrt) for full-disk context
23:36
Retrieve NRT HMI full-disk data (hmi.ME_720s_fd10_nrt) via NetDRMS, and extract patches using hmi.MEharp_720s_nrt,
hmi.Bharp_720s_nrt series. Attempt 21:48:00 target record; if it does not exist, wait one minute and retry. (21:37)
If target record still does not exist, query for data in the following order retrieve closest available record within [-60,þ48]
of target: 21:36, 22:00, 21:24, 22:12, 21:12, 22:24, 21:00, 22:36, 20:48
23:37
Query E-SWDS for latest SWPC NRT flare events, AR assignments; simultaneous ftp query and transfer
23:54
0. Plot HARPs on full-disk Blos image, for DAFFS landing page (Fig. 12)
1. Update NWRA database with latest events via NOAA E-SWDS database query
2. Update NRT HARP/NOAA translation table in NWRA database
3. Extract GONG patches via NOAA E-SWDS database query of visible active regions
4. Generate parameters, forecasts
5. Link the main webpage to the new forecast buffer); the disambiguation is performed with a faster cooling
schedule. For any specific area, there may be detectable
differences on a pixel-by-pixel basis, however there is no
systematic under- or over-reporting of magnetic field strengths,
azimuthal angle differences, or noise levels (Bobra et al., 2014). Statistically, the distributions of resulting parameters generally
agree well between the NRT and definitive HMI data series. HARPs that only ever have a single NOAA number assigned (to
account for the frequent delay of NOAA number assignments). DAFFS
runs
autonomously
twice
daily
by
default,
producing
forecasts
issued
just
before
00:00 UT
and
12:00 UT for the event definitions and validity periods listed
in Table 1. 4.1 NRT data sources The timeline for producing a NRT
DAFFS forecast is summarized in Table 4. The needed NOAA data (up to date flare events and
coordinates of visible numbered active regions) are retrieved
through queries to “E-SWDS”. The needed data are also
retrieved from the public ftp service as backup. Differences between the SDO/HMI definitive and NRT data
arise at a few steps in the data reduction, and some are
demonstrated in Figure 11. Of note, not all of the full-disk is
inverted for the NRT release (only the NRT-HARP areas plus a The GONG data are retrieved from the NSO NRT
dissemination page, https://gong2.nso.edu/oQR/zqa/; searches Page 15 of 23 4.2 NRT DAFFS implementation specifics For both the HMI NRTand the GONG data for DAFFS, only
a subset of parameters are considered during training (<50%
of the full science-investigation list) in order to remove
redundancy and highly correlated variables (for example,
separately the positive magnetic flux, the negative magnetic
flux, and the total magnetic flux). At present, the MCT module
is not used for the NRT DAFFS, and data are only examined at a
single time; no dX/dt analysis is included. Metadata from hmi.Mharp_720s_nrt is used to match
HARPs to AR numbers. For later training efforts, back-
propagation of HARP/NOAA matches is performed for those Page 16 of 23 Page 16 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 11. Full-disk line-of-sight magnetograms from SDO/HMI for 2014.03.18 21:48 TAI. Left: NRT data showing the NRT HARPs and their
numbering, Right: Definitive data, showing definitive HARP boxes and their numbering. Of note are the differences in coverage and in regions
in the NRT which are merged for definitive HARPs. For both NRT and definitive HARPs, boxes may overlap but the “active pixels” (cf. Fig. 3)
will not. Fig. 11. Full-disk line-of-sight magnetograms from SDO/HMI for 2014.03.18 21:48 TAI. Left: NRT data showing the NRT HARPs and their
numbering, Right: Definitive data, showing definitive HARP boxes and their numbering. Of note are the differences in coverage and in regions
in the NRT which are merged for definitive HARPs. For both NRT and definitive HARPs, boxes may overlap but the “active pixels” (cf. Fig. 3)
will not. Automated graphical output is generated of the locations of
the new data within the parameter space for each event
definition (see Fig. 12). This allows the user to understand and
confirm the context for the given probability forecast, and
enables a user to track movement of a particular active region
over time (helping to gauge increasing or decreasing flaring
probability). are additionally automatically updated by a separate ftp-based
cron job from the NOAA public postings. Of note, NOAA flare
forecasts are also retrieved for later evaluation comparisons. GONG data outages With a world-wide 6-station network, data outages from
GONG are quite rare. When this does occur, following the
protocol for HMI outages, “missing” data values will be
assigned and a PFF-based forecast prepared. Performance metrics are generated on demand (see Sect. Hardware redundancy Not yet implemented. SDO/HMI data outages Periodically, there are delays in the SDO/HMI data
processing such that no applicable NRT data (see Table 4) are
available for a forecast. In this case, then “misssing” data
values are assigned and a PFF-based forecast with FLtot and
FL24 is prepared. g
Retraining The system is retrained on demand, and new variable-
combinations can be employed for the forecasts at that point if
so desired. This may impact forecasts as results can vary
significantly according to the climatology of the training set,
especially for larger and rarer events. j
Unassigned flares Unassigned Flares are flare events not assigned to a
particular active region. Fairly rare for large events (except
when they occur behind the limb), they are most frequent for
the small events, including C-type flares. For region-by-region
forecasts, if they are not assigned, they are not considered as
part of the prior flare parameters. For full-disk forecasts, they
are included in evaluation but not in the training, leading to a
systematic under prediction. 4.3 NRT DAFFS redundancy and operational details An operational system is only as good as its performance
when everything fails. While there is still significant room for
improvement, the following operational aspects are, or are
designed to be, part of the NRT DAFFS implementation:
N
f 4.2 NRT DAFFS implementation specifics 4.4), as is re-training the full system (which potentially results
in different parameter pairs being used from thence forward). Redundant forecasting In order to ensure robustness of the forecasts, DAFFS is
designed to consider and report on multiple top performing
models; in the case of 2-parameter combinations, forecasts
from the three top performing combinations which contain
unique parameters would be reported. This would provide
essentially an ensemble forecast that considers 6 parameters,
albeit without the sample-size requirements of training a true
6-variable NPDA forecast. Although not yet fully imple-
mented, this approach also improves the odds of successful
bad-data rejection. g
p
No forecast outages A forecast is always issued. If all redundancies fail,
climatology is used. Hardware redundancy p p
E-SWDS data outage g
The situation of a complete and long-term E-SWDS data
outage likely implies larger problems. E-SWDS uses a fail-
over server for any outages, and the NWRA database
connection will attempt to connect to it if the primary server
is not responding. The event lists and active-region locations Page 17 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 ng” page for the NRT DAFFS showing a full-disk line-of-sight magnetogram and defined HARPs f
hown: the version of the code running and the training interval being used. Bottom: a context plot fo
gion forecasts, contour indicate the event (red)/non-event (black) training-sample distributions, the
e green dots indicate the location of the recent data on these distribution plots. The left-hand table sh
OAA AR(s) as appropriate, the forecast, and the status flags for the data. The full DAFFS forecast f
he demonstration page at www.nwra.com/DAFFS_home/. Fig. 12. Top: “Landing” page for the NRT DAFFS showing a full-disk line-of-sight magnetogram and defined HARPs for context, and the full-
disk forecasts. Also shown: the version of the code running and the training interval being used. Bottom: a context plot for the C1.0þ, 24 h, 24 h
latency, region-by-region forecasts, contour indicate the event (red)/non-event (black) training-sample distributions, the blue contour is the 50%
forecast level, and the green dots indicate the location of the recent data on these distribution plots. The left-hand table shows the HARP number,
the corresponding NOAA AR(s) as appropriate, the forecast, and the status flags for the data. The full DAFFS forecast for this date is available
for readers through the demonstration page at www.nwra.com/DAFFS_home/. Page 18 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 and evaluation intervals (although full-disk forecasts negate a
few of these differences). Table 5. DAFFS forecasting parameter combinations (training
interval: 2012.10.01–2016.03.31). Event definition
Parameter combination
C þ 1
re, Itot
M þ 1
s(re), Ih
tot
X þ 1
FL12, &(Bz)
C þ 2
Ftot, log(ℛnwra)
M þ 2
Bz, log(ℛnwra)
X þ 2
FL24, &(Bz)
C þ 3
Bz, Ih
tot
M þ 3
Bz, Itot
X þ 3
FL12, Bz Table 5. DAFFS forecasting parameter combinations (training
interval: 2012.10.01–2016.03.31). That being said, DAFFS is running as an autonomous tool
designed to address operational needs. p p
E-SWDS data outage During the SBIR Phase-
I
(feasibility)
study,
an
NCI-based
demonstration
out-
performed the NOAA/SWPC forecasts as judged by BSSs
that evaluated head-to-head comparisons with matched event
definitions and testing intervals, as required by the topic
description (Sect. 1). This success enabled Phase-II (prototype
development) funding and the NRT operational forecasting
tool described here as DAFFS. 5 Future developments The described infrastructure has been designed for
flexibility at various junctures, and our hope is to implement
improvements at a number of them. Regarding NCI in general, we intend to investigate how to
optimize the adaptive-kernel NPDA, where the smoothing
parameters are a function of parameter density. This should
allow a better estimation of the PDF in high-kurtosis
distributions – a useful additional option for all scientific
questions for which NCI might be applied. Investigating
AKNPDA is a proposed task for future funding. Validation Validation is performed on demand, producing lists of
standard skill scores (Fig. 13); Reliability and ROC plots can
be generated automatically, as well (e.g. Fig. 14). Customization DAFFS can be customized for event definition, timing of
forecasts, and forecast validity periods. Additionally, the
categorical forecasts can be optimized against either of the two
error types (thus minimizing False Alarms or minimizing
Missed Events). p
p
g
Regarding DAFFS specifically3, we intend to finish
implementing
the
GONG-based
secondary
forecasting –
including then a direct comparison of performance as
compared to the system when HMI vector field data are
available. A bootstrap approach for the training data will be
implemented
to
provide
estimates
of
the
performance
uncertainties. The event definitions can be modified with
respect to forecast interval, latency, and event limits, and these
will be acted upon as requested. As mentioned above, parallel
forecasts reporting on multiple top-performing combinations
can be implemented for the NRT forecasting as a further check
against statistical flukes from appearing in the predicted
probabilities. Additionally, the DA threshold can be optimized
according to the costs of either type of error, or to maximize a
particular skill score. While this is not widely used when
testing the efficacy of new parameters, it can be of particular
importance to customers of the NRT tool. Of note, these
proposed enhancements all have some degree of research-
based known value to add, but will require resources to
implement. Hence, DAFFS is not open source and is not freely
available, as there is no automatic funding for NWRA (a small
business) to continue its support. However parties interested in
using it can be granted limited access for trial periods (see
www.nwra.com/DAFFS_home/),
and
“access
only
with
technical support” levels of contracts are available for very
minimal resource levels. Of note, data which are not retrieved for the NRT forecasts,
for whatever reason, are queued for retrieval later to ensure a
reasonably complete NRT data source database for training
purposes. 3 Upon proof state, this is now completed. 4.4 DAFFS results For very few of the event definitions do the ApSS scores
show substantial improvement over climatology (Fig. 13),
although the ROC plots and G1 coefficients demonstrate some
performance significantly away from the “no skill” (x = y) line. (Note that the Peirce (H&KSS) scores quoted in the DAFFS
evaluation, Figure 13, use Pth = 0.5 while the ROC plots quote
the
maximum
H&KSS achieved
by varying
the
Pth). Uncertainties are not (yet) quoted when generated from within
DAFFS, but the magnitude of the uncertainties in Table 2 can be
a guide. g
For probabilistic forecasts, the performances are worse for
the larger events (due to smaller sample sizes). In fact overall,
the larger the event and the longer the latency, generally the
worse the performance, which is typical (Barnes et al., 2016;
Murray et al., 2017). NCI is a research platform by which many questions can be
addressed through the quantitative analysis of appropriate
sample sizes. Forecasting solar flares and energetic events is
one such question; it is fairly well accepted that the present
forecasting methods, DAFFS included, are performing above
climatology – but not performing particularly well. The
reasons why this is so are starting to become clear: likely
culprits include a combination of human-defined events and 4.5 Performance context The results above reflect the general performance of the
baseline NRT DAFFS forecast tool. The results will change
according to the climatology and training interval, and as such
should be interpreted with some care. These results are also not
directly comparable to numbers quoted for other methods or
even to the NCI results above, as discussed in Barnes et al. (2016), because of differences in samples, event definitions, Page 19 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 13. To summarize the metrics for the NRT DAFFS we show a screen-shot from the output of the DAFFS self-evaluation code. Indicated are
the evaluation period (20140701–20170630), for which issuance time (23:54:00 UT), and then a variety of skill scores. Note that the H&KSS
quoted here is not the “Optimal” quoted above, it is evaluated with Pth = 0.5, which is the system default. “Event” means “event rate”; “FD”
indicates full-disk (rather than region-by-region) forecasts. Fig. 14. ROC Curve for DAFFS NRT forecasts (see Fig. 13). Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ,
24 h, X1.0þ, 24 h) for effectively 0 h, 24 h, and 48 h latencies (left:right). Top row: region-by-region, Bottom row: full disk forecasts. Also noted
on each plot are the Gini coefficients, the maximum H&KSS (TSS) achieved, and the probability threshold Pth used for that maximum H&KSS
score. Fig. 14. ROC Curve for DAFFS NRT forecasts (see Fig. 13). Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ,
24 h, X1.0þ, 24 h) for effectively 0 h, 24 h, and 48 h latencies (left:right). Top row: region-by-region, Bottom row: full disk forecasts. Also noted
on each plot are the Gini coefficients, the maximum H&KSS (TSS) achieved, and the probability threshold Pth used for that maximum H&KSS
score. Page 20 of 23 Page 20 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 2003b; Barnes & Leka, 2006; Leka & Barnes, 2007) to address
an expressed need (Barnes et al., 2007). As a matter of
practicality, DAFFS by default mimics the system established at
NOAA/SWPC in terms of event definition and output,
although it does not have to. Many of the details which make
this an operational system (and thus very different from the
NCI) are described, and early results are presented. Supplementary Material Supplementary Material Supplementary material supplied by the author. The Supplementary Material is available at https://www.swsc-
journal.org/10.1051/swsc/2018004/olm. Acknowledgements. The NCI was developed with funds from
numerous sources, including AFOSR contracts F49630-00-C-
004 and F49620-03-C-0019, NASA contracts NNH12CG10C,
NNX16AH05G, and NNH09CE72C, and NSF Grant 1630454. The DAFFS tool was developed under NOAA SBIR contracts
WC-133R-13-CN-0079 (Phase-I) and WC-133R-14-CN-0103
(Phase-II) with additional support from Lockheed-Martin
Space Systems contract #4103056734 for Solar-B FPP Phase E
support. The authors also acknowledge NWRA internal
development funds and the efforts of the two referees to
improve the presentation of this work. The editor thanks Brian
Welsch and an anonymous referee for their assistance in
evaluating this paper. (
)
Research regarding different event definitions can be
constructed within the NCI framework, according to (for
example) a CME or lack thereof, the duration of events and
total energy released, whatever appropriate database of
“events” is available. Presently the NOAA-defined event
catalogs form the basis of the GOES event definitions, but this
itself could be modified to use other event catalogs based on
other instruments. Of note, the NCI is not solely useful for flare research. Topics
which
have
been
investigated
within
the
NCI
framework include pre-emergence signatures (Barnes et al.,
2014), a research topic and approach that is ongoing, and
filament eruption (Barnes et al., 2017). The NCI is not, we
stress, in and of itself a forecasting tool; it uses DA to evaluate
how well samples from two known populations can be
distinguished. Indeed, NCI may be used with any appropriately
defined populations for diverse investigation topics. We
actively invite collaboration to use the NCI framework in
broad topics of solar physics. References Abramenko VI. 2005. Relationship between
magnetic power
spectrum and flare productivity in solar active regions. Astrophys
J 629: 1141–1149. DOI:10.1086/431732. Ahmed OW, Qahwaji R, Colak T, Higgins PA, Gallagher PT,
Bloomfield DS. 2013. Solar flare prediction using advanced feature
extraction, machine learning, and feature selection. Sol Phys 283:
157–175. DOI:10.1007/s11207-011-9896-1. 4.5 Performance context simply a limited amount of information from photospheric
magnetic field data that themselves may not directly be related
to the flare initiation activity (Leka & Barnes, 2017). As
different events, data, and approaches are investigated we
invite further collaborative efforts using NCI as means to
quantitatively test proposed improvements in establishing
distinguishing characteristics of flare-imminent active regions. DAFFS is presently in use by the Chief Observers of the
Hinode mission. While the primary data source (SDO/HMI)
has an uncertain lifetime, DAFFS was designed to continue
without those primary data although the long-term perfor-
mance degradation in that situation has yet to be determined. With the oncoming solar minimum and as-of-yet no defined
SDO follow-on mission, DAFFS will be supported and
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missions slated for operation as solar activity increases again. 5.1 Other research modules Described above are the data, parametrizations, and
analysis results for flaring vs. flare-quiet active regions using
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https://openalex.org/W4324133401 | https://www.qeios.com/read/GWWGDY/pdf | English | null | Review of: "Ecotheology: missiological perspective in awareness" | null | 2,023 | cc-by | 376 | Review of: "Ecotheology: missiological perspective in
awareness" Dan Smyer Yu1
1 Yunnan University Dan Smyer Yu1
1 Yunnan University Potential competing interests: No potential competing interests to declare. Qeios, CC-BY 4.0 · Review, March 14, 2023 Qeios ID: GWWGDY · https://doi.org/10.32388/GWWGDY Comments and suggestions from the reviewer This submission is potentially a good read if the authors are willing to do a well-rounded revision in these areas: This submission is potentially a good read if the authors are willing to do a well-rounded revision As this submission is Christian specific, the reviewer recommends a revision of the current title to something like this:
“Christian Ecotheology: Missiological Perspective in Awareness” or “Ecotheology: Christian Missiological Perspective in
Awareness.” From the interfaith perspective, Christianity does not exclusively own the word “theology”; The content of this submission suggests that it does not offer an explanation of what ecological theology means (p.1);
instead, it makes an attempt to explain the current environmental crisis and to offer a Christian perspective about how
humans should care for the planet earth. This said, the authors are recommended to revise the relevant passages in
the opening paragraph; It is not clear from what Christian denominational perspective the authors speak of their “ecotheology” and
“missiological perspective”; Other than from “library and web research,” the abstract of the submission claims “collected data from various sources;”
however, it does not explicitly inform readers of both the sources and contents of the data. Empirical data will be highly
appreciated if they are available; In “Result and Discussion” section, climate change is spoken of in general terms. In currently interdisciplinary studies of
climate change as a pressing issue of our time, climate change vary locally although climate scientists offer an
averaged assessment of the change. The authors may consider offering readers a picture of the local manifestation of
the global climate change in Indonesia; It is not clear what the authors try to convey about the “new paradigm” (p.4); It is not clear what the authors try to convey about the “new paradigm” (p.4); It would make more sense to relocate the section “Missiological Perspective Ecotheology in Indonesian Context” to the
earlier part of the submission. Proofreading/copyediting is definitely needed. Proofreading/copyediting is definitely needed. Qeios ID: GWWGDY · https://doi.org/10.32388/GWWGDY 1/1 |
https://openalex.org/W4237677366 | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0110205&type=printable | English | null | Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity | PloS one | 2,014 | cc-by | 272 | The PLOS ONE Staff The affiliations for the fourth and fifth authors are incorrect. Ilyas Khan is not affiliated with #4 but with #3 College of
Engineering
Majmaah University,
Majmaah, Saudi Arabia. Sharidan Shafie is not affiliated with #4 but with #4 Department
of mathematical Sciences, Faculty of science, University Teknol-
ogy Malaysia, UTM Johor Bahru, Johor, Malaysia. Correction: Thin Film Flow in MHD Third Grade Fluid on a
Vertical Belt with Temperature Dependent Viscosity The PLOS ONE Staff 1. Gul T, Islam S, Shah RA, Khan I, Shafie S (2014) Thin Film Flow in MHD
Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity.
PLoS ONE 9(6): e97552. doi:10.1371/journal.pone.0097552. Correction
Correction: Thin Film Flow in MHD Third Grade Fluid on a
Vertical Belt with Temperature Dependent Viscosity Correction
Correction: Thin Film Flow in MHD Third Grade Fluid on a
Vertical Belt with Temperature Dependent Viscosity Correction Correction: Thin Film Flow in MHD Third Grade Fluid on a
Vertical Belt with Temperature Dependent Viscosity PLOS ONE | www.plosone.org Reference Citation: The PLOS ONE Staff (2014) Correction: Thin Film Flow in MHD Third
Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity. PLoS
ONE 9(10): e110205. doi:10.1371/journal.pone.0110205 Published October 3, 2014
Copyright: 2014 The PLOS ONE Staff. This is an open-access article
distributed under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided
the original author and source are credited. PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 1 October 2014 | Volume 9 | Issue 10 | e110205 October 2014 | Volume 9 | Issue 10 | e110205 |
https://openalex.org/W4309734231 | https://zenodo.org/record/7788135/files/WJARR-2022-1197.pdf | English | null | Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric hospital, Aro, Abeokuta, Ogun state, Nigeria | World Journal Of Advanced Research and Reviews | 2,022 | cc-by | 4,765 | Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric
hospital, Aro, Abeokuta, Ogun state, Nigeria
Ogungbesan J. O 1, *, Maitanmi B 1, Aroyewun Oluwayemisi 2 and Maitanmi Julius O 1
1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria.
2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria.
World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754
Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022
Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric
hospital, Aro, Abeokuta, Ogun state, Nigeria
Ogungbesan J. O 1, *, Maitanmi B 1, Aroyewun Oluwayemisi 2 and Maitanmi Julius O 1
1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. 2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754
Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022
Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric
hospital, Aro, Abeokuta, Ogun state, Nigeria 1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. 2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022 Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Abstract Substance use is a societal and an important public health concern in this 21st century. The number of substance use
cases and relapse are increasing geenrally, thus slowing down the progress made in the care and treatment of
individuals with substance abuse disorders. The study identified determinant of relapse among the rehabilitated
substance use patients in Neuropsychiatric hospital, Aro, Abeokuta. The study adopted cross-sectional, selected 125 relapse substance use patients and their primary informal caregiver on
the wards and clinics at neuropsychiatric hospital, Aro, Abeokuta. An interviewer-administered structured
questionnaire was used to obtain data on determinants of relapse among the rehabilitated substance use patients and
the retrieved data was analysed using SPSS version 21 for descriptive statistics. The findings shows that nearly half (44.4%) of the respondents were below 20 years, majority (64.5%) were male,
40.3% married. Most (69.4%) of the respondents agreed that the patient have friends who use drugs, 71.0% of the
patients were currently relapsed, though majority (72.5%) of the patients were on treatment either outside or/and in-
ward under control compliance. Conclusively, higher proportion were currently relapsed and had varied factors correlating the relapse; male, under
20years. Hence the client needs be proactively managed to prevent relapse through prompt therapy / care of psychotic
patients lengthy to lead a high quality of life. Keywords: Relapse; Rehabilitated; Substance Use; Patient; Substance abuse School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. Copyright © 2022 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Corresponding author: Ogungbesan J. O or(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0. Copyright © 2022 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0. g
g
J
g, Babcock University, Ilishan-Remo, Ogun State, Nigeria. Corresponding author: Ogungbesan J. O 1. Introduction Additionally, the national survey on drug use and health in USA revealed that
23.5 million Americans aged 12years and older required treatment for illicit drug and alcohol abuse problem. Of this
number, an estimated 2.6million (11.2 %) individual receives treatment at a specialty facility (SAMHSA, 2009). According to Mohammed (2009) revealed that urge, craving, and drug temptation, negative or positive emotional state,
negative physical state, testing of personal control, family or others relationship conflicts, social and peer pressures to
use substances, and treatment related are correlate with relapse. Predominantly, relapse is one of the most severe
problems of mental illness especially among individual with substance use disorder. Despite the current trend in
modern treatment, the rate of relapse is alarming. Relapse is estimated as 40 – 75% between three (3) to twenty-four
(24) weeks after substance use disorder treatment globally (Hasin et al, 2013; Maehira et al, 2013; Hubbard et al, 2001). Consequently, relapse reduces the chances of substance use disorder individuals from living a productive and
responsive life thereby making them not to live up to personal and societal expectation and fulfil life goals. Nevertheless, relapse could occur at any time or stage of treatment; for instance, relapse occur as soon as clients
discharge home, on trial discharge, at admission, and/or after successfully avoiding substance use for some period of
time as well establishing a routine of substance abstinence. Studies have identified various factors contributing to
relapse including; non-adherence to medication regimen and flagrant disregard for relapse prevention strategies
(Kabisa, Biracyaza, Habagusenga, et al., 2021). According to Murmane and Howell (2011), reinstatement of drug use
after a period of non-use or abstinence is typically initiated by one or a combination of the three main triggers as stress,
re-exposure to the drug priming and environmental cues. Although, people of all ages use and abuse substances for a
variety of reasons including sensation seeking, peer group pressure, emotional stress, cognitive enhancement, the
desire to relieve depression and anxiety and the need to cope with physical illness (Baghurst& Kelley, 2013; Barnett,
2017; Cho et al., 2015). Similarly, there are regional variations in the prevalence rates of substance use in Nigeria. In
Nigeria, studies have identified young adults and middle-aged males, less educated individuals, individuals working in
technical or commercial jobs, people with marital home, urban areas dwellers and individuals from broken homes are
more associated with substance uses (Hamdi et al 2016). 1. Introduction Substance abuse is a foremost societal and important public health concern. Generally, is a mental illness due to the
nexus of mental and behavioural disorders. Often time, substance use is used in replace of substance abuse, as substance
abuse means using of substances (drugs) for purposes other than it is intended, and characterized with maladaptive
pattern of substance uses with a propensity of resulting in to significant impairment in functioning (Sampson et al.,
2017). An individual continues using substances despite cognitive, behavioural, and physiological symptoms (Hamdi et
al, 2013). Literally, substance abuse is also a drug abuse as it is a harmful, hazardous or excessive use of psychoactive drugs or
substances such as alcohol, pain medication, and other drugs in which the user consumes in amount that is different
from the prescribed dosage or for purposes other than that which is prescribed but solely for the aim of creating a World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 pleasurable effect (Leikin, 2017; WHO, 2015). Thus with the potential to cause physical, social and emotional harm to
the abuser. More so, the World Health Organisation (WHO) conceptualizes substance use as a chronic and relapsing
disease confronting the global community in the 21st century due to its relapsing propensities (Mandal, 2021). Subsequently, substance abuse relapse is a gradual or sudden stop or disappearance of abstinence or sobriety status
after drug abuse. However, the burden of substance abuse relapse is very high among individuals, family and the society
of people abusing substance. As those who are not involve in doing substance are more affected by the behaviour of
those doing substances. More so it constantly draining available resources for wellbeing as he might become a danger
to self or/and others in the society by causing crisis. In literature, there are evidences that substance abuse related
relapse across all age groups but more common among the adolescents and young adult that indulge in substance intake,
dependent and a chronic addictive doping/taking of substances. Thus, place severe burden on the informal and formal
caregivers managing them especially in the acute phase. The prevalence of chemical dependence relapse among substance abusers had been estimated to be 75 – 90 % within
the first year of treatment (Iqbal, 2008). 1. Introduction In general, several social vices are associated with substance
use notably, people with criminal tendencies and antisocial behaviours are often under the influence of substances or
drugs (Ksir, Oakley and Charles (2011). Objectives of the Study The aimed to determine the factors associated with relapse among rehabilitated substance use patients in
Neuropsychiatric hospital, Aro, Abeokuta.
To identify t h e biological determinants of relapse among the rehabilitated substance use patients
To identify the social determinants of relapse among the rehabilitated substance use patients
To identify psychological determinants of relapse among the rehabilitated substance use patients
To identify t h e biological determinants of relapse among the rehabilitated substance use patie
T id
if
h
i l d
i
f
l
h
h bili
d
b
i To identify the social determinants of relapse among the rehabilitated substance use patients
To identify psychological determinants of relapse among the rehabilitated substance use patients y
p
g
p
To identify psychological determinants of relapse among the rehabilitated substance use patien
To identify psychological determinants of relapse among the rehabilitated subs 2.1. Research Design The study utilized a hospital-based descriptive cross-sectional survey to identify determinants of relapse among
rehabilitated substance abuse patients at the Federal Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. The
study targeted at the rehabilitated substance abuse patient currently in relapse at the Federal Neuropsychiatric Hospital
Abeokuta, Ogun State. 748 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Determinants of Relapse among the Rehabilitated Substance Use Patients
Variables
Frequency
Percentage %
Age of patient in years
Below 20years
55
44.4
21-30years
36
29.0
31-40 years
20
16.1
41and above
13
10.5
Sex of patient
Male
80
64.5
Female
44
35.5
Marital status of patient
Single
48
38.7
Marriage
50
40.3
Divorced
16
13.0
Widowed
10
8.0
Has any of the patients’ family members ever abused drugs in the past
Yes
90
72.5
No
34
27.5
Specify relationship with patient
Parents
45
36.3
Sibling
30
24.2
Brother
27
21.7
Sister
22
17.8
Does the patient suffer from any other chronic infection/illness
Mental confusion
50
40.3
Brain damage
36
29.0
Lung disease
22
17.7
Increase stain on the liver
16
13.0
Specific drug(s) is the patient abusing most
Skunk
52
42.0
Cannabis
30
24.2
Crystal meth
27
21.8
Colorado
15
12.0
Age did the patient start educing the drugs? Below 1 years
50
40.3
2-4 years
41
33.0
Above 5 years
33
26.7
For how long has the patient been abusing drugs? Below 6 month
58
46.7
6-12 month
40
32.3
13-18 month
26
21.0 Table 1 Biological Determinants of Relapse among the Rehabilitated Substance Use Patients 749 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 A total sample size of 125 relapse patients were conveniently selected. The data was collected with the aid of
questionnaire. The caregivers of patient were met at the different wards and clinics, introduced and explained to gain
the consent of participants. The collected data was analysed with SPSS version 25 for descriptive statistics. A total sample size of 125 relapse patients were conveniently selected. The data was collected with the aid of
questionnaire. The caregivers of patient were met at the different wards and clinics, introduced and explained to gain
the consent of participants. The collected data was analysed with SPSS version 25 for descriptive statistics. e 2 Social Determinants of Relapse Among The Rehabilitated Substance Use Patients
Variables
Frequency
Percentage %
Does the patient have friends who use drugs? 2.1. Research Design Yes
86
69.4%
No
38
30.6%
What is the patient's educational level? None
42
33.9%
Primary
36
29.0%
Secondary
30
24.2%
Post-secondary
16
12.9%
What is the patient's occupation? Employed
50
40.3%
Unemployed
40
32.2%
Schooling
34
27.5%
How accessible are the drugs that the patient commonly abuses? Readily Accessible
68
54.8%
Rarely Accessible
30
24.2 %
Never Accessible
26
21.0%
How affordable are the drugs that the patient commonly abuses? Readily Affordable
52
42.0%
Rarely Affordable
48
38.7%
Never Affordable
24
19.3%
How often does the patient do drug with friend? Very often
60
48.3%
Rarely often
42
33.9%
Never
22
17.8%
How often does the patient engage in social vices such as fight, rape or scatter the house? Very often
70
56.4%
Rarely often
36
29.0%
Never
18
14.6%
How often does the patient get arrested by the law enforcement agent such as Police or NDLEA? Very often
66
53.3%
Rarely often
48
38.7%
Never
10
8.0%
How often have you tried to stop the patient from doing drug? Very often
80
64.6%
Rarely often
36
29.0%
Never
8
6.4% able 2 Social Determinants of Relapse Among The Rehabilitated Substance Use Patients 750 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Table 3 Psychological Determinants of Relapse among the Rehabilitated Substance Use Patients
Variables
Frequency
Percentage %
For how long has the patient been ill (current relapse episode)? Below 4 weeks
88
71.0%
1-2 month
22
17.7%
3 month and above
14
11.3%
On average how many times in a year does this illness (relapses) usually occur to the patient after
successful treatment? Two
80
64.5%
Three or more
44
35.5%
Does the patient comply to the prescribed medication when his/he recondition is under control
(compliance)? Yes
90
72.5%
No
34
27.5%
Does the patient belong to any support group therapy
Yes
100
80.6%
No
24
19.4%
In the last one year, has the patient felt the need to stop drinking or any other substance? Yes
104
83.8%
No
20
16.2%
In your own opinion, do you think frequent family conflict contribute to patient frequent relapse? Yes
98
79.0%
No
26
21.0%
Does the patient ever use any of the following maladaptive coping tactics e.g. smoking, drinking alcohol,
chewing Mira, aggression/fights, etc when faced with negative life events and stress? Yes
88
71.0%
No
36
29.0%
Does the patients have any Personality problem (e.g. 2.1. Research Design introvert, extrovert, impulsive behaviors ,tendency to
violence, quarrel some, shyetc
Yes
99
79.9%
No
25
20.1%
Does the patient often have any negative thoughts
Yes
100
80.6%
No
24
19.4%
Are the generative life events that are associated with the present condition of the patient? Yes
94
75.8%
No
30
24.2%
Does the patient exhibit positive coping mechanisms when faced with stressful events? Yes
88
71.0%
No
36
29.0% l Determinants of Relapse among the Rehabilitated Substance Use Patients Table 3 Psychological Determinants of Relapse among the Rehabilitated Substance Use Patients 751 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Table 1 shows that nearly half 44.4% of the respondents were below 20 years, and 10.5% 41 and above. Majority 64.5%
were male, about 38.7% were single, 40.3% were marriage, 13.0% were divorced, while the 8.0% were widowed. The
informal caregivers included; parents 36.3%, 24.2% siblings. About 42.0% of the respondent took Skunk, 24.2%
Cannabis, 21.8% Crystal meth, while the remaining 12.0% used Colorado. Majority 40.3% started drug 1 years, 33.0%
between 2-4 years, and 26.7% above 5 years. Majority 46.7% claimed that they had been on a specific drug below 6
month, 32.3% between 6-12 month, and 21.0% 13-18 months. Table 2 shows that 69.4% of the respondents had friends who used drugs, about 33.9% of the respondents had no
formal education, 29.0% had primary, and 24.2% secondary. Two-fifth 40.3% were employed, 32.2% unemployed, and
the remaining 27.5% were schooling. Majorly 54.8% of the drug claimed to be readily accessible and about 42.0% were
quite affordable. About half 56.4% of the respondents often engaged in social vices such as fight, rape or scatter the
house, 53.3% of the respondents had been arrested by the law enforcement agents such as Police or NDLEA, two-third
64.6% of the respondents had tried to stop doing drugs before but finds it hard. Table 3 shows that 71.0% of the respondents had current relapse episode of less than four weeks, few 11.3% had it in
3 month and above. About 64.5% of the respondent said that relapse occurred twice to the patient after successful
treatment, majority 72.5% of the respondents claimed that the patient comply to the prescribed medication when
his/her condition is under control. About 80.6% of the respondents said that the patient belong to a support group
therapy. 2.1. Research Design Most 79.0% of the respondent agreed that the frequent family conflict contributed to patient relapse, and
71.0% of the respondent claimed that the patient ever used maladaptive coping tactics e.g. smoking, drinking alcohol,
chewing Mira, aggression/fights, etc when faced with negative life events and stress. Most 79.9% of the respondents
agreed that the patients have personality problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to violence,
quarrel some, shyetc, while 20.1% did not agreed with the patients have any Personality problem. Majority 80.6% of
the respondents agreed that the patient often had negative thoughts, 75.8% of the respondents agreed that the
generative life events that are associated with the present condition of the patient. Two-third 71.0% of the respondents
agreed that the patient exhibit positive coping mechanisms when faced with stressful events. 3.1. Social determinants of relapse among the rehabilitated substance use patients The present study finds that majority of the respondent agreed that the patient have friends who use drugs, and one-
third. One-third of the respondents had no formal education and others had formal education at various levels, 40.3%
of the respondent were employed, 32.2% of the respondent were unemployed, while the remaining 27.5% were
schooling, Thus, contrary to Swanepoel, Stephen, and Gretel, (2016) that found poverty, unemployment and community
adversity been a major contributing factors to relapse in substance abuse people. Half of the respondents readily access
drugs that commonly abuses. Most of the respondents have tried to stop the patient from doing drugs and few never
tried. This goes with Campbell and Ettore (2011) that social support is a major factor influencing relapse to drugs in
males and females. The researchers found that men are more supported from home and in their working environment. Women on the other hand tend to be cut off and secluded from the community and their partners tend to be unfriendly. Also Swanepoel, Stephen, and Gretel, (2016). Poverty, unemployment and community adversity have been major
contributing factors to relapse in substance misuse 3. Discussion This present findings is in conversely with Carson et al. 2016, in a study conducted in Canada found that, older patients
have a lower relapse rate as compared to young patients. The study associated the difference as due to other age-related
factors which impact positively on abstinence post treatment such as higher self-efficacy, greater motivation and social
networks among adults. Also, Farkhondeh et al. 2015, agreed that marital status and addiction relapse bear a sufficient
relationship. The highest frequency of addiction relapse is observed in single persons, people who have lost spouse
through death and those who are divorced Limitation Due to descriptive nature of the study, some importance social demographic data, personal factors, social factor and
clinical factors such as, level of income were not recorded. More so, not all factors associated with relapse are considered in the study, factor such as family relationship, genetic
factor/hereditary. Generalization of the study should be done with caution as some of the psychotic relapse cases might
not be reported Disclosure of conflict of interest No conflict of interest. Implication of the Findings for Nursing Practicing psychiatric nurses should always consider the influence of patient’s demographic-personal characteristics
on health decisions as well as treatment adherence when caring for any patient as this will help identify some of the
factors that might be contributing to silment and treatment. They need to improve their knowledge on treatment
adherence and personal factors that can devoid frequent relapse of patients. The findings of the study would help
patients and their relatives to know more about the association between the personal, social and clinical factors that
associated with relapse of psychotic illness. 4. Conclusion This study was carried out on relapse among the rehabilitated substance use patient in Neuropsychiatric Hospital, Aro,
Abeokuta, Ogun State. Relevant and related literatures were reviewed. Purposive sampling technique used for this
study. The study sampled 125 respondents out of 160 that constituted the population. Instrument used for data
collection was self-administered questionnaire which was divided into four sections. The analysis done using
descriptive statistics such as simple percentage while the presentation will be done using tables and graphs. Recommendations The following are the recommendations from this study. •
The therapy / care of psychotic patients must be lengthy if they are to have a high quality of life. In order to
prevent the factors linked with relapse, the researcher suggests involving the patient's health care
provider/professionals, family/relatives, community, and religious body in the care of the patient. •
The therapy / care of psychotic patients must be lengthy if they are to have a high quality of life. In order to
prevent the factors linked with relapse, the researcher suggests involving the patient's health care
provider/professionals, family/relatives, community, and religious body in the care of the patient. y
y
g
y
•
Non-governmental organisations and affluent members of society should be encouraged to become more
involved in the care of psychotic patients in order to lessen the burden and cost of treatment, which includes
the purchase of medication and the transportation of the patient and their family members. •
Non-governmental organisations and affluent members of society should be encouraged to become more
involved in the care of psychotic patients in order to lessen the burden and cost of treatment, which includes
the purchase of medication and the transportation of the patient and their family members. •
Government should establish hospitals/clinics that are cheap for both poor and wealthy mentally ill individuals
in order to lessen the burden/cost of treatment, which includes the purchase of medication and the emigration
of the mentally sick and their relatives. •
Government should establish hospitals/clinics that are cheap for both poor and wealthy mentally ill individuals
in order to lessen the burden/cost of treatment, which includes the purchase of medication and the emigration
of the mentally sick and their relatives. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 said the patient exhibit positive coping mechanisms when faced with stressful events, this goes in line with (Hames
2013). In a study of untreated heavy drinkers in Britain and their readiness to change, the investigators found that,
stress is among the leading causes of relapse among drug addicts. They noted that though all forms of stress can't be
avoided, setting priority changes in lifestyle and relationships helps a recovering patient to avoid incidences that spark
tension and other negative emotions associated with relapse. Also, Scott, Hemphill, Sampat, Bhaven (2011) shows that,
emotional devastation of drug addiction is experienced by the addicts themselves, spouses, children and close friends
and the emotional reactions range from pain, stress, discouragement, shame and self-guilty. said the patient exhibit positive coping mechanisms when faced with stressful events, this goes in line with (Hames
2013). In a study of untreated heavy drinkers in Britain and their readiness to change, the investigators found that,
stress is among the leading causes of relapse among drug addicts. They noted that though all forms of stress can't be
avoided, setting priority changes in lifestyle and relationships helps a recovering patient to avoid incidences that spark
tension and other negative emotions associated with relapse. Also, Scott, Hemphill, Sampat, Bhaven (2011) shows that,
emotional devastation of drug addiction is experienced by the addicts themselves, spouses, children and close friends
and the emotional reactions range from pain, stress, discouragement, shame and self-guilty. [1]
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Psychiatric
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(APA)
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last three month and above, 64.5% of the respondent agreed that he usually occur to the patient after successful
treatment, while the remaining 35.5% were three or more, 72.5% of the respondents agreed that Does the patient
comply to the prescribed medication when his/he recondition is under control compliance while 27.5% did not support
the patient comply to the prescribed medication. Most of the respondents agreed that the patients have personality
problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to violence, quarrel some, shyetc, while 20.1% did not
agreed with the patients have any Personality problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to
violence, quarrel some, shyetc, likewise most patient often have negative thoughts. About two-third of the respondents 752 No conflict of interest. References [1]
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https://openalex.org/W2009263746 | https://europepmc.org/articles/pmc3712680?pdf=render | English | null | Desmoid Tumors in Pregnant and Postpartum Women | Cancers | 2,012 | cc-by | 4,639 | lliam A. Robinson *,1, Colette McMillan 2, Amy Kendall 3 and Nathan Pearlman *,4 Department of Medicine, University of Colorado Denver, Denver, CO 80045, USA Department of Medicine, University of Colorado Denver, Denver, CO 80045, USA
2 Department of Pharmacy, University of Colorado Denver, Denver, CO 80045, USA;
E-Mail: colette.mcmillan@uch.edu (C.M.) 3 Department of the Tumor Registry, University of Colorado Denver, Denver, CO 80045, USA;
E-Mail: amy.kendall@uch.edu (A.K.) 4 Department of Surgery, University of Colorado Denver, Denver, CO 80045, USA * Authors to whom correspondence should be addressed; E-Mails: william.robinson@ucdenver.edu
(W.A.R.); nathan.pearlman@ucdenver.edu (N.P.); Tel.: +1-303-724-3872 (W.A.R.);
Fax: +1-303-724-3889 (W.A.R.); Tel.: +1-303-724-2728 (N.P.); Fax: +1-303-724-7377(N.P.). * Authors to whom correspondence should be addressed; E-Mails: william.robinson@ucdenver.edu
(W.A.R.); nathan.pearlman@ucdenver.edu (N.P.); Tel.: +1-303-724-3872 (W.A.R.);
Fax: +1-303-724-3889 (W.A.R.); Tel.: +1-303-724-2728 (N.P.); Fax: +1-303-724-7377(N.P.). Received: 4 January 2012; in revised form: 11 February 2012 / Accepted: 13 February 2012 /
Published: 21 February 2012 Received: 4 January 2012; in revised form: 11 February 2012 / Accepted: 13 February 2012 /
Published: 21 February 2012 Abstract: We report here a review of the current medical literature on pregnancy associated
desmoids, including 10 cases of our own. The pertinent findings are that a large percentage
of desmoids in females arise in and around pregnancy. Most occur in the abdominal
muscles, particularly the right rectus abdominus, perhaps related to trauma from abdominal
stretching and fetal movement. While these tumors may regress spontaneously after
delivery most can be surgically resected with low recurrence rates even with R1 resections
and this is clearly the treatment of choice. Subsequent pregnancies do not appear to result
in recurrence in either FAP or non FAP patients. It is not clear from currently available
data whether pregnancy associated desmoids are molecularly distinct from other desmoids. Keywords: desmoid; pregnancy; post-partum; female Cancers 2012, 4, 184-192; doi:10.3390/cancers4010184 Cancers 2012, 4, 184-192; doi:10.3390/cancers4010184 Cancers 2012, 4 In a previous
paper we described four women who all developed post-partum desmoids in the same location, namely
the right rectus abdominus muscle. We speculated that this might have resulted from tearing or
stretching of the abdominal wall musculature during fetal growth. It is well known that desmoids may
be associated with trauma of different sorts. Against such a theory is the fact that in other case reports
of pregnancy associated desmoids the tumor has developed in a remote location such as the larynx [3–22]. Others have attempted to link the hormonal and immune system changes that occur with pregnancy
with desmoid development. The possible role of these factors is suggested by the description
of spontaneous desmoid regression after delivery [23]. Further the possible role of estrogen is
suggested by the occasional report of desmoids tumors responding to treatment with the anti-estrogen
tamoxifen [24,25]. In contrast however is the finding that it is very uncommon to find estrogen
receptors expressed on desmoids, even those that respond to tamoxifen. To date therefore the only
thing clear in this unique association is that no clear explanation has been forthcoming. Here we have
reviewed our own cases of pregnancy associated desmoids and the current literature in an attempt
develops better understanding and future directions for research and management. Cancers 2012, 4 Since then there have multiple single case reports and a few small series including one from our
institutions [2]. There have been various definitions of pregnancy associated desmoid. For the purpose
of this paper we have elected to define as pregnancy associated desmoids those that arose, or were
discovered during pregnancy, grew during pregnancy or developed postpartum within three years after
delivery. The reason(s) for the association between pregnancy and development of desmoids remain
unclear. A number of possible explanation have been put forward, none very satisfactory. In a previous
paper we described four women who all developed post-partum desmoids in the same location, namely
the right rectus abdominus muscle. We speculated that this might have resulted from tearing or
stretching of the abdominal wall musculature during fetal growth. It is well known that desmoids may
be associated with trauma of different sorts. Against such a theory is the fact that in other case reports
of pregnancy associated desmoids the tumor has developed in a remote location such as the larynx [3–22]. Others have attempted to link the hormonal and immune system changes that occur with pregnancy
with desmoid development. The possible role of these factors is suggested by the description
of spontaneous desmoid regression after delivery [23]. Further the possible role of estrogen is
suggested by the occasional report of desmoids tumors responding to treatment with the anti-estrogen
tamoxifen [24,25]. In contrast however is the finding that it is very uncommon to find estrogen
receptors expressed on desmoids, even those that respond to tamoxifen. To date therefore the only
thing clear in this unique association is that no clear explanation has been forthcoming. Here we have
reviewed our own cases of pregnancy associated desmoids and the current literature in an attempt
develops better understanding and future directions for research and management. Since then there have multiple single case reports and a few small series including one from our
institutions [2]. There have been various definitions of pregnancy associated desmoid. For the purpose
of this paper we have elected to define as pregnancy associated desmoids those that arose, or were
discovered during pregnancy, grew during pregnancy or developed postpartum within three years after
delivery. The reason(s) for the association between pregnancy and development of desmoids remain
unclear. A number of possible explanation have been put forward, none very satisfactory. 1. Introduction Pregnancy associated desmoids tumors have been a subject of interest since the first description by
Macfarlene in 1832 [1]. He described a young postpartum woman who had a large fibrous abdominal
wall tumor. This was also the first description of surgical resection of a pregnancy associated desmoid. 185 2. Methods All cases with histologically proven desmoid tumors in the Tumor Registry of our institution from 1980
through August 2011 were initially identified. There were 56 total cases of which there were 24 males
and 32 females. Among the females 10 fit our criteria for pregnancy associated desmoid: arising in
pregnancy, growth of a previously identified desmoid during pregnancy or development in 36 months
after parturition. We used this definition since these are slowly growing tumors and it is likely that
they were present at the time of pregnancy. Thus in our series 18% of all patients seen here during this
time period had a pregnancy associated desmoid. Perhaps more striking is the fact that of all females
with desmoids in our registry 31% were pregnancy associated. Details of these patients are shown in
Table 1. Four of these were included in a prior paper [2]. In the current series the patients ranged in age
from 22 to 39 years with a mean age of 32 and a median age of 33 years. Nine of the 10 cases
developed the tumor after completion of pregnancy at an average of 12 months postpartum. One was
found in the last month of pregnancy. The most common site was the right rectus abdominus muscle in
6 cases; two were in the left rectus abdominus, one in the mesentery and one on the back in a patient
with Gardner’s Syndrome. Surgical resection was the method of primary treatment in 10 patients. The
tumors ranged in size from 2 to 16 cm with an average size of 4.5 cm. Two of these had microscopically
positive margins, but none of the patients who had surgical resection; even with positive surgical
margins have had local or systemic recurrence at a mean follow-up of 3.4 years. No patient received
further therapy after surgery. One patient was treated with tamoxifen followed by gleevec prior to
surgery with minimal benefit. Two patients subsequently had full term pregnancies without 186 Cancers 2012, 4 Cancers 2012, 4 complications or desmoid recurrence. Two patients have active tumors not thought to be amenable to
surgical resection and are currently being treated with tamoxifen and clinoril. Except for the patient
with Gardner’s Syndrome no patient had a family history of desmoids tumors. Table 1. Clinical characteristics of 10 patients with pregnancy associated desmoid tumors
seen at the University of Colorado. 2. Methods y
Patient Age FAP Pre or post
Site
Treatment
Delivery
ER
Size
(cm)
Outcome
1
39
No
Post 12 mon
Rt rectus
Surg
CS
NA
5
NED 5 years
2
39
No
Post 1 mon
Rt rectus
Surg
CS
NA
2
NED 5 years
3
33
No
Post 36 mon
Rt rectus
Surg
CS
NA
7.5
NED 2 years
4
32
No
Post 12 mon
Rt rectus
Surg
Vag
NA
16
NED 5 years
5
36
No
Post 13 mon
Rt rectus
Surg
CS
NA
2
NED 6 years
6
33
No
Post 4 mon
Left rectus Surg
Vag
Neg
8
NED 2 years
7
26
Yes
Post 12 mon
Back
Tam/chemo
Vag
Neg
37
Alive with 2 years
8
33
No
Preg 40 wk
Left rectus Tam/chemo
CS
Neg
8
Alive with 1 years
9
29
No
Post 6 mon
Mesentery
Surg
CS
NA
5
NED 3 years
10
22
No
Post 25 mon
Rt rectus
Surg
CS
NA
7
NED 3 years
Age range: 22–39 years; Mean: 32 years; mon: month(s), wk: weeks; Rt rectus: right rectus; Size
range: 2–37 cm, Mean: 9.75 cm; NED: No evidence of disease. Alive = alive with tumor remaining. 3. Literature Review We reviewed the available literature for reports of pregnancy associated desmoids and this data,
minus our own cases, is detailed below in Table 2 [3–22]. We included only those reports in which
there was sufficient data on the age of the patient, size of the tumor, location and method of treatment. We also found an abstract describing 15 cases, but this series has not been reported in a full manuscript
and is described separately below. For the review we found 20 full length reports in the literature with
a total of 24 cases that fit the criteria described and provided sufficient data for analysis. The patients
ranged in age from 17 to 42 years with an average age of 27. Seven cases were associated with FAP
mutations. The remaining were either non FAP or no mention was made of the genetic status. In 15 cases
the desmoid arose during pregnancy, in five during the post-partum period and in four patients a pre-
existing desmoid grew during pregnancy. In 14 of the 24 cases (58%) the desmoid involved the
muscles of the abdominal wall. The mesentery was the next most common site and the remainder were
in a wide variety of locations including the larynx in one case. Most were in the 5 to 10 cm size range,
but one in case a tumor in the rectus abdominus grew to 192 cm at 39 weeks gestation. Most of these
patients were treated with surgical resection Due to inadequate reporting we are unable to make
definitive comments regarding outcome and recurrence in patients other than our own described above. In addition to these cases Rocha et al. [23] have described, in abstract form, limited details of
pregnancy associated desmoids seen at The Brigham and Women’s Hospital in Boston. They reviewed
207 total cases of desmoid tumors in their registry and identified 16 of these (8%) as having a
pregnancy associated desmoid. Similar to our series, described above, most (75%) were extraabdominal,
but the individual sites were not specified. None of these were FAP associated. All 16 patients had
surgical resection and of these nine (56%) were R0 and 7(44%) were R1 resections. At a median follow-up 187 Cancers 2012, 4 Cancers 2012, 4 of 39 months only two patients in this series had recurred, both after initial R1 resections. Both
underwent successful re-excision. 3. Literature Review These authors concluded that pregnancy associated desmoids
represent a less aggressive, subtype of desmoid tumors usually amenable to surgical resection. Table 2. Pregnancy associated desmoid. A review of the literature. Author(s)
Ref. Age of
Patient
FAP
Number of
Pregnancies
Delivery
Pre, During,
or Post
Pregnancy
Size
Location
Treatment
Outcome
ER
Ober et al. [3]
18
N/A
1
(unknown)
Pre
1–2 cm
Left popliteal
fossa
Surg
NED
1 year
N/A
Khoo, S.K. [4]
25
No
2
Vag
During
8 × 5 ×
3 cm
obturator
Surg
NED
6 months
35
N/A
2
CS
During
11 week
gestation
(unknown)
Right
obturator
No
treatment
N/A
Caldwell,
E.H. [5]
26
N/A
4
(unknown)
Post
15 × 17 cm
Lower
abdominal
wall
No
treatment
NED
5 years
N/A
Knightly
et al. [6]
18
N/A
1
CS
Post
(unknown)
Right upper
quadrant
Surg;
XRT;
chemo
(unknown)
Harvey
et al. [7]
23
Yes
1
(unknown)
During
3rd trimester
N/A
Mesentry
Surg
(unknown)
24
Yes
1
(unknown)
Post
12 × 10 ×
5 cm
Mesentry
Surg
NED
3 years
34
Yes
1
(unknown)
Post
(unknown)
Terminal
ileus
Surg
(unknown)
Camiel &
Solish [8]
22
No
2
(unknown)
During
7th month
14 × 10 cm
Right, upper
anterior
abdominal
wall
Surg
N/A
Ezra et al. [9]
35
No
1
Vag
Pre
15 × 13 cm
Abdominal
wall
Surg
NED
2 years
N/A
Sportiello &
Hoogerland
[10]
40
N/A
1
CS
During
3rd trimester
10 × 8 ×
6 cm
Pelvic mass
Surg;
XRT;
chemo
NED at
27 months
N/A
Allen &
Novotny
[11]
19
No
1
(unknown)
Pre
3 × 3 cm
Right labium
Surg; XRT
NED at
12 months
Kunieda
et al. [12]
27
N/A
1
(unknown)
During
8th month
9 × 7.5 cm
Chest wall,
xphoid
Surg
NED
Neg
Way &
Culham
[13]
28
N/A
3
Vag
Post
3 × 4 ×
2.5 cm
Left rectus
abdominal
muscle
Surg
NED Table 2. Pregnancy associated desmoid. A review of the literature. 188 Cancers 2012, 4 Cancers 2012, 4 Table 2. Cont. Author(s)
Ref. Age of
Patient
FAP
Number of
Pregnancies
Delivery
Pre, During,
or Post
Pregnancy
Size
Location
Treatment
Outcome
ER
Way &
Culham
[13]
28
N/A
1
(unknown)
Post
1.3 × 1.2 cm
Left upper
rectus
muscle just
below the
costal
margin
Surg
NED
Neg
Gherman
et al. 3. Literature Review [14]
25
N/A
1
Vag
During
20 weeks
gestation
2.3 × 1.2 ×
1.6 cm
Larynx
Surg
(unknown)
de Cian
et al. [15]
42
N/A
2
CS
During
12 weeks
gestation
8 × 5 cm
Right rectus
abdominus
c-section
scar
Surg
NED
15 months
NE
G
Firoozmand
& Prager
[16]
27
Yes
1
(unknown)
During
23 weeks
gestation
17 × 14 ×
10 cm
J pouch
Surg
N/A
N/A
Mulik et al. [17]
35
Yes
5
Vag; CS
During
18 weeks
gestation
5 × 4 cm
4 × 4 cm
Rectus
sheath
Surg
No follow
up
Molelekwa,
V. [18]
31
N/A
2
CS
During
20 weeks
gestation
2.7 ×
4.5 cm
Left lower
quadrant
abdominal
mass
Surg
N/A
Durkin et
al. [19]
29
N/A
1
Vag
During
1st trimester
3.5 × 7.2 cm
Left rectus
abdominis
muscle
Surg;
chemo
NED
2.5 years
Sun et al. [20]
28
N/A
1
CS
Post
12.2 × 11.5
× 8.5 cm
Mesentery
abdomen
Surg
NED
12 months
Viriyaroj
et al. [21]
17
N/A
1
(unknown)
During
5th month
28 × 21 ×
18 cm
Lower
abdominal
wall
Surg
NED
8 months
Le Roc'h
et al. [22]
18
N/A
1
Vag
Pre
192 cm3
Rectus
muscle of the
abdomen
No
treatment
N/A
N/A Table 2. Cont. Cancers 2012, 4 Cancers 2012, 4 Cancers 2012, 4 without desmoids. The age(s) were not given for the patients in the series reported by Rocha et al. [23]. Most, patients, both in our own series and our review had a prior pregnancy often with a caesarian
section. While desmoids have been reported to arise in caesarian section scars this appears to be
uncommon. The most common site is in the abdominal musculature particularly the right rectus
abdominus muscle. Since these tumors are known to arise in areas of trauma we have speculated that
this results from stretching of the abdominal muscles and fascia during gestation. This suggestion of
causation does not explain however the development of desmoids in other areas during and after
pregnancy indicating that other factors are also involved. The most likely factors are the hormonal and
immunologic changes that occur during pregnancy. The fact that some desmoids have been reported to regress without treatment after termination of
pregnancy indicates that such factors may be in play. The most important of these are probably
hormonal. This suggestion is strengthened by reports of spontaneous regression of pregnancy
associated desmoids after delivery and without treatment. Further are many reports that some
desmoids, both in pregnant and non-pregnant patients, respond to treatment with the anti-estrogen
tamoxifen or the related drug toremifene [24]. This is not a simple estrogen related phenomenon
however. Very few desmoids have been reported to express significant estrogen receptors. This may be
due to inadequate methods of investigation in the past. These receptors are almost always present if
carefully searched for, although their significance is unknown. The effects of tamoxifen are
considerably more broad and complex than blocking estrogen uptake [25]. The doses used for
desmoids are usually much higher (200 mg/day) [25] than typically used in the treatment of breast
cancer (20 mg/day) and usually combined with a non-steroidal anti-inflammatory drug such as
sulindac. The response rate to tamoxifen therapy in all desmoids is however in the range of 50% [24]
and understanding the mechanisms involved is likely to lead to better understanding of development
and new therapies. Finally regression of desmoids has been reported to occur in women as they go
through menopause. In contrast prior pregnancy has been reported to ameliorate the course of intra-abdominal desmoids
in patients with FAP [26]. 4. Discussion We review here 50 cases of pregnancy associated desmoid tumors including 10 cases from our own
institution. These appear to be a unique form of desmoids comprising 8 to 18% of all desmoid tumors
in cancer registries. They are usually sporadic but may be associated with the FAP syndrome. If we
exclude patients with FAP there does not appear to be any common features that mark women at risk
for this problem. The patients in our series were perhaps older (mean age 32 years) than pregnant women 189 Cancers 2012, 4 Cancers 2012, 4 of the three patients did not have mutations of CTNNB1, but did have loss of parts of 5q including the
area encoding APC. Together these findings provide a link to the development of spontaneous
desmoids and those occurring in FAP patients as the same pathways are involved. Although longer
term studies are needed it would appear that those patients without mutations of CTNNB1, such as
pregnancy associated desmoids, have a more favorable prognosis for unclear reasons. These same
authors [29] have recently reported on outcome and prognostic factors in 426 patients with desmoid
tumors. Of these 32 (7.5%) had abdominal wall pregnancy associated desmoids with a 10 year
progression survival of 62%, the highest of any subgroup in this large series. One of the questions frequently asked by patients with pregnancy associated desmoids is what the risk
of recurrence with subsequent pregnancies is. We could not find any non FAP cases in which this occurred. In our own series two patients had subsequent pregnancies, Rocha’s series had one [23] and Way et al. [13]
reported two further patients with no recurrence with a subsequent pregnancy. Of interest in this regard
is a patient reported by Caldwell [5] who described a 26 year old woman who a large, unresectable
desmoid during pregnancy which regressed without therapy even during a subsequent pregnancy. 5. Conclusions Desmoid tumors in females are often associated with pregnancy or occur post-partum. The reasons
behind this association are unclear. The most common sites are in the abdominal muscles, but they
have been reported in multiple other areas of the body. Surgical resection is the treatment of choice
and is usually curative even when surgical margins are involved. Subsequent pregnancies do not
appear to be contraindicated. Acknowledgements We thank Brenda Batlle for her help in preparation of the manuscript. Cancers 2012, 4 These authors compared the growth and progression of FAP related
desmoids in 22 never pregnant patients with 25 similar patients who had been pregnant at least once. The patients who had been pregnant had smaller tumors, less surgery and a more benign course
overall. These authors go as to far as to suggest that consideration should be given to possible therapy
with hormone combinations of progesterone, prolactin and estrogen. It should be noted that these
findings were reported only for FAP related desmoids and whether they are applicable to sporadic
pregnancy associated desmoids is not clear. In order to better understand the mechanisms involved in the development of desmoids and develop
new therapies a number of studies have examined molecular pathways, though not specifically in
pregnancy associated desmoids. Heinrich et al. [27] examined tumor specimens from 19 patients
looking for possible imatinib targets. No mutations were found in KIT, PDGFRA or PDGFRB, but 16
of the 19 had mutations involving the WNT pathway (APC or CTNNB1). These findings provide a
link to the development of spontaneous desmoids and those occurring in FAP patients as the same
pathways are involved. These findings were confirmed by Salas et al. in a larger study of 194 patients [28]
using comparative genomic and DNA sequencing. This study included 13 women of child bearing age,
during or shortly following pregnancy. Of these detailed molecular data is reported for only three. Two 190 Cancers 2012, 4 Cancers 2012, 4 Cancers 2012, 4 8. Camiel, M.R.; Solish, G.I. Desmoid tumor during pregnancy. Am. J. Obstet. Gynecol. 1982, 144,
988–989. 9. Ezra, Y.;Krausz, M.M.; Rivkind, A.; Antebey, S.O. Successful pregnancy and normal delivery
with Marlex mesh replacement of the abdominal wall. Am. J. Obstet. Gynecol. 1990, 162, 97–98. 10. Sportiello, D.J.; Hoogerland, D.L. A recurrent pelvic desmoid tumor successfully treated with
tamoxifen. Cancer 1991, 67, 1443–1446. 11. Allen, M.V.; Novotny, D.B. Desmoid tumor of the vulva associated with pregnancy. Arch. Pathol. Lab. Med. 1997, 121, 512–514. 12. Kunieda, K.; Saji, S.; Tanaka, Y.; Katoh, M.; Fucada, D.; Shimokawa, K. An abdominal desmoid
tumor involving the xyphoid and costal chondrium associated with pregnancy: Report of a case. Surg. Today 1999, 29, 927–930. 13. Way, J.C.; Culham, B.A. Desmoid tumour. The risk of recurrent or new disease with subsequent
pregnancy: A case report. Can. J. Surg. 1999, 42, 51–54. 14. Gherman, R.B.; Bowen, E.; Eggleston, M.K.; Karakia, D. Desmoid tumor of the larynx
complicating pregnancy: A case report. Am. J. Obstet. Gynecol. 1999, 180, 1036–1037. 15. de Cian, F.; Delay, E.; Rudigoz, R.C.; Ranchere, D.; Rivoire, M. Desmoid tumor arising in a
cesarean section scar during pregnancy: Monitoring and management. Gynecol. Oncol. 1999, 75,
145–148. 16. Firoozmand, E.; Prager, E. Pelvic desmoid tumor: threat to mother and fetus. Am. Surg. 2001, 67,
1213–1215. 17. Mulik, V.; Griffiths, A.N.; Beattie, R.B. Desmoid tumours with familial adenomatous polyposis
in pregnancy. J. Obstet. Gynaecol. 2003, 23, 307–308. 18. Molelekwa, V. Conservative management of a desmoid tumour in pregnancy. J. Obstet. Gynaecol. 2004, 24, 700. 19. Durkin, A.J.; Korkolis, D.P.; Al-Saif, O.; Zervos, E.E. Full-term gestation and transvaginal
delivery after wide resection of an abdominal desmoid tumor during pregnancy. J. Surg. Oncol. 2005, 89, 86–90. 20. Sun, L.; Wu, H.; Zhuang, Y.Z.; Guan, Y.S. A rare case of pregnancy complicated by mesenteric
mass: What does chylous ascites tell us? World J. Gastroenterol. 2007, 13, 1632–1635. 21. Viriyaroj, V.;Yingsakmongkol, N.; Pasukdee, P.; Rermluk, N. A large abdominal desmoid tumor
associated with pregnancy. J. Med. Assoc. Thai. 2009, 92, S72–S75. 22. Le Roc'h, A.; Montaigne, K.; Leblond, P.; Subtil, D.; Boukerrou, M. Desmoid tumour of the
rectus abdominis muscle during pregnancy. J. Obstet. Gynaecol. 2009, 29, 668–669. 23. Rocha, F.; George, S.; Fletcher, C.; Bertagnolli, M.; Butrynski, J.; Demetri, G.; Morgan, J.;
Wagner, A.; Raut, C. Pregnancy-associated desmoid tumors: A distinct clinical entity. Ann. Surg. Oncol. References 1. Macfarlane, J. Clinical Reports of the Surgical Practice of the Glasgow Royal Infirmary; David
Robertson: Glasgow, UK, 1832; pp. xvi, 314. 1. Macfarlane, J. Clinical Reports of the Surgical Practice of the Glasgow Royal Infirmary; David
Robertson: Glasgow, UK, 1832; pp. xvi, 314. 2. Carneiro, C.; Hurtubis, C.; Sing, M.; Robinson, W. Desmoid tumors of the right rectus abdominus
muscle in postpartum women. Arch. Gynecol. Obstet. 2009, 279, 869–873. 2. Carneiro, C.; Hurtubis, C.; Sing, M.; Robinson, W. Desmoid tumors of the right rectus abdominus
muscle in postpartum women. Arch. Gynecol. Obstet. 2009, 279, 869–873. 3. Ober, W.B.; Velardo, J.T.; Greene, R.T.; Taylor, R.J. Desmoid tumor of the popliteal space
occurring during pregnancy: Report of a case with bioassays. J. Natl. Cancer Inst. 1955, 16, 569–577. 4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of 3. Ober, W.B.; Velardo, J.T.; Greene, R.T.; Taylor, R.J. Desmoid tumor of the popliteal space
occurring during pregnancy: Report of a case with bioassays. J. Natl. Cancer Inst. 1955, 16, 569–577. g
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4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of
four patients. Aust. N. Z. J. Surg. 1972, 42, 170–174. 4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of
four patients. Aust. N. Z. J. Surg. 1972, 42, 170–174. 5. Caldwell, E.H. Desmoid tumor: Musculoaponeurotic fibrosis of the abdominal wall. Surgery
1976, 79, 104–106. 5. Caldwell, E.H. Desmoid tumor: Musculoaponeurotic fibrosis of the abdominal wall. Surgery
1976, 79, 104–106. 6. Knightly, J.J.; Machiedo, G.W.; Merke, E.A.; Blackwood, G.M. Giant recurrent desmoid tumor:
A case report. Am. Surg. 1977, 43, 613–616. 6. Knightly, J.J.; Machiedo, G.W.; Merke, E.A.; Blackwood, G.M. Giant recurrent desmoid tumor:
A case report. Am. Surg. 1977, 43, 613–616. 7. Harvey, J.C.; Quan, S.H.; Fortner, J.G. Gardner’s syndrome complicated by mesenteric desmoid
tumors. Surgery 1979, 85, 475–477. 7. Harvey, J.C.; Quan, S.H.; Fortner, J.G. Gardner’s syndrome complicated by mesenteric desmoid
tumors. Surgery 1979, 85, 475–477. 191 © 2012 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/). Cancers 2012, 4 2008, 15, 66. 24. Bocale, D.; Rotelli, M.T.; Cavallini, A.; Altomare, D.F. Anti-oestrogen therapy in the treatment of
desmoid tumours. A systematic review. Colorectal Dis. 2011, 13, e388–e395. 25. Hansmann, A. High-dose tamoxifen and sulindac as first-line treatment for desmoid tumors. Cancer 2004, 100, 612–620. 26. Church, J.M.; McGannon, E. Prior pregnancy ameliorates the course of intra-abdominal desmoid
tumors in patients with familial adenomatous polyposis. Dis. Colon Rectum 2000, 43, 445–450. 192 Cancers 2012, 4 27. Heinrich, M.C.; McArthur, G.; Demetri, G.; Joensuu, H.; Bono, P.; Herrmann, R.; Hirte, H.;
Cresta, S.; Koslin, B.; Corless, C.; et al. Clinical and molecular studies of the effect of imatinib on
advanced aggressive fibromatosis (desmoid tumor). J. Clin. Oncol. 2006, 24, 1195–1203. 27. Heinrich, M.C.; McArthur, G.; Demetri, G.; Joensuu, H.; Bono, P.; Herrmann, R.; Hirte, H.;
Cresta, S.; Koslin, B.; Corless, C.; et al. Clinical and molecular studies of the effect of imatinib on
advanced aggressive fibromatosis (desmoid tumor). J. Clin. Oncol. 2006, 24, 1195–1203. 28. Salas, S.; Chibon, F.; Noguchi, T.; Terrier, P.; Rancher-Vince, D.; Lagarde, P.; Benard, J.; Forger, S.;
Blanchard, C.; Domont, J.; et al. Molecular characterization by array comparative genomic
hybridization and DNA sequencing of 194 desmoid tumors. Genes Chromosomes Cancer 2010,
49, 560–568. 29. Salas, S.; Dufresne, A.; Bui, B.; Blay, J.Y.; Terrier, P.; Ranchere-Vince, D.; Bonvalot, S.;
Stoeckle, E.; Guillou, L.; Le Cesne, A.; et al. Prognostic factors influencing progression-free
survival determined from a series of sporadic desmoid tumors: A wait-and-see policy according to
tumor presentation. J. Clin. Oncol. 2011, 29, 3553–3558. © 2012 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/). |
https://openalex.org/W4245565794 | https://www.cambridge.org/core/services/aop-cambridge-core/content/view/F3B625A7CAF0AA679ED2D8337CDE8C21/S0140078900012621a.pdf/div-class-title-professor-sir-desmond-pond-1978-1981-div.pdf | English | null | Professor Sir Desmond Pond (1978–1981) | The bulletin of the Royal College of Psychiatrists/Bulletin of the Royal College of Psychiatrists | 1,981 | cc-by | 5,545 | Professor Sir Desmond Pond (1978-1981) Sir Martin Roth and Professor Linford Rees have well
documented the achievements of the past ten years, to which
I can add but little except to say how proud I am to have
been able to join in with these activities and try to continue
their far-sighted policies. Nevertheless, there is much that
remains to be done, not so much because of what we have
failed to do as because of the constantly changing situation
in which we work. views more at the undergraduate than the postgraduate level. We are probably further on than most specialties in pro
viding better arrangements for part-time trainees and part-
time consultant appointments, though there is still a long
way to go. More difficult is the question of the ratio of
trainees to consultants, though there is now movement here,
at least at the levels of DHSS and Joint Consultants Com
mittee policy planning. More consultants has always been
our policy, but it carries with it the inevitable consequence
that some hospitals will be without trainees. What sort of
non-trainee, non-consultant doctors may share the work
load with the consultant staff is so far an unsolved issue, but
1 think we are nearer than most specialties to having and
accepting a role for career-grade part-time (and probably
whole-time) specialists. However. I do not think we have
adequately
considered the advantages
of using general
practitioners more, nor the possibilities of the non-medical
professionals,
like
community
psychiatric
nurses,
counsellors, clinical psychologists, etc. As an example, I should like first to mention recruitment
and manpower. Though I raised this as a major issue when I
became President, little progress has been made. However,
the general lines of future policy are now clearer, and the will
to implement change will undoubtedly be increased by the
recommendations of the House of Commons Select Com
mittee under RenéeShort, whose report has just been pub
lished. The
main difficulty is that,
though
manpower
problems are different in different specialties, we have, never
theless, to keep roughly in step with the career structure of
the medical profession as a whole. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner.
During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa.
The Research
Committee
is not only always ready to help
individual
research
workers
in
the
plan
methodology of their research, but has also la
College's first research project, an inquiry into EC
Other standing committees have also gone fr
to strength. The Programmes and Meetings
arranges excellent meetings throughout the year,
tion Committee, in its manifold activities, plays a
the College's affairs, the Collegiate Trainees C
actively
engaged
and
is
particularly
conce
manpower
and the
Membership Examination
training throughout the United Kingdom and
Ireland.
A key person during the period preceding the
the College and throughout the past decade has
Natalie Cobbing who. as Secretary of the Colleg
a co-ordinating role without which the College
function effectively. We are indebted to her a
leagues, and to Mr and Mrs Brooks, for all the
have so faithfully given the College.
This has really been a very brief summary of
important activities of the College, and inevita
been unable to mention all its achievements an
who have contributed to its success during the p
The College continues to evolve and has alread
status and recognition throughout the world, fo
can all bejustly proud. This has really been a very brief summary of some of the
important activities of the College, and inevitably 1 have
been unable to mention all its achievements and all those
who have contributed to its success during the past decade. The College continues to evolve and has already gained in
status and recognition throughout the world, for which we
can all bejustly proud. The Research
Committee
is not only always ready to help Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner.
During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa.
The Research
Committee
is not only always ready to help
individual
research
workers
in
the
plan
methodology of their research, but has also la
College's first research project, an inquiry into EC
Other standing committees have also gone fr
to strength. The Programmes and Meetings
arranges excellent meetings throughout the year,
tion Committee, in its manifold activities, plays a
the College's affairs, the Collegiate Trainees C
actively
engaged
and
is
particularly
conce
manpower
and the
Membership Examination
training throughout the United Kingdom and
Ireland.
A key person during the period preceding the
the College and throughout the past decade has
Natalie Cobbing who. as Secretary of the Colleg
a co-ordinating role without which the College
function effectively. We are indebted to her a
leagues, and to Mr and Mrs Brooks, for all the
have so faithfully given the College.
This has really been a very brief summary of
important activities of the College, and inevita
been unable to mention all its achievements an
who have contributed to its success during the p
The College continues to evolve and has alread
status and recognition throughout the world, fo
can all bejustly proud. All these appear to
be thriving in a very healthy manner. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner. g
y
y
During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa. Other standing committees have also gone from strength
to strength. The Programmes and Meetings Committee
arranges excellent meetings throughout the year, the Educa
tion Committee, in its manifold activities, plays a vital part in
the College's affairs, the Collegiate Trainees Committee is
actively
engaged
and
is
particularly
concerned
with
manpower
and the
Membership Examination and with
training throughout the United Kingdom and Republic of
Ireland. A key person during the period preceding the inception of
the College and throughout the past decade has been Miss
Natalie Cobbing who. as Secretary of the College, exercises
a co-ordinating role without which the College could not
function effectively. We are indebted to her and her col
leagues, and to Mr and Mrs Brooks, for all the work they
have so faithfully given the College. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner.
During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa.
The Research
Committee
is not only always ready to help
individual
research
workers
in
the
plan
methodology of their research, but has also la
College's first research project, an inquiry into EC
Other standing committees have also gone fr
to strength. The Programmes and Meetings
arranges excellent meetings throughout the year,
tion Committee, in its manifold activities, plays a
the College's affairs, the Collegiate Trainees C
actively
engaged
and
is
particularly
conce
manpower
and the
Membership Examination
training throughout the United Kingdom and
Ireland.
A key person during the period preceding the
the College and throughout the past decade has
Natalie Cobbing who. as Secretary of the Colleg
a co-ordinating role without which the College
function effectively. We are indebted to her a
leagues, and to Mr and Mrs Brooks, for all the
have so faithfully given the College.
This has really been a very brief summary of
important activities of the College, and inevita
been unable to mention all its achievements an
who have contributed to its success during the p
The College continues to evolve and has alread
status and recognition throughout the world, fo
can all bejustly proud. This has really been a very brief summary of
important activities of the College, and inevita
been unable to mention all its achievements an
who have contributed to its success during the p
The College continues to evolve and has alread
status and recognition throughout the world, fo
can all bejustly proud. are those for Dependence
chiatry. All these appear to
er. has taken an active inter
particularly with regard to
tical purposes (see Sidney
y 1981. p 94). The College
ondemning this abuse, par
y Presidency, I was able to
ral Council of the Bar to
mmission jointly with the
investigate allegations of
was not received from the
. The College proposed a
Assembly
of
the
World
in Hawaii, which after
d New Zealand College of
e Assembly. The World
o committees, one to deal
and the College set up its
er matters relating to the
er the Chairmanship of Dr
has considered allegations
other countries, including
. only always ready to help
individual
research
workers
in
the
plannin
methodology of their research, but has also launc
College's first research project, an inquiry into ECT. Other standing committees have also gone from
to strength. The Programmes and Meetings Com
arranges excellent meetings throughout the year, the
tion Committee, in its manifold activities, plays a vita
the College's affairs, the Collegiate Trainees Comm
actively
engaged
and
is
particularly
concerne
manpower
and the
Membership Examination an
training throughout the United Kingdom and Rep
Ireland. A key person during the period preceding the ince
the College and throughout the past decade has be
Natalie Cobbing who. as Secretary of the College, e
a co-ordinating role without which the College co
function effectively. We are indebted to her and h
leagues, and to Mr and Mrs Brooks, for all the wo
have so faithfully given the College. This has really been a very brief summary of som
important activities of the College, and inevitably
been unable to mention all its achievements and a
who have contributed to its success during the past
The College continues to evolve and has already ga
status and recognition throughout the world, for w
can all bejustly proud. individual
research
workers
in
the
planning
and
methodology of their research, but has also launched the
College's first research project, an inquiry into ECT. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner.
During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa.
The Research
Committee
is not only always ready to help
individual
research
workers
in
the
plan
methodology of their research, but has also la
College's first research project, an inquiry into EC
Other standing committees have also gone fr
to strength. The Programmes and Meetings
arranges excellent meetings throughout the year,
tion Committee, in its manifold activities, plays a
the College's affairs, the Collegiate Trainees C
actively
engaged
and
is
particularly
conce
manpower
and the
Membership Examination
training throughout the United Kingdom and
Ireland.
A key person during the period preceding the
the College and throughout the past decade has
Natalie Cobbing who. as Secretary of the Colleg
a co-ordinating role without which the College
function effectively. We are indebted to her a
leagues, and to Mr and Mrs Brooks, for all the
have so faithfully given the College.
This has really been a very brief summary of
important activities of the College, and inevita
been unable to mention all its achievements an
who have contributed to its success during the p
The College continues to evolve and has alread
status and recognition throughout the world, fo
can all bejustly proud. Psychiatry. Other active Groups are those for Dependence
and Addiction and Biological Psychiatry. All these appear to
be thriving in a very healthy manner. During these years the College has taken an active inter
est in the matter of human rights, particularly with regard to
the abuse of psychiatry for political purposes (see Sidney
Levine's article in the Bulletin, May 1981. p 94). The College
passed a number of resolutions condemning this abuse, par
ticularly in the USSR. During my Presidency, I was able to
enlist the agreement of the General Council of the Bar to
take part in an investigatory commission jointly with the
College to visit the USSR and investigate allegations of
psychiatric abuse, but permission was not received from the
USSR for the visit to take place. The College proposed a
resolution
for
the
General
Assembly
of
the
World
Psychiatric
Association
meeting in Hawaii, which after
amendment by the Australian and New Zealand College of
Psychiatrists, was passed by the Assembly. The World
Psychiatric Association set up two committees, one to deal
with ethical matters in psychiatry, and the College set up its
own special committee to consider matters relating to the
political abuse of psychiatry, under the Chairmanship of Dr
Peter Sainsbury. This committee has considered allegations
of the abuse of psychiatry in other countries, including
Argentina. Chile and South Africa. The Research
Committee
is not only always ready to help
individual
research
workers
in
the
plan
methodology of their research, but has also la
College's first research project, an inquiry into EC
Other standing committees have also gone fr
to strength. The Programmes and Meetings
arranges excellent meetings throughout the year,
tion Committee, in its manifold activities, plays a
the College's affairs, the Collegiate Trainees C
actively
engaged
and
is
particularly
conce
manpower
and the
Membership Examination
training throughout the United Kingdom and
Ireland. A key person during the period preceding the
the College and throughout the past decade has
Natalie Cobbing who. as Secretary of the Colleg
a co-ordinating role without which the College
function effectively. We are indebted to her a
leagues, and to Mr and Mrs Brooks, for all the
have so faithfully given the College. Professor Sir Desmond Pond (1978-1981) We are
particularly
fortunate
in having very good
relations with the doctors in the DHSS concerned with
mental health in all its aspects. Not all the other Royal
Colleges have such close contacts. It has enabled us to have
informal discussions about many sensitive medico-political
issues before they reach the level of formal negotiation. Perhaps Sir Henry
Yellowlees' distinguished psychiatric
forebears have had a benign ghostly influence! As I write we
are awaiting the news of a possible new Mental Health Act. and this will undoubtedly be a major issue for our new Presi
dent—wecould not be in safer and stronger hands to steer
us through this and the many other problems that will
doubtless emerge in the next few years. class Journal with an international reputation. But it has little
influence in the corridors of power. I have often wondered
why it is less influential than many of the bodies to which
most of its members belong. Probably it is because ACPP
does not control entry into any profession, nor training
schemes, nor certificates of competence. These functions
which the existing organization that do these things, such as
the medical Royal Colleges, guard very jealously, and I
suspect that they would be very reluctant to give them up or
even accept the need for rationalization across disciplines. at least three areas in which we have many common inter
ests with numerous other professional groups: the first, the
whole matter of training in psychotherapy and counselling. Trainees differ greatly in the intensity of their training, the
breadth
of
their
experience
and
their
background
of
academic knowledge, and the various levels do not corre
spond easily to usual professional boundaries. I believe that
there is enough in common between all of the methods of
treatment for a greater effort to be made to integrate train
ing schemes. Secondly, there ought to be certain common
standards of professional behaviour. A start has been made
in this direction in the long on-going Committee on Con
fidentiality. In spite of tremendous efforts by Professor
Linford Rees and Dr Brian Ward, the Chairman
and
Secretary,
respectively, of this inter-disciplinary
group,
agreement
is proving difficult to
reach,
though
much
valuable discussion has taken place and it is hoped that a
report will soon be published. Professor Sir Desmond Pond (1978-1981) The Zangwill Committee
Report on a Code of Behaviour for Behaviour Therapy is
another example of trying to apply standards of profes
sional behaviour across disciplines. The Registration of
Psychotherapists
is a third topic where standards
and
training matters overlap. Finally, many of these organiza
tions, including ourselves, have common interests in the pre
vention of mental disorder and in treatment in the com
munity. The community-based work inevitably implies going
beyond the treatment of the individual patient which is the
traditional role of the doctor. It implies going beyond even
the treatment of the family which is now well-established in
psychiatry. I am not sure how many of us are ready to be
involved even indirectly in changing the attitudes
and
behaviour of social groups, including some sort of social
action. The problems here will probably be the most intract
able, as social and political actions are hard to separate and
political action is something that many professional people
fight shy of. class Journal with an international reputation. But it has little
influence in the corridors of power. I have often wondered
why it is less influential than many of the bodies to which
most of its members belong. Probably it is because ACPP
does not control entry into any profession, nor training
schemes, nor certificates of competence. These functions
which the existing organization that do these things, such as
the medical Royal Colleges, guard very jealously, and I
suspect that they would be very reluctant to give them up or
even accept the need for rationalization across disciplines. Although many people express satisfaction at the flourish
ing state of the numerous Sections and Groups that the
College has and of the numerous meetings held (even includ
ing committees!), I must express some concern at this
proliferation—we might do better if we met less often for
longer. The central core of general psychiatry needs to be
jealously maintained as it is of primary importance for us all. Medicine and surgery, of course, have similar fissiparous
tendencies, but I am sure the Royal College of Physicians
and the Royal College of Surgeons are right to insist on the
MRCP and the FRCS, repectively, as general examinations
without which specialization and further training cannot be
undertaken. on 1 January, 1982. There are still some subscriptions out
standing, and in their own interest members are requested to
make prompt payment of their dues. on 1 January, 1982. There are still some subscriptions out
standing, and in their own interest members are requested to
make prompt payment of their dues.
The response from members who signed mandates to
enable subscriptions to be paid by direct debit has exceeded
our early expectations. However, it is hoped that members
who have not already agreed to this method of payment will
soon do so. Thus continuity of payment is assured even
though the subscription varies and no further action is
required by the member. Notification of the amount due will
be seni annually.
C. M. B. PAREHonorary Treasurer Professor Sir Desmond Pond (1978-1981) What I say in this connection could be seen to
be in conflict with what I have said in the previous para
graph about the need for multidisciplinary training and
standards, but I think the contradiction is probably healthy,
and I hope it will continue to stimulate discussion and
debate. We are
particularly
fortunate
in having very good
relations with the doctors in the DHSS concerned with
mental health in all its aspects. Not all the other Royal
Colleges have such close contacts. It has enabled us to have
informal discussions about many sensitive medico-political
issues before they reach the level of formal negotiation. Perhaps Sir Henry
Yellowlees' distinguished psychiatric
forebears have had a benign ghostly influence! As I write we
are awaiting the news of a possible new Mental Health Act. and this will undoubtedly be a major issue for our new Presi
dent—wecould not be in safer and stronger hands to steer
us through this and the many other problems that will
doubtless emerge in the next few years. As many of you know, before I became President of this
College I was Chairman
of the Association
of Child
Psychology and Psychiatry. This is a flourishing multi
disciplinary body whose membership is rightly increasing all
the time. I hope that all child psychiatrists feel that they
should belong to it. Amongst other things, it publishes a first Annual Subscription on 1 January, 1982. There are still some subscriptions out
standing, and in their own interest members are requested to
make prompt payment of their dues.
The response from members who signed mandates to
enable subscriptions to be paid by direct debit has exceeded
our early expectations. However, it is hoped that members
who have not already agreed to this method of payment will
soon do so. Thus continuity of payment is assured even
though the subscription varies and no further action is
required by the member. Notification of the amount due will
be seni annually.
C. M. B. PAREHonorary Treasurer Professor Sir Desmond Pond (1978-1981) Our recruitment from
British graduates may improve as a result of the 'popular'
specialties of general medicine and surgery making greater
efforts to bring home to graduates the advantages of going
into the 'shortage' specialties, though it is difficult to know
quite what determines popularity and unpopularity among
us and whether efforts should be made to change students' This last consideration brings me to the second matter on
which further action is increasingly necessary. This is to
remedy the lack of a proper body to represent the interests of
the numerous workers in the psychosocial caring field.There
are many ad hoc committees and standing committees, but
no on-going body which can speak with authority. There are 223 https://doi.org/10.1192/S0140078900012621 Published online by Cambridge University Press at least three areas in which we have many common inter
ests with numerous other professional groups: the first, the
whole matter of training in psychotherapy and counselling. Trainees differ greatly in the intensity of their training, the
breadth
of
their
experience
and
their
background
of
academic knowledge, and the various levels do not corre
spond easily to usual professional boundaries. I believe that
there is enough in common between all of the methods of
treatment for a greater effort to be made to integrate train
ing schemes. Secondly, there ought to be certain common
standards of professional behaviour. A start has been made
in this direction in the long on-going Committee on Con
fidentiality. In spite of tremendous efforts by Professor
Linford Rees and Dr Brian Ward, the Chairman
and
Secretary,
respectively, of this inter-disciplinary
group,
agreement
is proving difficult to
reach,
though
much
valuable discussion has taken place and it is hoped that a
report will soon be published. The Zangwill Committee
Report on a Code of Behaviour for Behaviour Therapy is
another example of trying to apply standards of profes
sional behaviour across disciplines. The Registration of
Psychotherapists
is a third topic where standards
and
training matters overlap. Finally, many of these organiza
tions, including ourselves, have common interests in the pre
vention of mental disorder and in treatment in the com
munity. The community-based work inevitably implies going
beyond the treatment of the individual patient which is the
traditional role of the doctor. It implies going beyond even
the treatment of the family which is now well-established in
psychiatry. Professor Sir Desmond Pond (1978-1981) I am not sure how many of us are ready to be
involved even indirectly in changing the attitudes
and
behaviour of social groups, including some sort of social
action. The problems here will probably be the most intract
able, as social and political actions are hard to separate and
political action is something that many professional people
fight shy of. As many of you know, before I became President of this
College I was Chairman
of the Association
of Child
Psychology and Psychiatry. This is a flourishing multi
disciplinary body whose membership is rightly increasing all
the time. I hope that all child psychiatrists feel that they
should belong to it. Amongst other things, it publishes a first
class Journal with an international reputation. But it has little
influence in the corridors of power. I have often wondered
why it is less influential than many of the bodies to which
most of its members belong. Probably it is because ACPP
does not control entry into any profession, nor training
schemes, nor certificates of competence. These functions
which the existing organization that do these things, such as
the medical Royal Colleges, guard very jealously, and I
suspect that they would be very reluctant to give them up or
even accept the need for rationalization across disciplines. Although many people express satisfaction at the flourish
ing state of the numerous Sections and Groups that the
College has and of the numerous meetings held (even includ
ing committees!), I must express some concern at this
proliferation—we might do better if we met less often for
longer. The central core of general psychiatry needs to be
jealously maintained as it is of primary importance for us all. Medicine and surgery, of course, have similar fissiparous
tendencies, but I am sure the Royal College of Physicians
and the Royal College of Surgeons are right to insist on the
MRCP and the FRCS, repectively, as general examinations
without which specialization and further training cannot be
undertaken. What I say in this connection could be seen to
be in conflict with what I have said in the previous para
graph about the need for multidisciplinary training and
standards, but I think the contradiction is probably healthy,
and I hope it will continue to stimulate discussion and
debate. Annual Subscription It was with great reluctance that subscription rates for
United Kingdom members were increased at the Annual
General Meeting in July 1981. Details appear in the Minutes
of the Annual Meeting on page 232. You are reminded that
your subscription falls due on 1 January, 1982. and that if
you do not pay by direct debit or banker's order payment
should now be sent to me at the College. on 1 January, 1982. There are still some subscriptions out
standing, and in their own interest members are requested to
make prompt payment of their dues. on 1 January, 1982. There are still some subscriptions out
standing, and in their own interest members are requested to
make prompt payment of their dues. The response from members who signed mandates to
enable subscriptions to be paid by direct debit has exceeded
our early expectations. However, it is hoped that members
who have not already agreed to this method of payment will
soon do so. Thus continuity of payment is assured even
though the subscription varies and no further action is
required by the member. Notification of the amount due will
be seni annually. C. M. B. PAREHonorary Treasurer The response from members who signed mandates to
enable subscriptions to be paid by direct debit has exceeded
our early expectations. However, it is hoped that members
who have not already agreed to this method of payment will
soon do so. Thus continuity of payment is assured even
though the subscription varies and no further action is
required by the member. Notification of the amount due will
be seni annually. C. M. B. PAREHonorary Treasurer Members whose subscriptions are outstanding for the
current year were informed at the beginning of September
that unless payment was received by the end of October,
they would cease to receive the British Journal of Psychiatry 224 https://doi.org/10.1192/S0140078900012621 Published online by Cambridge University Press |
https://openalex.org/W3217604012 | https://nottingham-repository.worktribe.com/preview/6841342/Weng%20PLOS%20ONE%202021.pdf | English | null | Determining propensity for sub-optimal low-density lipoprotein cholesterol response to statins and future risk of cardiovascular disease | PloS one | 2,021 | cc-by | 9,514 | PLOS ONE PLOS ONE RESEARCH ARTICLE Editor: Carmine Pizzi, University of Bologna, ITALY Received: April 7, 2021
Accepted: November 17, 2021
Published: December 2, 2021 OPEN ACCESS Citation: Weng SF, Akyea RK, Man KKC, Lau WCY,
Iyen B, Blais JE, et al. (2021) Determining
propensity for sub-optimal low-density lipoprotein
cholesterol response to statins and future risk of
cardiovascular disease. PLoS ONE 16(12):
e0260839. https://doi.org/10.1371/journal. pone.0260839 Citation: Weng SF, Akyea RK, Man KKC, Lau WCY,
Iyen B, Blais JE, et al. (2021) Determining
propensity for sub-optimal low-density lipoprotein
cholesterol response to statins and future risk of
cardiovascular disease. PLoS ONE 16(12):
e0260839. https://doi.org/10.1371/journal. pone.0260839 RESEARCH ARTICLE
Determining propensity for sub-optimal low-
density lipoprotein cholesterol response to
statins and future risk of cardiovascular
disease Stephen Franklin Weng1☯, Ralph Kwame AkyeaID1☯*, Kenneth KC ManID2,3, Wallis C. Y. Lau2,3, Barbara IyenID1, Joseph Edgar BlaisID3, Esther W. Chan3, Chung Wah Siu4,
Nadeem Qureshi1‡, Ian C. K. Wong2,3‡, Joe Kai1‡ a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 1 Primary Care Stratified Medicine (PRISM), Division of Primary Care, University of Nottingham, Nottingham,
United Kingdom, 2 Centre for Medicine Optimisation Research and Education (CMORE), Research
Department of Practice and Policy, UCL School of Pharmacy, London, United Kingdom, 3 Centre for Safe
Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of
Medicine, University of Hong Kong, Hong Kong, China, 4 Cardiology Division, Department of Medicine, Li Ka
Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China ☯These authors contributed equally to this work. ‡ These authors also contributed equally to this work. * Ralph.Akyea1@nottingham.ac.uk Background Variability in low-density lipoprotein cholesterol (LDL-C) response to statins is underappreci-
ated. We characterised patients by their statin response (SR), baseline risk of cardiovascu-
lar disease (CVD) and 10-year CVD outcomes. Editor: Carmine Pizzi, University of Bologna, ITALY Introduction Funding: Funded by scientific donation by AMGEN
Ltd. The funders of the study had no role in study
design, data collection, data analysis, data
interpretation, or writing of the report. Cardiovascular disease (CVD) is a significant cause of mortality and morbidity, accounting for
almost a third of all deaths globally [1]. Statins, the most widely prescribed class of drug world-
wide, are an effective and low-cost solution in lowering cholesterol levels and reducing future risk
of CVD [2]. Statin use is set to rise further in many countries as guidelines recommend their use
in greater proportions of the population [3, 4]. In the United States alone, the proportion of adults
whom statins are indicated has increased from 17.9% (21.8 million) to 27.8% (39.2 million) from
2002 to 2013 [5], with similar magnitude increases in most European [6] and Asian countries [7]. Following meta-analyses of cholesterol treatment trials [8, 9], the safety and intended per-
centage reductions in LDL-C achieved by specific statins (and their doses) have been well-
established. Guidelines in the United States (US), United Kingdom (UK), Europe (EU) and
Hong Kong (HK) recommend intended LDL-C reduction targets for statin therapy to reduce
CVD. The 2013 American College of Cardiology/American Heart Association (ACC/AHA)
guideline suggests a fixed dose (or intensity) of statin depending on absolute CVD risk, with
intended LDL-C reduction of 30–50% [4]. The UK National Institute of Clinical Excellence
(NICE) Guideline aims for a greater than 40% reduction in non-high-density lipoprotein cho-
lesterol (non-HDL-C) [3]. An LDL-C reduction of 50% is recommended by European Society
of Cardiology guidelines [10]. Hong Kong primary prevention guidelines follow similar ACC/
AHA, NICE, and ESC guideline targets for LDL-C reduction [11]. Cardiovascular disease (CVD) is a significant cause of mortality and morbidity, accounting for
almost a third of all deaths globally [1]. Statins, the most widely prescribed class of drug world-
wide, are an effective and low-cost solution in lowering cholesterol levels and reducing future risk
of CVD [2]. Statin use is set to rise further in many countries as guidelines recommend their use
in greater proportions of the population [3, 4]. In the United States alone, the proportion of adults
whom statins are indicated has increased from 17.9% (21.8 million) to 27.8% (39.2 million) from
2002 to 2013 [5], with similar magnitude increases in most European [6] and Asian countries [7]. Introduction Competing interests: NQ is a member of the most
recent NICE Familial Hypercholesterolaemia & Lipid
Modification Guideline Development Groups (CG71
& CG181). SW, IW are members of the Clinical
Practice Research Datalink (CPRD) Independent
Scientific Advisory Committee (ISAC). RKA
currently holds an NIHR-SPCR funded studentship
(2018-2021). SW reports honorarium from
AMGEN and is also an employee of Janssen. KM
holds the CW Malpethorpe Fellowship Award and
reports personal fees from IQVIA Ltd have been
received outside the submitted work. JB is
supported by the Hong Kong Research Grants
Council as a recipient of the Hong Kong PhD
Fellowship Scheme. EC and IW report grants from
Amgen. The remaining authors have no competing
interests. This does not alter our adherence to
PLOS ONE policies on sharing data and materials. Following meta-analyses of cholesterol treatment trials [8, 9], the safety and intended per-
centage reductions in LDL-C achieved by specific statins (and their doses) have been well-
established. Guidelines in the United States (US), United Kingdom (UK), Europe (EU) and
Hong Kong (HK) recommend intended LDL-C reduction targets for statin therapy to reduce
CVD. The 2013 American College of Cardiology/American Heart Association (ACC/AHA)
guideline suggests a fixed dose (or intensity) of statin depending on absolute CVD risk, with
intended LDL-C reduction of 30–50% [4]. The UK National Institute of Clinical Excellence
(NICE) Guideline aims for a greater than 40% reduction in non-high-density lipoprotein cho-
lesterol (non-HDL-C) [3]. An LDL-C reduction of 50% is recommended by European Society
of Cardiology guidelines [10]. Hong Kong primary prevention guidelines follow similar ACC/
AHA, NICE, and ESC guideline targets for LDL-C reduction [11]. These guidelines are designed to curb CVD deaths; however, recent evidence has shown
that over 50% of a cohort of 165,411 patients prescribed statins for primary prevention in the
UK fail to reach treatment targets, which significantly increases risk of heart disease and stroke
[12]. The reasons are varied, but there is evidence to suggest individual variability in LDL-C
response [13] and significant non-adherence [14]. It is unclear which patient characteristics
may be associated with variation in LDL-C reduction after commencing statin therapy for pri-
mary prevention of CVD and if these clinical characteristics can be used to predict an individ-
ual’s likelihood of achieving recommended LDL-C targets. Methods and results Peer Review History: PLOS recognizes the
benefits of transparency in the peer review
process; therefore, we enable the publication of
all of the content of peer review and author
responses alongside final, published articles. The
editorial history of this article is available here:
https://doi.org/10.1371/journal.pone.0260839 A multivariable model was developed using 183,213 United Kingdom (UK) patients without
CVD to predict probability of sub-optimal SR, defined by guidelines as <40% reduction in
LDL-C. We externally validated the model in a Hong Kong (HK) cohort (n = 170,904). Patients were stratified into four groups by predicted SR and 10-year CVD risk score: [SR1]
optimal SR & low risk; [SR2] sub-optimal SR & low risk; [SR3] optimal SR & high risk; [SR4]
sub-optimal SR & high risk; and 10-year hazard ratios (HR) determined for first major
adverse cardiovascular event (MACE). Our SR model included 12 characteristics, with an
area under the curve of 0.70 (95% confidence interval [CI] 0.70–0.71; UK) and 0.68 (95% CI
0.67–0.68; HK). HRs for MACE in predicted sub-optimal SR with low CVD risk groups (SR2
to SR1) were 1.39 (95% CI 1.35–1.43, p<0.001; UK) and 1.14 (95% CI 1.11–1.17, p<0.001;
HK). In both cohorts, patients with predicted sub-optimal SR with high CVD risk (SR4 to
SR3) had elevated risk of MACE (UK HR 1.36, 95% CI 1.32–1.40, p<0.001: HK HR 1.25,
95% CI 1.21–1.28, p<0.001). Copyright: © 2021 Weng et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Data Availability Statement: The third-party data
for this study were obtained from the Clinical
Practice Research Datalink (CPRD) and the
University of Hong Kong/Hospital Authority Hong 1 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD Kong West Cluster. CPRD is a research service that
provides primary care and linked data for public
health research. CPRD and University of Hong
Kong/Hospital Authority data governance and our
own license to use data do not allow us to
distribute or make available patient data directly to
other parties. However, data is available upon
application to CPRD (www.cprd.com) and the
University of Hong Kong/Hospital Authority (www. ha.org.hk). Conclusions Patients with sub-optimal response to statins experienced significantly more MACE, regard-
less of baseline CVD risk. To enhance cholesterol management for primary prevention,
statin response should be considered alongside risk assessment. Introduction There are currently no
management strategies in clinical practice to determine if patients will experience sub-optimal
reduction in LDL-C when prescribed statins, nor the impact this may have on future CVD out-
comes. First, we conducted an international study using two large geographically distinct
cohorts to characterise LDL-C response to statin therapy in relation to baseline cardiovascular
risk. We then determined the association between LDL-C response, baseline CVD risk and
future CVD outcomes. Outcomes The primary outcome for this analysis was the incidence of first major adverse cardiovascular
event (MACE) over 10-year follow-up after initiation of statins. We defined MACE as a com-
posite of coronary heart disease (CHD), stroke, transient ischemic attack (TIA), peripheral
vascular disease (PVD), and cardiovascular (CV) death [19]. CHD included acute myocardial
infarction, coronary revascularisations, stable and unstable angina. CVD events were identi-
fied from linked primary, secondary, and death registries. These are coded diagnoses based on
National Health Service (NHS) Read codes and ICD-10 in the UK and mapped to ICD-9-CM
in HK. Secondary outcomes include all-cause mortality, and CVD outcomes by sub-type. Data source This study used the anonymized electronic health records from the UK Clinical Practice
Research Datalink (CPRD) and the Hong Kong (HK) Clinical Data Analysis and Reporting
System (CDARS). 2 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD CPRD contains anonymized patient data for more than 15 million patients and is represen-
tative of the general UK population [15]. CPRD is one of the largest quality-assured databases
of longitudinal medical records from primary care in the world, with over 800 UK primary
medical care practices. Regulatory approval for this study (protocol number: 17_200RA) was
obtained from the CPRD Independent Scientific Advisory Committee. The CDARS contains data from the Hong Kong Hospital Authority, which serves a popula-
tion of over 7.4 million through 43 hospitals and institutions, 48 specialist outpatient clinics,
73 general outpatient clinics, covering approximately 80% of all hospital admissions in Hong
Kong [16]. The use of CDARS data for this study was approved by the Institutional Review
Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (protocol
number: UW 17–135). Study population The study cohorts comprised 183,213 patients initiating statin therapy with repeat prescrip-
tions between 3rd September 1990 and 7th June 2016 in UK CPRD and 170,904 patients
between 1st of January 2003 and 31st of December 2011 in HK CDARS. Patients were eligible
for inclusion if they were registered with their health care provider for at least 12 months. Patients were required to have at least two recorded LDL-C measurements (directly mea-
sured). The baseline LDL measure was within 12 months before or at the initiation of statins
and the follow-up measure was within 24 months after initiation of statins. Patients on statin
treatment for primary prevention of CVD who failed to achieve greater than 40% reduction in
their untreated baseline LDL-C, recorded within the first 24 months, were defined as sub-opti-
mal LDL-C responders. This was based on the lower bound expected reduction of LDL-C rec-
ommended in CVD prevention guidelines [3, 10, 11, 17] and also recognised in meta-analyses
[8]. Percentage LDL-C reduction, which considers individual baseline levels, has been shown
to have better prognostic value than attained LDL-C for future CVD events [18]. For on-treat-
ment response, the most recent LDL-C record at or closest to 24 months was used. This was
because many routine annual medication reviews or cholesterol assessments in clinical prac-
tice are unlikely to be documented in the EHRs until beyond 12 months. All individuals with a diagnosis of CVD (defined as coronary heart disease, cerebrovascular
disease and peripheral arterial disease) before initiating statin therapy were excluded. Candi-
date predictors (documented in S1 Table) were assessed for inclusion by clinical review and
prior evidence. Study design and statistical analyses The study involved two phases, detailed in the study flowchart (Fig 1). Phase I involved the
development and validation of the statin response (SR) propensity model and Phase II strati-
fied groups according to statin response and evaluated future CVD and mortality outcomes. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 3 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Fig 1 https://doi.org/10.1371/journal.pone.0260839.g001 Full methods on model development, validation, statistical methods and evaluation of future
CVD outcomes are detailed in S1 Text. Stata SE version 15 and RStudio were used for all analysis. Full methods on model development, validation, statistical methods and evaluation of future
CVD outcomes are detailed in S1 Text. Stata SE version 15 and RStudio were used for all analysis. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 Characteristics of the cohorts Within 24 months following initiation of statin therapy, 51.3% of UK patients had sub-optimal
cholesterol response in the derivation cohort. However, a higher proportion of HK patients
had a sub-optimal LDL-C response (60.8%) compared to the UK. Both derivation and valida-
tion cohorts had similar mean age, mean baseline LDL-C, and proportion of females. Baseline
mean LDL-C was higher in UK patients than in HK patients (156.5 mg/dL and 156.6 mg/dL
for UK cohorts compared to 149.8 mg/dL for the HK cohort). Higher potency statins tended
to be prescribed more frequently in in the UK than in HK (with 23.6% prescribed low potency
in the UK compared to 68.5% prescribed low potency in HK). Full baseline characteristics are
presented in Table 1, with S2 Table detailing the grouping of statins based on potency. Disease outcomes over 10-year follow-up for both cohorts are shown in Fig 2. Overall,
there were 40,928 cases of MACE (22.3%) in the UK population and 37,777 cases of MACE PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 4 / 17 PLOS ONE PLOS ONE Propensity of LDL-C response to statins and CVD Table 1. Clinical characteristics of patients initiating statin treatment and free from cardiovascular disease at baseline (n = 183,213). PLOS ONE Characteristic
Units
UK CPRD derivation cohort
UK CPRD internal validation
cohort
HK CDARS external validation
cohort
Total sample size
N
128,248
54,965
170,904
Follow-up time (years)
Median
(IQR)
5.29 (2.28–8.78)
5.26 (2.29–8.70)
6.92 (3.78–8.61)
Sex (Females)
N (%)
60,891 (47.5)
26,161 (47.6)
89,315 (52.3)
Sub-optimal LDL-C response to statin
N (%)
65,777 (51.3)
28,141 (51.2)
103,899 (60.8)
Age (years)
Mean (SD)
62.9 (11.9)
62.9 (11.8)
63.0 (12.0)
Median
(IQR)
63.0 (55.0–71.0)
63.0 (55.0–71.0)
62.8 (54.7–72.0)
Baseline LDL-C (mg/dL)
Mean (SD)
156.5 (44.2)
156.6 (44.2)
150.0 (41.2)
Median
(IQR)
154.7 (127.6–184.1)
154.7 (127.6–184.5)
147.6 (125.0–171.9)
Body mass index (kg/m2)
Mean (SD)
28.72 (4.63)
28.70 (4.61)
N/A
Median
(IQR)
28.3 (25.9–30.8)
28.25 (25.9–30.8)
Systolic blood pressure (mmHg)
Mean (SD)
142 (19)
142 (19)
N/A
Median
(IQR)
140 (130–150)
140 (130–150)
Diastolic blood pressure (mmHg)
Mean (SD)
82 (10)
82 (10)
N/A
Median
(IQR)
81 (76–88)
81 (76–88)
Ethnicity
White
N (%)
11,026 (8.6)
4,738 (8.6)
Asian
563 (0.4)
262 (0.5)
Black/African/Caribbean
448 (0.3)
180 (0.3)
Mixed/multiple
684 (0.5)
282 (0.5)
Other
380 (0.3)
163 (0.3)
Unknown
115,147 (89.8)
49,340 (89.8)
Comorbidities (prior to 1st statin)
Atrial fibrillation
N (%)
4,200 (3.3)
1,821 (3.3)
3,828 (2.2)
Chronic kidney disease
N (%)
3,574 (2.8)
1,592 (2.9)
3,150 (1.8)
Diabetes
N (%)
20,843 (16.3)
8,928 (16.2)
32,457 (19.0)
Dyslipidaemias
N (%)
10,262 (8.0)
4,375 (8.0)
10,059 (5.9)
Family history of cardiovascular
disease
N (%)
13,491 (10.5)
5,837 (10.6)
N/A
Family history of hyperlipidaemia
N (%)
281 (0.2)
120 (0.2)
N/A
Treated hypertension
N (%)
33,631 (26.2)
14,319 (26.1)
22,670 (13.3)
Hypothyroidism
N (%)
5,340 (4.2)
2,243 (4.1)
2,636 (1.5)
Liver disease
N (%)
1,221 (1.0)
517 (0.9)
497 (0.3)
Migraine
N (%)
2,766 (2.2)
1,182 (2.2)
359 (0.2)
Nephrotic syndrome
N (%)
83 (0.1)
40 (0.1)
1,062 (0.6)
Rheumatoid arthritis
N (%)
1,185 (0.9)
480 (0.9)
1,377 (0.8)
Systemic lupus erythematosus
N (%)
157 (0.1)
54 (0.1)
622 (0.4)
Medications (prescribed within 12 months prior to 1st statin)
Medication count
Median
(IQR)
4 (1–6)
4 (1–6)
8 (5–12)
Antipsychotics
N (%)
5,421 (4.2)
2,295 (4.2)
3,279 (1.9)
Other lipid lowering medication
N (%)
535 (0.4)
223 (0.4)
10,885 (6.4)
Oral corticosteroids
N (%)
5,390 (4.2)
2,396 (4.4)
8,906 (5.2)
(Continued) atients initiating statin treatment and free from cardiovascular disease at baseline (n = 183,213). PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 5 / 17 According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. PLOS ONE PLOS ONE Propensity of LDL-C response to statins and CVD Table 1. (Continued)
Characteristic
Units
UK CPRD derivation cohort
UK CPRD internal validation
cohort
HK CDARS external validation
cohort
Potency of initial statin prescribed†
Low
N (%)
30,310 (23.6)
12,994 (23.6)
11,7107 (68.5)
Medium
90,514 (70.6)
38,747 (70.5)
47,825 (28.0)
High
7,424 (5.8)
3,224 (5.9)
5,972 (3.5)
Missing data
Missing body mass index
N (%)
57,782 (45.1)
24,641 (44.8)
N/A
Missing systolic blood pressure
N (%)
15,076 (11.8)
6,354 (11.6)
N/A
Missing diastolic blood pressure
N (%)
15,029 (11.7)
6,337 (11.5)
N/A Table 1. (Continued)
Characteristic
Units
UK CPRD derivation cohort
UK CPRD internal validation
cohort
HK CDARS external validation
cohort
Potency of initial statin prescribed†
Low
N (%)
30,310 (23.6)
12,994 (23.6)
11,7107 (68.5)
Medium
90,514 (70.6)
38,747 (70.5)
47,825 (28.0)
High
7,424 (5.8)
3,224 (5.9)
5,972 (3.5)
Missing data
Missing body mass index
N (%)
57,782 (45.1)
24,641 (44.8)
N/A
Missing systolic blood pressure
N (%)
15,076 (11.8)
6,354 (11.6)
N/A
Missing diastolic blood pressure
N (%)
15,029 (11.7)
6,337 (11.5)
N/A
According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. † Statin potency–see S2 Table for detailed definitions. CDARS: Clinical Data Analysis and Reporting System; CPRD: Clinical Practice Research Datalink; HK: Hong Kong; IQR: interquartile range; LDL-C: low-density
lipoprotein cholesterol; SD: standard deviation; UK: United Kingdom. According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. Fig 2. https://doi.org/10.1371/journal.pone.0260839.g002 https://doi.org/10.1371/journal.pone.0260839.g002 6 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD (22.1%) in the HK population. There were some notable differences between the proportion of
stroke/TIA and CHD between cohorts, the most common MACE outcomes. There was a
higher proportion of CHD (14.9%) and PVD (2.6%) outcomes in UK patients compared to
HK patients (10.2% CHD, 0.9% PVD). There was a lower proportion of stroke/TIA (3.8%) in
UK patients compared to HK patients (8.4%). The proportion of non-CVD death in the HK
patients (13.9%) was twice that of UK patients (6.2%). Development of sub-optimal LDL-C statin response model The multivariable logistic model using the derivation cohort retained age, sex, atrial fibrillation
(AF), diabetes, dyslipidaemia, potency or intensity of initial statin prescribed, treated hyper-
tension, prescription of corticosteroid and other lipid lowering medications, LDL-C level at
time of statin prescription and medication count. S3 Table provides the adjusted odds ratios,
with regression coefficients and constants presented in S4 Table. The results of the model showed those with higher baseline levels of LDL-C, atrial fibrilla-
tion (in men only), diabetes, treated hypertension, increasing number of concurrent medica-
tions (in men only), high potency statins, and other lipid lowering drugs (in men only) were
less likely to have sub-optimal LDL-C reduction. Dyslipidaemias and corticosteroids were
associated with a higher likelihood of sub-optimal LDL-C reduction. The interaction terms
showed that when considered in relation to higher LDL-C levels, those on higher potency stat-
ins and had a diagnosis of dyslipidaemias were less likely to have sub-optimal response. Validation of sub-optimal LDL-C statin response model The discriminatory accuracy of the model in predicting sub-optimal LDL-C response per-
formed similarly in both UK cohorts (derivation AUROC 0.704, 95% CI 0.701–0.707, internal
validation AUROC 0.703 (95% CI 0.698–0.707) with a slightly lower performance in the HK
cohort (external validation AUC 0.677 (95% CI 0.675–0.680) (Table 2). Calibrations plots (S1 Fig) show that the model was perfectly calibrated (slope = 1.0) for
UK populations by comparing the predicted and observed probability of sub-optimal statin
response across each tenth of predicted probabilities. For HK populations, the model under-
predicted risk with predicted probabilities consistently lower than observed probabilities
(slope = 0.86). An adjustment to the intercept term of the risk model in the HK population
would improve its calibration. The sensitivity and specificity plots for the model are presented in S2 Fig. The optimum
trade-off occurred at 50% probability as determined by the maximum product index [20]
between sensitivity and specificity (shown at the intersection), and hence we classified individ-
uals with SR propensity >50% as “predicted sub-optimal response” and individuals 50% as
“predicted optimal response”. This binary classification resulted in a sensitivity of 64% (95%
CI 63.4% - 64.5%) and specificity of 64.9% (95% CI 64.3% - 65.5%). Table 2. Model discrimination for sub-optimal LDL-C response to statins. Statin Optimisation Model
Sample Size
AUROC (95% CI)
Standard Error
Derivation cohort: UK CPRD
128,248
0.704 (0.701–0.707)
0.002
Internal validation cohort: UK CPRD
54,965
0.703 (0.698–0.707)
0.002
External validation cohort: HK CDARS
170,904
0.677 (0.675–0.680)
0.001
Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice
Research Datalink; HK: Hong Kong; UK: United Kingdom. https://doi.org/10.1371/journal.pone.0260839.t002 Table 2. Model discrimination for sub-optimal LDL-C response to statins. Statin Optimisation Model
Sample Size
AUROC (95% CI)
Standard Error
Derivation cohort: UK CPRD
128,248
0.704 (0.701–0.707)
0.002
Internal validation cohort: UK CPRD
54,965
0.703 (0.698–0.707)
0.002
External validation cohort: HK CDARS
170,904
0.677 (0.675–0.680)
0.001
Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice
Research Datalink; HK: Hong Kong; UK: United Kingdom. https://doi.org/10.1371/journal.pone.0260839.t002
PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021
7 / 17 Table 2. Model discrimination for sub-optimal LDL-C response to statins. Validation of sub-optimal LDL-C statin response model Statin Optimisation Model
Sample Size
AUROC (95% CI)
Standard Error
Derivation cohort: UK CPRD
128,248
0.704 (0.701–0.707)
0.002
Internal validation cohort: UK CPRD
54,965
0.703 (0.698–0.707)
0.002
External validation cohort: HK CDARS
170,904
0.677 (0.675–0.680)
0.001
Jack-knife procedure to estimate standard errors. Table 2. Model discrimination for sub-optimal LDL-C response to statins. Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice
Research Datalink; HK: Hong Kong; UK: United Kingdom. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 7 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Table 3. Model performance stratified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). Statin Adherence Rate
(%)
Mean reduction in LDL-C
(SD), mg/dL
Percentage mean reduction in
LDL-C (%)
Percentage achieving targeted 40%
reduction in LDL-C
AUROC c-statistic
(95% CI)
<20%
-17.1 (36.7)
-19.1%
9.9%
0.637 (0.606–0.670)
20-< 40%
-30.6 (41.6)
-35.8%
22.2%
0.633 (0.613–0.653)
40-< 60%
-44.2 (61.3)
-53.7%
35.0%
0.642 (0.627–0.658)
60-< 80%
-54.6 (40.5)
-69.9%
48.2%
0.672 (0.661–0.684)
80%
-65.7 (76.7)
-81.6%
58.2%
0.737 (0.731–0.742)
Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates
representing discontinuation periods are based on statin pack size and prescribed daily dosage. AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD: atified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). r 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). Table 3. Model performance stratified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates
representing discontinuation periods are based on statin pack size and prescribed daily dosage. AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD:
standard deviation. https://doi.org/10.1371/journal.pone.0260839.t003 Impact of adherence on model Approximately 60% of the UK validation cohort (n = 33,491) had a discontinuation period
over two-years from starting statins. The statin adherence rate had explained 11% of the varia-
tion in the mean reduction in LDL-C (Pearson’s r = -0.33; R^2 = 0.108) and followed an
expected inverse association with both absolute and percentage mean reduction in LDL-C and
positive association with percentage patients achieving the targeted 40% reduction in LDL-C
from baseline (Table 3). The model performance ranged from AUROC of 0.637 (95% CI
0.606–0.670) for patients who had <20% adherence to an AUROC of 0.737 (95% CI 0.731–
0.742) in patients who had 80% adherence. Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates
representing discontinuation periods are based on statin pack size and prescribed daily dosage.
AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD:
standard deviation. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 Stratifying groups by LDL-C statin response and CVD risk Ten-year CVD risk recommended by ESC guidelines and two-year sub-optimal LDL-C reduc-
tion propensity was calculated for all patients in both cohorts from baseline risk factors (histo-
grams and distributions shown in S3 Fig). By jointly stratifying patients into “high” (> 5%) or
“low” ( 5%) CVD risk and “sub-optimal” (> 50%) or “optimal” ( 50%) LDL-C reduction,
four groups for statin response (SR) were created (shown in S4 Fig). For the UK cohort, 45,684 patients (24.9%) were predicted to have optimal statin response
and low CVD risk (SR1), 64,997 patients (35.5%) were predicted to have sub-optimal statin
response and low CVD risk (SR2), 48,460 patients (26.5%) were predicted to have optimal
statin response and high CVD risk (SR3), and 24,072 patients (13.1%) were predicted to have
sub-optimal statin response and high CVD risk. For the HK cohort, 47,842 patients (27.9%)
were predicted to have optimal statin response and low CVD risk (SR1), 61,725 patients
(36.1%) were predicted to have sub-optimal statin response and low CVD risk (SR2), 43,514
patients (25.4%) were predicted to have optimal statin response and high CVD risk (SR3), and
17,823 patients (10.4%) were predicted to have sub-optimal statin response and high CVD
risk. Characteristics of the groups for the UK patients are provided in S5 Table and HK patients
in S6 Table. For UK patients, classified as being at low CVD risk, patients predicted to have
sub-optimal compared to optimal response were more likely to be male (55.6% compared to
41.5%), less likely to be treated for hypertension (17.5% compared to 26.7%), with lower mean
LDL-C (133.4 mg/dL compared to 187.6 mg/dL), and more frequently initiated on a low
potency statin (34.2% compared to 5.4%). Following similar trends, UK patients classified as
being at high CVD risk, patients predicted to have sub-optimal response were more likely to
be male (64.6% compared to 52.6%), with lower mean LDL-C (123.2 mg/dL compared to PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 8 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD 174.9 mg/dL), less likely to be treated for hypertension (27.4% compared to 35.4%), and were
much more likely to initiated on a low potency statin (52.8% compared to 12.2%). In HK patients, SR groups were also significantly different across groups but with some dif-
ferences compared to UK patients. Stratifying groups by LDL-C statin response and CVD risk In HK patients classified as being at low CVD risk, patients
predicted to have sub-optimal compared to optimal response were more likely to be male
(53.3% compared to 32.1%), lower mean LDL-C (207.4 mg/dL compared to 259.8 mg/dL), less
likely to be diabetic (14.2% compared to 23.4%), and less likely to be treated for hypertension
(7.1% compared to 14.5%). Similarly, HK patients predicted to have sub-optimal compared to
optimal response in high CVD risk groups also were more likely to be male (70.9% compared
to 47.6%), have lower mean LDL-C (113.6 mg/dL compared to 166.7 mg/dL), less likely to be
diabetic (11.0% compare to 24.2%) or treated for hypertension (10.1% compared to 22.0%). Potency of statin prescribing remained stable in HK patients across all groups, favouring lower
dosage statins compared to UK patients. Similar to UK patients, HK patients in high CVD risk
groups were generally older, with higher numbers of men, medication count, and smokers. Long-term follow-up MACE outcomes Long-term follow-up MACE outcomes Incidence rates (per 1000 person-years) over 10-years for MACE increased significantly across
groups (S7 Table). Increasing incidence across SR groups followed similar trends for all-cause
mortality, CHD, stroke/TIA, PVD and CVD death for both cohorts. CHD was the most com-
mon MACE event to occur during follow-up. Cumulative incidence graphs for 10-year MACE
are displayed in Fig 4. In high CVD risk groups, the absolute difference in MACE cumulative
event rate at the end of 10-year follow-up was 8% greater in UK patients and 11% greater in
HK patients between predicted sub-optimal statin responders (SR4) and predicted optimal
statin responders (SR3). Even in low-risk CVD groups, the absolute difference in MACE
cumulative event rate at the end of 10-year follow-up was 5% greater in UK patients and 7%
greater in HK patients between predicted sub-optimal statin responders (SR2) and predicted
optimal statin responders (SR1). Ten-year models (Table 4) showed that predicted sub-optimal SR in patients with low
CVD risk (comparing SR2 to SR1), resulted in hazard ratios for MACE of 1.39 (95% CI 1.35–
1.43, p < 0.001) for UK patients and 1.14 (95% CI 1.11–1.17, p < 0.001) for HK patients. Pre-
dicted sub-optimal SR in patients with high CVD risk (comparing SR4 to SR3) resulted in haz-
ard ratios for MACE of 1.36 (95% CI 1.32–1.40, p < 0.001) for UK patients and 1.25 (95% CI
1.21–1.28, p < 0.001) for HK patients. In UK patients, the risk of constituent MACE outcomes
increased significantly in patients predicted to be sub-optimal responders for CHD, stroke/
TIA, and PVD in both high and low CVD risk groups. There was an increased risk of all-cause
mortality in UK patients in high CVD risk groups but not in low CVD risk groups. There was
no significant difference in CVD death in UK patients. In HK patients, risk of CHD was
increased in both low and high CVD risk groups in predicted sub-optimal SR groups. Stroke/
TIA and PVD was, however, only increased for sub-optimal SR in high CVD risk groups. Sub-
optimal SR groups had significantly lower risks of CVD death and all-cause mortality in
patients with low CVD risk (HR<1.0), which can be explained by this group being younger
and healthier. Two-year follow-up of LDL-C reduction Baseline and 2-year follow-up LDL-C levels after statin initiation for UK and HK patients are
shown in Fig 3. Higher baseline LDL-C levels resulted in more prominent reductions in
LDL-C over two years. In UK patients, low and high CVD risk groups, respectively, achieved
40.5% and 41.9% reduction in mean LDL-C in predicted optimal response groups whereas the
mean reduction in LDL-C in predicted sub-optimal responders was only 26.8% and 28.6%. In
HK patients, low and high CVD risk groups, respectively, achieved 35.0% and 36.7% reduction
in mean LDL-C in predicted optimal response groups whereas the mean reduction in LDL-C
in predicted sub-optimal responders was only 20.5% and 22.4%. Overall, variability of the
LDL-C response in patients in both UK and HK cohorts remained quite high ranging from
60% reduction in LDL-C to increase of 50% in LDL-C after two years of treatment (S5 Fig). Fig 3. https://doi.org/10.1371/journal.pone.0260839.g003 https://doi.org/10.1371/journal.pone.0260839.g003 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 9 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 Discussion This international study in two countries has identified clinical characteristics of patients that
predict variation in LDL-C in response to statin therapy commenced for primary prevention
of CVD. We have found that irrespective of their baseline CVD risk, patients with poorer
LDL-C response experience much greater rates and risk of adverse cardiovascular outcomes
than those likely to achieve target reductions in LDL-C. Groups who have low predicted likeli-
hood to achieve LDL-C treatment targets will experience overall 5–10 more CVD events per
1000 person-years with low baseline CVD risk. The effect is even greater in populations with
high baseline CVD risk, with 19–20 more CVD events per 1000-years, compared to population
groups with predicted optimal response. An individual’s response to statins should be considered alongside cardiovascular risk
assessment to enhance cholesterol treatment strategies and to inform shared decision-making
with patients as part of primary prevention of CVD. To our knowledge, this is the first study to
demonstrate sub-optimal LDL-C response to statins can be reliably predicted. Our statin
response model uses patient characteristics that are routinely available in electronic health rec-
ords and was robust in both validation cohorts. Considering the effects of adherence, we
showed the model predicts LDL-C response when patients are more compliant to their medi-
cines, suggesting there is biological variation in treatment response. In less compliant individ-
uals, expectedly, there is less certainty in predicting LDL-C response. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 10 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base
line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response
[21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with
higher levels of inflammation and thus interact with the effectiveness of statins. Patients in
Fig 4. https://doi.org/10.1371/journal.pone.0260839.g004
al.pone.0260839
December 2, 2021
11 / Fig 4. https://doi.org/10.1371/journal.pone.0260839.g004 https://doi.org/10.1371/journal.pone.0260839.g004 https://doi.org/10.1371/journal.pone.0260839.g004 Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base-
line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response
[21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with
higher levels of inflammation and thus interact with the effectiveness of statins. PLOS ONE PLOS ONE PLOS ONE Table 4. Hazard ratios (95% confidence intervals) for 10-year major adverse cardiovascular events and all-cause mortality for predicted statin response and cardio-
vascular risk groups. Group
MACE
All-Cause Mortality
Specific CVD Outcomes
CHD
Stroke/TIA
PVD
CVD Death
United Kingdom CPRD cohort 10-year outcomes
Number of events, N (%)
40,928 (22.3)
13,199 (7.2)
27,257 (14.9)
7,017 (3.8)
4,835 (2.6)
1,819 (1.0)
SR2: Predicted sub-optimal statin response
& low CVD risk†
1.39 (1.35–1.43)
0.94 (0.88–1.01)
1.45 (1.40–1.50)
1.30 (1.21–1.41)
1.27 (1.16–1.38)
0.86 (0.72–1.03)
SR4: Predicted sub-optimal statin response
& high CVD risk‡
1.36 (1.32–1.40)
1.10 (1.06–1.15)
1.47 (1.42–1.52)
1.24 (1.16–1.32)
1.18 (1.09–1.28)
1.10 (0.98–1.23)
Hong Kong CDARS cohort 10-year outcomes
Number of events, N (%)
37,777 (22.1)
28,321 (16.5)
17,371 (10.2)
14,321 (8.4)
1,554 (0.9)
4,531 (2.7)
SR2: Predicted sub-optimal statin response
& low CVD risk†
1.14 (1.11–1.17)
0.78 (0.75–0.82)
1.51 (1.45–1.57)
1.00 (0.95–1.04)
0.95 (0.83–1.09)
0.73 (0.66–0.81)
SR4: Predicted sub-optimal statin response
& high CVD risk‡
1.25 (1.21–1.28)
1.06 (1.03–1.09)
1.69 (1.60–1.78)
1.10 (1.04–1.16)
1.17 (1.00–1.37)
0.97 (0.90–1.05)
p <0.05. †reference group: SR1-predicted optimal statin response & low CVD risk. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE:
major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. -year major adverse cardiovascular events and all-cause mortality for predicted statin response and cardio- †reference group: SR1-predicted optimal statin response & low CVD risk. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE:
major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE:
major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE:
major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. Discussion Patients in Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base-
line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response
[21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with
higher levels of inflammation and thus interact with the effectiveness of statins. Patients in PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 11 / 17 Propensity of LDL-C response to statins and CVD PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE The strengths of this study include its large sample size, long-term follow-up, from general
patient populations in two countries, derived from high quality electronic patient health PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 12 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD records. Data linkages to hospital records and death registries enhanced the quality of outcome
ascertainment for the cohorts of patients derived from these databases. Although the model
was developed using a UK cohort, the applicability of the model in the ethnically different HK
cohort, enhances external validity and generalisability of more aggressive lipid management
across both Western and Asian populations. By adopting an open cohort design and account-
ing for statin type and intensity, the predicted statin response and event rates across time peri-
ods reflect real-world changes in practice over time. Both populations have experienced
prescribing trends towards stronger statin intensity over time [7, 28]. Some limitations of this study are recognized. Although the proxy for statin adherence
explained a third of the variation in LDL-C response, prescribing records cannot confirm
whether a patient actually takes their medication, which is a shared limitation of all observa-
tional studies and trials. Moreover, patients who are on cardioprotective therapies are likely to
be on other medications other than statins and are more likely to discontinue multiple thera-
pies, which has also been shown to influence the mortality outcomes [29]. In common with
other large population studies using routinely collected data, this limitation together with oth-
ers including ascertainment and information bias, potential bias due to missing data and
unmeasured confounding is acknowledged. Newer medications such as PCSK9 are not yet
indicated for primary prevention, hence no data was available to assess its effect on cholesterol
response. We used the ESC guidelines to stratify CVD risk due to its simplicity, accessibility to
the published risk equations, and being recommended by ESC and HK guideline committees
as acceptable for use in both the UK and HK. We acknowledge that different national guide-
lines may recommend use of other CVD risk equations. Finally, we did not consider the effects
of medication switching during follow-up. Future analysis could consider modelling the effects
of time-varying exposure periods to account for any changes of dosing. Conclusions Predicted sub-optimal LDL-C lowering response to statins consistently resulted in higher rates
of MACE. To enhance cholesterol management for primary prevention of CVD, clinicians
should consider a patient’s likely response to statins as a component of CVD risk assessment. PLOS ONE both cohorts who were less likely to achieve targeted LDL-C reduction were also more likely to
have lower baseline LDL-C levels and be initiated on low potency statins. However, there was
greater use of more potent statins in the UK cohort compared to the HK cohort, while greater
use of other non-statin lipid lowering drugs in the HK cohort compared to the UK cohort. Recent updates to cholesterol guidelines have broadened the population of individuals eligi-
ble for statins for primary prevention [3, 10, 11, 17]. For example, the UK NICE guideline [3]
now suggest statin therapy be considered for individuals who have a cardiovascular risk
score > 10%, which has been reduced from a previous threshold of > 20%. In the current
study, over half of patients who initiated statins had a sub-optimal LDL-C response in both
HK and UK. This would equate to about 6.1 million of the estimated 12 million adults aged
30–84 in the UK who could be eligible for statins, for primary prevention [23]. Other factors, such as physical activity, diet and statin or treatment side-effects (which are
less reliably recorded) should clearly also be considerations alongside statin alternatives to
achieve shared clinical decision making with patients for appropriate cholesterol management. However, identifying patients likely to have sub-optimal LDL-C response to statins could
enable clinicians to be more aggressive in cholesterol management by identifying those who
need closer monitoring, or initiated on higher statin doses, given in combination with ezeti-
mibe [24]. Recent evidence suggests that reduction in cardiovascular events is significant even
to ultra-low levels of LDL-C less than 0.2 mmol/L (7.7 mg/dL) [25]. Our study shows that
many patients are initiated on low dose statins in the predicted sub-optimal groups suggesting
many clinicians may not be aware of the clinical benefits of a stronger treatment regime even
in those with lower baseline levels of LDL-C with high risk of CVD. Medications that aim to reduce LDL-C such as PCSK9 inhibitors and Ezetimibe [26, 27] are
presently indicated for both primary and secondary prevention of CVD. When taken in combina-
tion with statin and diet therapies, additional reduction in LDL-C levels have been shown in trials. Supporting information S1 Fig. Validation plots for logistic model applied in (a) UK CPRD internal validation cohort,
n = 54,985 and (b) HK CDARS external validation cohort, n = 170,904. E:O–log of the
expected/observed number of events; CITL–calibration-in-the-large; AUC–area under the
curve; slope–calibration slope. The circles represent deciles of patients grouped by similar pre-
dicted risk. The distribution of patients (stratified by outcome) is indicated with spikes at the
bottom of the graph. Patients with sub-optimal response are represented by spikes above the
x-axis (red line), and patients with optimal response, below the x-axis). (DOCX) S2 Fig. Plot of sensitivity and specificity to determine optimum cut-off for the classifica-
tion of sub-optimal LDL response risk to statins using the standard approach model in the
UK CPRD validation cohort (n = 54,985).
(DOCX) S2 Fig. Plot of sensitivity and specificity to determine optimum cut-off for the classifica-
tion of sub-optimal LDL response risk to statins using the standard approach model in the
UK CPRD validation cohort (n = 54,985). (DOCX) S3 Fig. Histograms of predicted 10-year CVD risk score by ESC guidelines and 2-year pro-
pensity of sub-optimal LDL-C reduction for UK and HK cohorts. (DOCX) S3 Fig. Histograms of predicted 10-year CVD risk score by ESC guidelines and 2-year pro-
pensity of sub-optimal LDL-C reduction for UK and HK cohorts. (DOCX) 13 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD S4 Fig. Joint stratification of 10-year CVD risk by ESC guidelines and 2-year propensity of
sub-optimal LDL-C reduction in both UK and HK patient cohorts. ESC: European Society
of Cardiology CVD SCORE >5% is defined as high CVD risk; Low-density lipoprotein choles-
terol statin response propensity of > 50% is defined as sub-optimal response. (DOCX) S4 Fig. Joint stratification of 10-year CVD risk by ESC guidelines and 2-year propensity of
sub-optimal LDL-C reduction in both UK and HK patient cohorts. ESC: European Society
of Cardiology CVD SCORE >5% is defined as high CVD risk; Low-density lipoprotein choles-
terol statin response propensity of > 50% is defined as sub-optimal response. (DOCX) S5 Fig. Waterfall plots of 2-year percentage LDL-C reduction from baseline based on initi-
ated statin potency. Potency classification by expected LDL-C reduction (see S2 Table for
specific statin types); 20%–30%: low potency; 31%–40%: medium potency; Above 40%: high
potency. (DOCX) S1 Table. Potential predictors of sub-optimal statin response propensity model. The choice
of medications of medications is informed by review of clinical guidelines and previous litera-
ture on CVD risk (UK NICE Guidelines, QRISK3). (DOCX) S2 Table. Grouping of statins by potency. 1 20%–30%: low intensity; 2 31%–40%: medium
intensity; 3 Above 40%: high intensity. Note: combination therapies with a statin and ezetimibe
10 mg would push potency up one group (i.e., low to medium, medium to high). (DOCX) S3 Table. Multivariable logistic regression for mutually adjusted diagnostic variables of
sub-optimal LDL-C response to statins using UK CPRD derivation cohort (n = 128,298). p < 0.05; No–reference category for dichotomous variables. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac-
tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics. Unit: per mmol/L. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac-
tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics.
Unit: per mmol/L.
(DOCX) S5 Table. Characteristics of 183,213 patients from the UK CPRD dataset by statin response
group based on ESC score. + Significance determined by Kruskal-Wallis non-parametric H
test between two or more groups; ESC: European Society of Cardiology; CPRD: Clinical Prac-
tice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipoprotein; CVD:
cardiovascular disease; SR1 –Patients with predicted optimal statin response and low CVD
risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk; SR3 –
Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with pre-
dicted sub-optimal statin response and high CVD risk. (DOCX) S5 Table. Characteristics of 183,213 patients from the UK CPRD dataset by statin response
group based on ESC score. + Significance determined by Kruskal-Wallis non-parametric H
test between two or more groups; ESC: European Society of Cardiology; CPRD: Clinical Prac-
tice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipoprotein; CVD:
cardiovascular disease; SR1 –Patients with predicted optimal statin response and low CVD
risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk; SR3 –
Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with pre-
dicted sub-optimal statin response and high CVD risk. (DOCX) S6 Table. Characteristics of 170,904 patients from the HK CDARS dataset by statin
response group based on ESC score. + Significance determined by Kruskal-Wallis non-
parametric H test between two or more groups; ESC: European Society of Cardiology; CPRD:
Clinical Practice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipopro-
tein; CVD: cardiovascular disease; SR1 –Patients with predicted optimal statin response and
low CVD risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk;
SR3 –Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with
predicted sub-optimal statin response and high CVD risk. (DOCX) PLOS ONE | https://doi.org/10.1371/journal.pone.0260839
December 2, 2021 14 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD S7 Table. 10-year incidence rates (per 1000 person-years) for major adverse cardiovascular
events (MACE) and all-cause mortality for predicted statin response and ESC cardiovascu-
lar risk groups. 95% Confidence Intervals are provided in () for all incidence rates. SR1 –
Patients with predicted optimal statin response and low CVD risk; SR2 –Patients with pre-
dicted sub-optimal statin response and low CVD risk; SR3 –Patients with predicted optimal
statin response and high CVD risk; SR4 –Patients with predicted sub-optimal statin response
and high CVD risk. Acknowledgments We are grateful to all the patients contributing data to both CPRD and CDARS. We are grateful to all the patients contributing data to both CPRD and CDARS. Author Contributions Conceptualization: Stephen Franklin Weng, Nadeem Qureshi, Joe Kai. Data curation: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau, Joseph Edgar Blais. Formal analysis: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau. Funding acquisition: Stephen Franklin Weng. Investigation: Stephen Franklin Weng, Kenneth KC Man, Wallis C. Y. Lau, Barbara Iyen. Methodology: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau, Nadeem Qureshi, Ian C. K. Wong, Joe Kai. Project administration: Stephen Franklin Weng. Resources: Stephen Franklin Weng. Resources: Stephen Franklin Weng. Supervision: Stephen Franklin Weng, Ian C. K. Wong. Supervision: Stephen Franklin Weng, Ian C. K. Wong. Validation: Stephen Franklin Weng. Visualization: Stephen Franklin Weng, Ralph Kwame Akyea. Visualization: Stephen Franklin Weng, Ralph Kwame Akyea. Writing – original draft: Stephen Franklin Weng, Ralph Kwame Akyea. Writing – review & editing: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man,
Wallis C. Y. Lau, Barbara Iyen, Joseph Edgar Blais, Esther W. Chan, Chung Wah Siu,
Nadeem Qureshi, Ian C. K. Wong, Joe Kai. S1 Text. Supplemental methods.
(DOCX) S1 Text. Supplemental methods. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac-
tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics.
Unit: per mmol/L.
(DOCX) ESC: European Society of Cardiology; CPRD: Clinical Practice Research
Datalink; CDARS: Clinical Data Analysis and Reporting System; CVD: cardiovascular disease;
TIA: Transient Ischemic Attack; CHD: Coronary Heart Disease; PVD: Peripheral Vascular
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Guideline on the Assessment of Cardiovascular Risk. Circulation. 2014; 129: S49–S73. https://doi.org/
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26551986 19. Hicks KA, Mahaffey KW, Mehran R, Nissen SE, Wiviott SD, Dunn B, et al. 2017 Cardiovascular and
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et al. Benefit of Adding Ezetimibe to Statin Therapy on Cardiovascular Outcomes and Safety in Patients
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CIRCULATIONAHA.117.030950 PMID: 29263150 25. Giugliano RP, Pedersen TR, Park J-G, De Ferrari GM, Gaciong ZA, Ceska R, et al. Clinical efficacy and
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https://openalex.org/W2021168705 | https://ahea.pitt.edu/ojs/index.php/ahea/article/download/155/222 | English | null | Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe. Budapest and New York: Central European University Press. 386 pp. | Hungarian cultural studies | 2,015 | cc-by | 3,080 | Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finlan Christianity and Modernity in Eastern Europe is a collection of thirteen essays about the
results of a collaborative project that lasted from 2005 to 2010 and involved over twenty
historians from Europe and North America who sought to “address methodological approaches
and interpretative problems in the larger fields of church history and religious studies” (XV). The
volume proposes two major goals, one of which is to show the significance of Christianity in
Eastern Europe to unfamiliar readers who are searching for the meaning of Christianity and/or
religion in the twentieth and twenty-first centuries. The way these goals are formulated suggests
that from the perspective of history studies, these essays focus on the interrelatedness of what is
defined as Eastern Europe (geography), Christianity (religion) and modernity (historical period),
and emphasize the relevance of this interrelatedness within a broad context of inquiries. The
contributors also aim to show how in reality the relationship of time, place and religion was and
is far more complex than what is suggested by currently pervasive stereotypes. p
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In the abovementioned framework, the contributions of editors Bruce R. Berglund and
Brian Porter-Szűcs act as an instrumental infrastructure that provides the reader with necessary
insights into the project as well as some of the results presented in the essays of the other
historian contributors. In his introductory chapter, Porter-Szűcs refers to Hans Georg Gadamer’s
(1900-2002) term of hermeneutic circles to describe the contributors of the volume as mediators
and translators who “are moving from explanation to a search for meaning and understanding
[…] to narrow the gap between alien worldviews and to appreciate as fully as possible the
motives and the goals of historical agents (without […] surrendering one’s own critical
perspectives)” (9-10). In order to achieve this goal, the contributors not only have to pay careful
attention to individual subjectivity and agency, but also critically reconsider those theories and
terminologies that previously failed to reflect the everyday experiences and actions of believers. These considerations entail a critical approach to existing historiographies and their foci of
interest by keeping in mind that Christianity is more than publicly confessed doctrines, officially
accepted theologies and institutional embodiments. New articles in this journal are licensed under a Creative Commons Attribution 4.0 International License.
This journal is published by the University Library System of the University of Pittsburgh as part of its
D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press
ISSN 1936-8879 (online) Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity
and Modernity in Eastern Europe. Budapest and New York: Central
European University Press. 386 pp. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland However,
the purpose of such a broad definition is to empathize how Christianity and any of its conceptual
counterparts can be meaningfully addressed, discussed and reflected upon from the perspective
of human agents and their approach to and understanding of the world through their respective
beliefs. After reading the essays, one may conclude that these abstractions of Christianity are
simply tools for addressing questions about identity. For instance, Natalia Shlikhta’s essay on the
Ukrainian Greek Catholic Church or Galia Valtchinova’s inquiries into what it means to be
Orthodox Christian in Bulgarian society are but two poles that address the fluidity of human
identities as studied through the abstraction of Christianity, while both Paul Hanebrink’s research
on interwar Christian Hungary and James Felak’s case study of individuals in Slovakia aim to
show that identities should be conceived as reflexive processes instead of as static worldviews
(see also Michal Pagis, “Religious Self-Constitution: A Relational Perspective,” in Courtney
Bender et al. eds., Religion on the Edge; Oxford: Oxford University Press, 96-97). ,
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The concept of modernity in this volume emerges within the fluid dynamic of human
agency described above and is conceived as a rubric denoting “tumultuous transformations”
within, mainly, the twentieth century such as “capitalist industrialization and the Great
Depression, the rise of the radical right and racial politics, World War II, Stalinism, the actually
existing socialism from the 1960s to the 1980s, and the apparent triumph of neoliberalism since
the 1990s” (17). Within this broad framework that emphasizes the fluidity and diversity of
human agents and the worldviews they produce, the volume suggests that those who study
modernity and its relationship with Christianity should be able to interpret the acts of the will
made under various socio-political settings of the various nation-states. The following essays of
the volume translate these concerns into a fascinating array of topics based on will and person,
two crucial concepts “when questions of action and agency” are concerned according to Thomas
Pfau’s Minding the Modern: Human Agency, Intellectual Traditions, and Responsible
Knowledge (Notre Dame: University of Notre Dame Press, 2013, 14). For instance, human rights
(Katharina Kunter), education (Hanebrink), peace (David Doellinger), belief and socio-political
order (Patrick Hyder Patterson), religious diversity (James Bjork and Andreas Kossert), as well
as the person and his/her situatedness (Anca Şincan) within culture (Martin C. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland One of the ways in which the contributing historians of the volume bring human agency
into a focal point is by making a clear distinction between Christianity defined as “a set of broad
frameworks for perceiving and understanding the world” and Christians viewed as “the people
who lived within those frameworks” (3), with both definitions kept intentionally vague in order
to capture the fluidity of human agents and their relationship to the world. Both categories are
defined so loosely that they could essentially be replaced by any other identifier such as Judaism,
Islam, “worldview,” “culture” or even “modernity.” The book does acknowledge the nondescript
nature of these definitions and soon clarifies that Christianity is discussed in this volume as a New articles in this journal are licensed under a Creative Commons Attribution 4.0 International License. This journal is published by the University Library System of the University of Pittsburgh as part of its
D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press
ISSN 1936-8879 (online) ISSN 1936-8879 (online) Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 broader category encompassing many subcategories such as Catholics, Protestants and Orthodox
Christians, and where Protestants are broken down further into Lutherans and Calvinists, the
Catholics into Ukrainian Greek Catholics, and the Orthodox believers are categorized according
to their respective nation states. These additional categories are just as vague as the original
categories of Christianity or Christians, which may be the reason why in his attempt to provide a
working definition for Christianity, Porter-Szűcs came to the conclusion that “Christianity is
delineated yet fluid, constraining yet enabling and always under construction” (13). Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Putna) are but a
few topics through which the diverse history of “modernity” is presented to the reader. The way the conceptual framework of the project translates into essays also reveals the
methodological struggle of combining the abstractions of Christianity and “modernity,”
especially when we consider that the noun “modernity” and its derivative adjective “modern”
can be used to denote a worldview, an understanding of the world as well as one’s identity and
place in the social order. The fact that most of the essays do not or hardly use the terms
“modernity” or “modern” further underlines the necessity of addressing the theoretical questions
entailed in examining the relationship of Christians, Christianity and modernity. In this regard,
the discussion initiated by some of the contributors to the volume could certainly benefit from
dwelling more substantially into on theological understandings of modernity and touching on The way the conceptual framework of the project translates into essays also reveals the
methodological struggle of combining the abstractions of Christianity and “modernity,” 406 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 other aspects of everyday life such as family, sexuality, gender, leadership and entrepreneurship. “Modernity,” then, is largely presented in the volume as an un-problematized and invariably
masculine construct, with a few exceptions such as Valtchinova’s article on the “remaking” of
religion in Socialist Bulgaria, in which the author offers a deconstruction of the traditionally
accepted religious field in Bulgaria through the case of Vanga (Evangelia) Pandeva Gushterova
(1911-1996). Vanga was a blind and poor Orthodox woman who attracted a massive following
on account of her visions, premonitions and spiritual experiences and soon caught the attention
of political leaders as well, who viewed her as challenging politics to address the issue of
religion in Bulgaria. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Valtchinova illustrates how in their eagerness to settle the issue of faith and
modernity in Bulgaria, different political ideologies as well as the Orthodox Church continuously
assessed Vanga in ways that strengthened their own arguments. The third key term of the volume is Eastern Europe, which at first glance seems to
suggest area studies but which comes to be used across the essays in ways that do not clarify to
the reader whether the volume’s choice of terminology hides an epistemological assumption of
the legitimacy of an east-west paradigm or not. The transparency of the term is greatly reduced
by the way several contributors seemingly use the terms “Central and Eastern Europe” and “East
Central Europe” to refer to the same area, and how the concept of “Eastern Europe” is also
broken down into certain nation states for the purposes of individual contributors, but the fact
that the case of the German Democratic Republic strongly features in the selection (Kunter and
Doellinger) seems to confirm the presence of an east-west axis. Nevertheless, whenever the
construct of “Eastern Europe” becomes a focal point in research, this happens through the
identification and geographical demarcation of regions where “the social, economic, and political
processes that have characterized the continent’s modernity were experienced belatedly, if at all”
and where “communist regimes held power from the 1940s to the 1989s” (16). Berglund builds
on Walter Brueggemann’s theological conceptualization of place to argue that “Eastern Europe”
is also a “conceptual place, with no visible boundaries or objective features, yet it remains fixed
in most people’s geographic imaginations” and in this sense, “it can influence religious belief
and practice” (330). Berglund’s argument also implies that the juxtaposition of the elements
mentioned in the title of the volume could be perceived as a triangulation of the concepts of
Christianity, modernity and Eastern Europe. y
y
p
Hanebrink partly explores the dynamics of the above mentioned triangulation in an article
titled “Christianity, Nation, State: The Case of Christian Hungary,” in which he contemplates the
complexities of Christianity and the Hungarian socio-political order by examining the interwar
period rhetoric of Hungary being or once again becoming a purely Christian nation. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Hanebrink
eases his readers into the subject through a detailed description of the interwar period in
Hungary, during which both politicians and church leaders engaged in politics called for a moral
revival and the revitalization of Christianity and Christian values in Hungarian society as the
only path towards a brighter future for the Hungarian nation. Hanebrink then proceeds to
deconstruct the apparently unified program for realizing a Christian Hungary by highlighting the
conflicts, negotiations and compromises among Christians from every tier of society and
regardless of their economic, political or religious affiliation as they faced the pressing question
of what was the right relationship between religion and state in the age of modernity. As a result,
the reader is presented with a wide spectrum of options between nationalism and missionization,
where the consensus between Hungarian Christians invariably seems to have emerged with
regard to the subject of the “Jewish question.” Hanebrink argues that the line of Anti-Semitic
rhetoric calling for a united Christian nation stems from the 1880’s, a time when the concept of a 407 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern
Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7
(2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Christian Hungary was envisioned “against the predations of “Jewish power” (64) and can be
traced up to “the moment of crisis” in 1944 (81). This article also supports Berglund’s argument
about Eastern Europe as a place (versus “space”) with historical meanings where certain things
are remembered in certain ways and through remembrance, and where different identities remain
and manage to relate in spite of all their contradictions. g
p
One of the volume’s strong points, as demonstrated above, is that it offers fresh takes on
old questions, but looking at the relationship of the editors’ programmatic framework and its
implementation by the contributions might cause a sense of dissatisfaction in readers as the
frame seems to be larger than the actual picture portrayed. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland While I do not dispute the legitimacy
of focusing on Catholics, Protestants and Orthodox Christians and investigating their
participation in the history of the twentieth and twenty-first centuries in Eastern Europe, it would
have been useful to include other Christians in a discussion of modernity as it was exactly within
this historical period that the issue of diversity in the Eastern European region was further
complicated by the emergence of Christian Others (see Catherine Wanner, Communities of the
Converted: Ukrainians and Global Evangelism; New York: Cornell University Press, 2007). In
this regard, concepts such as Berglund’s “spiritual geography” become even more problematic
since Berglund’s own construct of religiosity is largely based on Catholic or Orthodox
terminology (e.g. sacred sites, holy lands, sacramental places), and as such may prove
inapplicable to other tenets of Christianity that would be worth investigating. The reader is also
left wondering why the historians contributing to the volume neglected the primary sources of
other religions such as Judaism or Islam in addressing the question of how non-Christians
assessed the role of Christians and Christianity in shaping the history of Eastern Europe. Some of
these questions could have been addressed either through a more detailed description of the
process of essay selection for the volume, or by a narrower framework that stretches no further
than the actual picture emerging within it. g
p
One of the volume’s strong points, as demonstrated above, is that it offers fresh takes on
old questions, but looking at the relationship of the editors’ programmatic framework and its
implementation by the contributions might cause a sense of dissatisfaction in readers as the
frame seems to be larger than the actual picture portrayed. While I do not dispute the legitimacy
of focusing on Catholics, Protestants and Orthodox Christians and investigating their Although the reflective reader might be able to see the triangulation of Christianity,
modernity and Eastern Europe throughout the essays, the purpose of the volume might have been
better served by establishing a connection between the presented case studies and the rest of the
world at large. Offering levels of comparison and extending the east-west dichotomy (Kossert)
would have certainly been beneficial to readers who are not familiar with the Eastern European
region but have an extended knowledge about other parts of the world. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Placing the issue of
Christianity and modernity in Eastern Europe within an extended global framework would have
also allowed readers to engage more easily in dialogue with the volume, especially when it
invites us to perceive Eastern Europe as “a relational story, a drama of differences perceived and
real, of associations and rejections” (353). Nevertheless, even if these shortcomings might leave
some readers frustrated, one should keep in mind Berglund’s words of hope that the “volume
will open up new lines of research” into what he calls “East European Christianity” (332). As a volume of selected essays addressing the interrelatedness of geography, religion and
a historical period, Christianity and Modernity in Eastern Europe will appeal to a large spectrum
of readers. It calls for historians to explore new ways of writing/composing historiographies on
Christianity and modernity, challenges theologians to enter into a dialogue with non-theological
research on Christianity and modernity, and invites students of Hungarian Cultural Studies to
investigate the ways in which the contributing historians tackle these basic concepts. All these
directions and possibilities would make the volume an exciting addition to academic courses
centered on the juxtaposition of Christianity and modernity. 408 |
https://openalex.org/W2156627402 | https://www.hal.inserm.fr/inserm-00663642/file/cc10270.pdf | English | null | High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction | Critical care | 2,011 | cc-by | 8,543 | To cite this version: Yonathan Freund,
Camille Chenevier-Gobeaux,
Pascale Bonnet,
Yann-Erick Claessens,
Jean-
Christophe Allo, et al.. High-sensitivity versus conventional troponin in the emergency department for
the diagnosis of acute myocardial infarction.. Critical Care, 2011, 15 (3), pp.R147. 10.1186/cc10270. inserm-00663642 High-sensitivity versus conventional troponin in the
emergency department for the diagnosis of acute
myocardial infarction. Yonathan Freund, Camille Chenevier-Gobeaux, Pascale Bonnet, Yann-Erick
Claessens, Jean-Christophe Allo, Benoit Doumenc, François Leumani,
Claudine Cosson, Bruno Riou, Patrick Ray HAL Id: inserm-00663642 L’archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d’enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés. HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers. Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 RESEARCH RESEARCH Open Access * Correspondence: yonatman@gmail.com
1Department of Emergency Medicine and Surgery, Hôpital Pitié-Salpétrière,
Assistance Publique-Hôpitaux de Paris (APHP), Université Pierre et Marie
Curie-Paris 6 (UPMC), 47-83 boulevard de l’hôpital, F-75651 Paris cedex 13,
France
Full list of author information is available at the end of the article © 2011 Freund et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. Abstract Introduction: Recently, newer assays for cardiac troponin (cTn) have been developed which are able to detect
changes in concentration of the biomarker at or below the 99th percentile for a normal population. The objective
of this study was to compare the diagnostic performance of a new high-sensitivity troponin T (HsTnT) assay to that
of conventional cTnI for the diagnosis of acute myocardial infarction (AMI) according to pretest probability (PTP). Methods: In consecutive patients who presented to our emergency departments with chest pain suggestive of
AMI, levels of HsTnT were measured at presentation, blinded to the emergency physicians, who were asked to
estimate the empirical PTP of AMI. The discharge diagnosis was adjudicated by two independent experts on the
basis of all available data. Results: A total of 317 patients were included, comprising 149 (47%) who were considered to have low PTP, 109
(34%) who were considered to have moderate PTP and 59 (19%) who were considered to have high PTP. AMI was
confirmed in 45 patients (14%), 22 (9%) of whom were considered to have low to moderate PTP and 23 (39%) of
whom were considered to have high PTP (P < 0.001). In the low to moderate PTP group, HsTnT levels ≥0.014 μg/
L identified AMI with a higher sensitivity than cTnI (91%, 95% confidence interval (95% CI) 79 to 100, vs. 77% (95%
CI 60 to 95); P = 0.001), but the negative predictive value was not different (99% (95% CI 98 to 100) vs. 98% (95%
CI 96 to 100)). There was no difference in area under the receiver operating characteristic (ROC) curve between
HsTnT and cTnI (0.93 (95% CI 0.90 to 0.98) vs. 0.94 (95% CI 0.88 to 0.97), respectively). Conclusions: In patients with low to moderate PTP of AMI, HsTnT is slightly more useful than cTnI. Our results
confirm that the use of HsTnT has a higher sensitivity than conventional cTnI. High-sensitivity versus conventional troponin in
the emergency department for the diagnosis of
acute myocardial infarction Yonathan Freund1*, Camille Chenevier-Gobeaux2, Pascale Bonnet1, Yann-Erick Claessens3, Jean-Christophe Allo3,
Benoit Doumenc4, François Leumani1, Claudine Cosson5, Bruno Riou1,6 and Patrick Ray1,6 Introduction with suspected acute coronary syndrome (ACS), including
risk stratification of ACS, and the use of cTn measure-
ments is recommended by current guidelines [6]. A cutoff
point at the 99th percentile has been endorsed, as values
above this level have repeatedly proven to be associated
with adverse cardiovascular outcomes, including death
[7-13]. However, the delay (4 to 6 hours, and 12 hours for
peak level) in its elevation remains of concern, since it can
delay AMI diagnosis and its treatment and increases the
burden on EDs. Thus, cTn measurement does not reliably
exclude AMI without repeated negative measurements
over the course of 4 to 6 hours. These last years, newer
assays have been developed, and High Sensitivity Troponin
(HsTn) has been associated with higher sensitivity and Early detection of acute myocardial infarction (AMI)
remains a major concern, with approximately 15 million
patients per year presenting to US emergency departments
(EDs) with symptoms suggestive of the diagnosis [1,2]. Among such patients, a strong association between ele-
vated cardiac troponin (cTn) levels and myocardial necro-
sis has been clearly demonstrated [3-5]. Conventional cTn
has revolutionised the management of patients presenting Page 2 of 9 Page 2 of 9 Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 NPV than conventional cTn. Recent studies have shown
excellent diagnostic performance, even with early presen-
tation to the ED [14], and a better diagnostic accuracy
than cTn [15]. However, the latter studies did not evaluate
the diagnostic accuracy of high-sensitivity troponin T
(HsTnT) according to the pretest probability (PTP) of
AMI. For example, ST elevation on an electrocardiogram
of a patient with chest pain would be diagnosed as AMI,
and then the patient would undergo cardiac catheteriza-
tion without any measurement of a cardiac biomarker. Furthermore, one of the potential strengths of HsTnT
might be the exclusion of AMI earlier than it would be
with conventional cTn measurement as suggested by pre-
vious studies [15]. Therefore, the objectives of the current
study were to confirm whether HsTnT is more sensitive
than conventional cTnI to detect AMI according to the
patient’s PTP. evaluation and treatment or directly to the catheteriza-
tion laboratory for primary percutaneous coronary inter-
vention. However, the timing and treatment of patients
were left to the discretion of the attending physicians
according to the suspected diagnosis. Introduction ED physicians in
charge were blinded to the results of HsTnT, and biolo-
gists were blinded to the emergency diagnosis suspected
by physicians. To determine the etiologic diagnosis of chest pain at
presentation for each patient, two independent experts
(ED physicians) who were blinded to the results of HsTnT
reviewed all available medical records (including patient
history, physical findings, results of laboratory and radiolo-
gic testing, ECG, echocardiography, cardiac exercise test,
coronary angiography and summary chart at discharge)
pertaining to the patient from the time of ED presentation
to 30-day follow-up. In the event of diagnostic disagree-
ment, cases were reviewed and adjudicated in conjunction
with a third expert (also an ED physician). Routine assessment As part of the routine assessment in our institutions, all
patients underwent an initial clinical evaluation that
included clinical history, a physical examination, 12-lead
electrocardiography (ECG), pulse oximetry, routine
blood tests and chest X-rays. After these routine tests
were done, and before cardiac biomarker results were
available, ED physicians were asked to offer an ‘empiri-
cal’ clinical probability of AMI (low, medium or high
PTP) based on cardiovascular risk factors, type of chest
pain, physical findings and electrocardiogram abnormal-
ities [17,18]. Conventional cardiac troponin I (cTnI) was
measured at presentation and, if needed, was repeated
after 3 to 9 hours as long as it was clinically indicated. Thus, according to the diagnosis of non-ST elevation
MI (NSTEMI) or ST elevation MI (STEMI), the patients
were admitted either to the cardiology unit for further To assess the influence of renal function on cTn mea-
surement accuracy, the creatinine level was measured in
each patient and then renal function was estimated
using the Modification of Diet in Renal Disease study
equation [19]. Materials and methods
Clinical setting AMI was diagnosed according to the joint European
Society of Cardiology/American College of Cardiology/
American Heart Association/World Heart Federation
Task Force redefinition of MI guidelines [6]. Diagnosis of
AMI required a cTnI increase above the 10% coefficient of
variation (CV) value associated with at least one of the fol-
lowing: symptoms of ischaemia, new ST-T changes or a
new Q wave on an electrocardiogram, imaging of new loss
of viable myocardium or normal cTnI on admission. Unstable angina was diagnosed in patients with constant
normal cTnI levels and a history or clinical symptoms
consistent with ACS. Predefined further diagnostic cate-
gories included AMI (STEMI with the presence of ST-
segment elevation in at least two continuous leads on
ECG, new onset of left bundle branch block or NSTEMI),
unstable angina, and a third group including cardiac but
not coronary symptoms (for example, stable angina, myo-
carditis, arrhythmias and heart failure), noncardiac symp-
toms (for example, pulmonary embolism) and chest pain
of unknown origin. During the period from August 2005 to January 2007 in
three urban teaching hospitals, we prospectively enrolled
consecutive hospital outpatients (> 18 years of age) who
presented to the ED with chest pain suggestive of ACS
with the onset or peak occurring within the previous 6
hours. Patients with acute or chronic kidney failure requir-
ing dialysis were excluded. The study was performed
according to the principles of the Declaration of Helsinki
and approved by the local ethics committee (Comité de
Protection des Personnes Ile-de-France VI, CHU Pitié-
Salpétrière Hospital, Paris, France). Because routine medi-
cal care was unchanged, waiver of informed consent was
authorised. We followed most of the recommendations
concerning the reporting of diagnostic studies set forth by
the Standards for Reporting of Diagnostic Accuracy initia-
tive [16]. Statistical analysis Continuous variables are presented as means ± SD or
medians (25th to 75th percentile), and categorical variables
are expressed as numbers and percentages. Continuous
variables were compared by using the Mann-Whitney U
test, and categorical variables were assessed using Pear-
son’s c2 test. Correlations among continuous variables
were assessed using the Spearman’s rank correlation coef-
ficient. Receiver operating characteristic (ROC) curves
were constructed to assess the sensitivity and specificity,
positive predictive value (PPV) and negative predictive
value (NPV), positive likelihood ratio (LR+) and negative
likelihood ratio (LR-) (all data presented with their 95%
confidence intervals (95% CIs)) throughout the concentra-
tions of cTnI and HScTnT to compare the accuracy of
these markers in the diagnosis of AMI. Comparison of
areas under the ROC curve was performed [20]. As this
comparison is recognised as potentially insensitive, the net
reclassification index (NRI) method was used as recently
described [21]. For tests with binary outcomes (such as
cTn for the diagnosis of AMI), NRI is defined as the gain
in certainty of the first test (cTnI) minus the gain in cer-
tainty of the second test (HScTnT) or, alternatively stated,
the difference of the sum of the sensitivity and specificity
expressed as follows: Table 1 Contingency data according to pretest
probabilitya
All patients
Patient characteristics
AMI
No AMI
Total
Positive cTnI
32
9
41
Negative cTnI
13
263
276
Total
45
272
317
Positive HsTnT
42
48
90
Negative HsTnT
3
224
227
Total
45
272
317
Low to moderate PTP
AMI
No AMI
Total
Positive cTnI
17
7
24
Negative cTnI
5
229
234
Total
22
236
258
Positive HsTnT
20
36
56
Negative HsTnT
2
200
202
Total
22
236
258
aNet reclassification improvement (NRI) from the use of highly sensitive
troponin T (HsTnT) was 7.9% (95% CI = 0.9 to 14.9; P = 0.034). Comparison of
the model including HsTnT with cTnI was significant for low PTP patients
(NRI = 10.3%, 95% CI = 1.9 to 18.7; P = 0.027), but NRI was not significantly
different in moderate PTP patients (NRI = 11.6%, 95% CI = -0.5 to 23.7; P =
0.084) or in high PTP patients (NRI = -14.4%, 95% CI = -32.6 to -3.6; P = 0.181). Table 1 Contingency data according to pretest
probabilitya NRIHScTnT vs. cTnI = (sensitivity + specificity)HScTnT −(sensitivity + specificity)cTnI. Results After 18 months, 317 consecutive patients were enrolled
in the study. The baseline characteristics of the patients
are shown in Table 2. The mean age of the patients was
57 ± 17 years (range, 40 to 90 years), and 205 (65%)
were men. There were significant proportions of older
adult patients (31% patients were age 65 years or older,
n = 98) and patients with a history of cardiovascular
events (26%, n = 83). Chest pain was considered typical
of ACS in 43% (n = 136) of the patients. In our study HScTnT measurement
d
l Heparinised samples collected upon admission and, if
available, samples collected 3 to 9 hours later were ana-
lysed. Plasmatic highly sensitive cardiac TnT (HScTnT)
concentrations were measured using the HScTnT one-
step electrochemiluminescence immunoassay on an
Elecsys 2010 analyzer (Roche Diagnostics, Meylan,
France). The measuring range extended from 0.003 to
10 μg/L. The threshold for this method is 0.014 μg/L and
corresponds to the 99th percentile. The CV was found to
be < 10% at 0.014 μg/L. In our laboratory, CVs obtained
in Roche Diagnostics quality controls containing 0.027
and 2.360 μg/L of HScTnT were < 4%. These analytical
performance levels were in accordance with data pro-
vided by the manufacturer. All hypothesis testing was two-tailed, and P < 0.05 was
considered statistically significant. Statistical analysis was
performed using StatView for Windows version 5.0 soft-
ware (SAS Institute, Cary, NC, USA) and MedCalc soft-
ware for ROC analysis (MedCalc Software, Mariarkerke,
Belgium). Graphs were built with GraphPad Prism 5
software (GraphPad Software Inc., La Jolla, CA, USA). Biochemical analysis In two EDs (Cochin Hospital and La Pitié Salpêtrière Hos-
pital, Paris, France), plasmatic cTnI concentrations were
routinely measured on an Xpand HM analyzer using the
Cardiac Troponin I one-step enzyme immunoassay system
(Siemens Healthcare Diagnostics Inc., Newark, NJ, USA). The measurement range extended from 0.04 to 40.00 μg/L. The threshold for this method (0.14 μg/L) corresponds to
the lowest substrate concentration that can be reproducibly Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Page 3 of 9 Page 3 of 9 measured with a CV ≤10%. In the remaining ED (Bicêtre
Hospital, Le Kremlin-Bicêtre, France), plasmatic cTnI con-
centrations were routinely measured on an Access analyser
(Beckman Coulter, Inc., Brea, CA, USA). The measurement
range of this one-step chemiluminescence immunoassay
extends from 0.01 to 100.00 μg/L. The threshold (10% CV)
given by the manufacturer is 0.06 μg/L. down in a category and the proportion of individuals
with nonevents who move up or down in a category. Table 1 is a contingency table comparing diagnostic
classifications according to cTnI and HsTnT, with shifts
between the two classifications, to represent the possible
benefit of HScTnT in terms of the number of patients
correctly reclassified. As stated in the Routine assess-
ment subsection above, we separated the study popula-
tion into two groups: one included the patients assessed
as having low or moderate PTP of AMI and the other
assessed as having high PTP of AMI. NRIHScTnT vs. cTnI = (sensitivity + specificity)HScTnT −(sensitivity + specificity)cTnI. Statistical analysis NRI is the combination of four components: the pro-
portion of individuals with events who move up or Freund et al. Statistical analysis Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Page 4 of 9 Page 4 of 9 Table 2 Baseline characteristics of the population according to the pretest probabilitya
Population characteristics
All patients
Low or moderate PTP
High PTP
P value*
Number of patients
317
258
59
Age, years
57 ± 17
56 ± 17
60 ± 17
0.168
Men
205 (65)
166 (64)
39 (66)
0.88
Systolic BP, mmHg
141 ± 28
141 ± 27
144 ± 30
0.396
Diastolic BP, mmHg
80 ± 16
80 ± 16
82 ± 16
0.428
Heart rate, beats/minute
85 ± 45
84 ± 23
80 ± 19
0.177
Pulse oxymetry, %
97 ± 3
97 ± 3
97 ± 2
0.651
TIMI risk score
1 (0 to 3)
1 (0 to 2)
2 (1 to 4)
< 0.001
Family history of CAD
100 (32)
77 (30)
23 (59)
0.161
Personal history of CAD
83 (26)
56 (22)
27 (46)
0.0003
Dyslipidemia
113 (36)
86 (33)
27 (46)
0.069
Smoking
128 (40)
99 (38)
29 (49)
0.145
Diabetes
44 (14)
31 (12)
13 (22)
0.059
Hypertension
116 (37)
89 (34)
27 (46)
0.134
History of heart failure
21 (7)
14 (5)
7 (12)
0.083
Typical thoracic pain
136 (43)
105 (41)
31 (53)
0.11
Positive cTnI at admission
41 (13)
24 (9)
17 (29)
< 0.001**
eGFR, mL/minute/1.73 m2
77 (62 to 94)
77 (64 to 94)
76 (56 to 91)
0.187
Treatment within first 24 hours after admission
Aspirin
119 (38)
79 (31)
40 (68)
<0.001
Clopidogrel
54 (17)
29 (11)
25 (42)
< 0.001
LMWH
68 (21)
41 (16)
27 (46)
< 0.001
Anti GPIIb/IIIa
3 (1)
1 (0)
2 (3)
0.09
Coronarography
83 (26)
51 (20)
32 (54)
< 0.001
Outcomes
Hospital admission
192 (61)
140 (54)
52 (88)
< 0.001
Admission to CCU
134 (42)
88 (34)
46 (78)
< 0.001
Final diagnosis
AMI
45 (14)
22 (9)
23 (39)
< 0.001
STEMI
13 (4)
0 (0)
13 (22)
< 0.001
NSTEMI
32 (10)
22 (9)
10 (17)
< 0.001
Unstable angina
11 (3)
4 (2)
7 (12)
< 0.001
Other diagnosis
261 (82)
232 (90)
29 (49)
< 0.001***
aAMI, acute myocardial infarction; BP, blood pressure; CAD, coronary artery disease; cTnI, conventional troponin I; eGFR, estimated glomerular filtration rate;
LMWH, low-molecular-weight heparin; anti-GPIIb/IIIa, Anti-glycoprotein IIb-IIIa; CCU, cardiologic care unit; NSTEMI, non-ST elevation myocardial infarction; PTP,
pretest probability; STEMI, ST elevated myocardial infarction. Statistical analysis TIMI, Thrombolysis in Myocardial Infarction. Results are expressed as means ± standard deviations,
medians (25th to 75th percentile) or n (%); *statistical comparisons are between low to moderate PTP and high PTP groups unless otherwise indicated; **P > 0. μg/L in Pitie-Salpetriere and Cochin, P > 0.06 μg/L in Bicêtre; ***Statistical comparison including stable angina (n = 63), pulmonary embolism (n = 16),
myopericarditis (n = 43), heart failure (n = 5) and others. Table 2 Baseline characteristics of the population according to the pretest probabilitya aAMI, acute myocardial infarction; BP, blood pressure; CAD, coronary artery disease; cTnI, conventional troponin I; eGFR, estimated glomerular filtration rate;
LMWH, low-molecular-weight heparin; anti-GPIIb/IIIa, Anti-glycoprotein IIb-IIIa; CCU, cardiologic care unit; NSTEMI, non-ST elevation myocardial infarction; PTP,
pretest probability; STEMI, ST elevated myocardial infarction. TIMI, Thrombolysis in Myocardial Infarction. Results are expressed as means ± standard deviations,
medians (25th to 75th percentile) or n (%); *statistical comparisons are between low to moderate PTP and high PTP groups unless otherwise indicated; **P > 0.14
μg/L in Pitie-Salpetriere and Cochin, P > 0.06 μg/L in Bicêtre; ***Statistical comparison including stable angina (n = 63), pulmonary embolism (n = 16),
myopericarditis (n = 43), heart failure (n = 5) and others. higher final diagnosis of AMI (39% vs. 9%) in the high
PTP group (P < 0.001). At 30 days after admission,
there were three deaths (two in the AMI group and one
in the other cause group) and four relapses of ACS (all
in the AMI group). population, 149 patients (47%) were assessed as having a
low PTP of AMI, 109 patients (34%) were assessed as
moderate and 59 patients (19%) were assessed as high. AMI was confirmed in 45 patients (14%), 13 of whom
had sustained STEMI, and all of these 13 patients were
in the high PTP group; 32 of the patients had sustained
NSTEMI. Table 2 shows that patients in the two groups
(high PTP and low or moderate PTP) had significantly
different characteristics. There was a higher rate of a
personal history of AMI in the high PTP group and a HsTnT diagnostic performances The area under the ROC curve (AUC) for the diagnosis
of AMI was 0.940 (95% Confidence Intervall 0.901 to
0.980) (P < 0.001) for initial cTnI compared to 0.926 Page 5 of 9 Page 5 of 9 Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI for the diagnosis of AMI according to pretest probabilitya
Patient characteristics
Sensitivity
Specificity
PPV
NPV
Acc
LR+
LR- Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI for the diagnosis of AMI according to pretest probabilitya
Patient characteristics
Sensitivity
Specificity
PPV
NPV
Acc
LR+
LR-
All patients (N = 317)
Positive cTnI
71 (55-84)
97 (94 to 98)
78 (62 to 89)
95 (92 to 97)
93 (90 to 96)
21.5 (20.1 to 22.9)
0.32 (0.23 to 0.36)
Positive HScTnT
93 (89 to 100)*
82 (77 to 87)*
47 (36 to 58)*
99 (96 to 100)
84 (79 to 88)*
5.3 (4.8 to 5.8)
0.08 (0.04 to 0.12)
Low to moderate PTP group (n = 258)
Positive cTnI
77 (54 to 92)
97 (94 to 99)
71 (49 to 87)
98 (95 to 99)
95 (92 to 97)
26.1 (24.0 to 28.1)
0.23 (0.17 to 0.30)
Positive HScTnT
91 (69 to 98)
85 (79 to 89)*
36 (24 to 49)**
99 (96 to 100)
85 (80 to 89)*
6.0 (5.3 to 6.6)
0.11 (0.06 to 0.15)
High PTP group (n = 59)
Positive cTnI
65 (43 to 83)
94 (79 to 99)
88 (62 to 98)
81 (65 to 91)*
83 (71 to 91)**
11.7 (10.1 to 13.4)
0.37 (0.18 to 0.55)
Positive HScTnT
96 (76 to 100)***
67 (49 to 81)***
65 (47 to 81)
96 (78 to 100)
78 (65 to 87)
2.9 (2.3 to 3.4)
0.07 (0 to 0.17)
aHScTnT, highly sensitive cardiac troponin T; PPV: positive predictive value; NPV: negative predictive value; Acc: diagnostic accuracy; LR: likelihood ratio. Values are expressed as percentages (except for LR) and their
95% confidence intervall. Positive cTnI > 0.14 μg/L in Pitie-Salpetriere and Ccochin, > 0.06 μg/L in Bicetre; positive HScTnT >0.014 μg/mL. *P < 0.05 versus positive cTnI in all patients; **P < 0.05 versus cTnI in low to
moderate PTP group; ***P < 0.05 versus cTnI in high PTP group. (0.881 to 0.971) (P < 0.001) for HsTnT. However, there
was no significant difference between AUCs (Figure 1). Net reclassification improvement Table 3 shows patient classification on the basis of using
cTnI or HsTnT to diagnose AMI and highlights the
shifts between the two classifications. HsTnT diagnostic performances ROC analysis indicated an optimal threshold of HsTnT
for the diagnosis of AMI at 0.014 μg/L, with a high sen-
sitivity of 89% (78 to 98) and a high specificity of 82%
(78 to 87). The overall diagnostic accuracy of HsTnT
was not significantly different compared to that of cTnI,
regardless of PTP. Similar results (data not shown) were
observed when we considered only NSTEMI patients
(that is, after exclusion of the 13 STEMI patients). For
the diagnosis of AMI, the sensitivities of HsTnT were
higher and the specificities were lower than those of
cTnI, regardless of PTP (Table 3). When we assessed
the low and moderate PTP populations, the sensitivity
of HsTnT was higher (91% (79 to 100) vs. 77% (60 to
95)) but NPV was not (99% (96 to 100) vs. 98% (95 to
99) for cTnI). Discussion
h During the past two decades, cTn has been adopted as
the preferred biomarker for the diagnosis of acute MI, a
position reaffirmed in recent consensus guidelines
[14,22]. However, until recently, cTn methods were
unable to deliver the requisite analytic performance at
the 99th percentile, an extremely low cutoff point within
the range of analytic ‘noise’ in most conventional assays. The present prospective multicenter study of unselected
patients who presented to the ED with chest pain of < 6 0,001
0,01
0,1
1
10
100
eGFR tertiles
cTnI µg/L
1
2
3
AMI
0
1
***
***
***
0.04
0.04
0.04
1.10
0.12
1.30
0,001
0,01
0,1
1
10
eGFR tertiles
cTnT µg/L
1
2
3
AMI
0
1
***
***
***
0.007
0.004
0.003
0.241
0.034
0.225
a)
b)
Figure 2 Boxplots for cTnI (A) and HSTnT (B) values as a function
of AMI and according to eGFR tertiles. ***P < 0.001 versus AMI
patients in the same eGFR tertile. Tertile 1 (eGFR < 67.2 mL-1 minute-1
1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 mL-1 minute-1 1.73 m-2) and
tertile 3 (eGFR ≥86.9 mL-1 minute-1 1.73 m-2). Medians are indicated
for each box. 0,01
0,1
1
10
100
cTnI µg/L
AMI
0
1
***
***
***
0.04
0.04
0.04
1.10
0.12
1.30
a) Second, we confirmed the value of 0.014 μg/L as an
optimal threshold [14,22]. We confirmed the high diag-
nostic accuracy of HsTnT; the AUC of HsTnT was 0.93,
similar to that found by investigators in previous studies. Thus, Keller et al. [22] and Reichlin et al. [14] found
AUCs that ranged from 0.94 to 0.96. However, and con-
versely to other reports, our findings do not show a better
AUC for HsTnT than for conventional cTnI measure-
ments. Several reasons could explain this discrepancy. First, we used cTnI (from Siemens and Beckman
Coulter) instead of cTnT as the comparator, thus with a
different assay than was previously used, and our com-
parator cTnI could have slightly better analytical quali-
ties than the one called the ‘standard assay’ that was
used in the Reichlin et al. study [14]. Second, in our
study, the AUC for cTnI, or ‘conventional troponin’,
that is, the comparator, was 0.94 (95% CI, 0.90 to 0.98),
which in fact is included in the 95% CIs of the AUCs of
other comparators previously used. For example, Christ
et al. Influence of renal function on cTn performances Patients were classified into tertiles: tertile 1 (estimated
glomerular filtration rate (eGFR) < 67.2 ml-1 minute-1
1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 ml-1 min-
ute-1 1.73 m-2) and tertile 3 (eGFR ≥86.9 ml-1 minute-1
1.73 m-2). Cardiac TnI levels were not significantly dif-
ferent across tertiles. However, HsTnT increased signifi-
cantly across tertiles (P < 0.001): the lower the eGFR,
the higher the HsTnT value. However, in each eGFR
tertile, cTnI and HsTnT levels remained significantly the higher the HsTnT value. However, in each eGFR
tertile, cTnI and HsTnT levels remained significantly
Figure 1 ROC curves for the diagnosis of AMI. Values were log-
transformed before analysis. AUC: area under the curve; cTnI:
conventional troponin I; HSTnT: highly sensitive troponin T. Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI fo
Patient characteristics
Sensitivity
Specificity
All patients (N = 317)
Positive cTnI
71 (55-84)
97 (94 to 98
Positive HScTnT
93 (89 to 100)*
82 (77 to 87)
Low to moderate PTP group (n = 258)
Positive cTnI
77 (54 to 92)
97 (94 to 99
Positive HScTnT
91 (69 to 98)
85 (79 to 89)
High PTP group (n = 59)
Positive cTnI
65 (43 to 83)
94 (79 to 99
Positive HScTnT
96 (76 to 100)***
67 (49 to 81)*
aHScTnT, highly sensitive cardiac troponin T; PPV: positive predictive value; NPV: negative p
95% confidence intervall. Positive cTnI > 0.14 μg/L in Pitie-Salpetriere and Ccochin, > 0.06
moderate PTP group; ***P < 0.05 versus cTnI in high PTP group. Figure 1 ROC curves for the diagnosis of AMI. Values were log-
transformed before analysis. AUC: area under the curve; cTnI:
conventional troponin I; HSTnT: highly sensitive troponin T. Figure 1 ROC curves for the diagnosis of AMI. Values were log-
transformed before analysis. AUC: area under the curve; cTnI:
conventional troponin I; HSTnT: highly sensitive troponin T. Figure 1 ROC curves for the diagnosis of AMI. Values were log-
transformed before analysis. AUC: area under the curve; cTnI:
conventional troponin I; HSTnT: highly sensitive troponin T. Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Page 6 of 9 Page 6 of 9 hours’ duration produced major different findings about
the new HsTnT assay. different between AMI and no AMI (P < 0.001 for
both) (Figure 2). Influence of renal function on cTn performances We found no significant differences in
the AUCs of cTnI and HsTnT regarding eGFR tertiles,
and the optimal threshold value of cTnI did not change
across tertiles. Conversely, the optimal threshold value
of HsTnT increased only in tertile 1 (0.036 μg/L com-
pared to 0.014 μg/L). First, the sensitivity of the HsTnT assay remains high
at all PTP levels. The excellent sensitivity of 93% was
comparable to that found in a previous study (84% to
90% [22]) and significantly higher than conventional
cTn (69% in our study and 72% previously described
[14]). However, despite its good sensitivity of 91% in the
low and moderate PTP groups, the use of HsTnT assays
would not allow physicians to rule out AMI in these
patients with a unique measurement of HsTnT, as the
NPV is not quite perfect, that is, a unique value < 0.014
μg/L cannot avoid a second blood test several hours
later to control HsTnT level. It should be noted that in
the high PTP group, HsTnT showed excellent diagnostic
accuracy, with 93% sensitivity (compared to 80% for
cTnI) and 96% NPV (compared to 93% for cTnI). Recently, Januzzi et al. [15] showed that HsTnT was
able to detect ACS more sensitively than a correspond-
ing conventional cTnT method in a population of low
to moderate PTP patients with chest pain. Limitations The main limitation of our study is the small sample of
patients, especially patients with AMI. We cannot
exclude the possibility that better results might have
been found with a larger sample. Our sample is compar-
able to those used in previous studies, however, and
most of all, we believe that the imperfect NPV that we
describe herein is the major result of our study, which
could not have been corrected by including more
patients. Our study has some other limitations. First, we per-
formed only a single measurement of HsTnT. We did not
evaluate its kinetics, which would have been interesting,
especially in the ‘grey zone’ (between 0.014 μg/L and 0.050
μg/L). A second value could have provided more data, as
previously described in the Giannitsis et al. study [27],
which reported that a doubling in the HsTnT concentra-
tion within 3 hours of chest pain (with first negative
HsTnT and no electrocardiogram abnormality) was asso-
ciated with a 100% PPV of a diagnosis of NSTEMI. Conventional cTn is widely used and is recommended
for the management of patients presenting with sus-
pected ACS [6]. However, the delay in detecting its ele-
vation prevents early, safe discharge from the ED
without repeated negative measurements during the
course of 4 to 6 hours. Recent studies have shown excel-
lent diagnostic performance of HsTnT measurement,
even with early presentation to the ED [14], and better
diagnostic accuracy than cTn [15]. Despite its higher
sensitivity, we did not find that HsTnT had better NPV,
diagnostic accuracy or AUC, conversely to the findings
of previous studies [15]. Furthermore, as expected, spe-
cificity and PPV were lower. The clinical setting, time of
inclusion, rate of AMI in our patient population and
our focus on low or moderate PTP of AMI could
explain this discrepancy. Second, we used empirical PTP and not a standardised,
validated one [17,18]. However, outcomes in the low and
moderate PTP population (only nine with confirmed
NSTEMI), and differences in clinical characteristics at
admission suggested that even though empirical, this eva-
luation by the clinician was accurate. Furthermore, one of
the strengths of our study was that it evaluated differ-
ences in diagnostic performance for the HsTnT regarding
PTP as demonstrated for D-dimers and empirical suspi-
cion of pulmonary embolism [28]. Discussion
h [23] found an AUC of the standard fourth-genera-
tion cTnT assay, that is, its comparator, of 0.89 (95% CI,
0.81 to 0.98). Unfortunately, Keller et al. [22] did not
detail the 95% CIs of their AUCs for cTn, and Reichlin
et al. [14] used an old standard assay which in fact
underestimated the diagnostic performance of the cTn
assay. Other reasons could explain this discrepancy in
the AUC of ROC curves for cTnI. Our inclusion criteria
differ from those of Reichlin et al. [14], Keller et al. [22]
and others who included patients with chest pain of less
than 12 hours’ duration with high rates of AMI and
unstable angina. Our population markedly differs from
those in previous studies. Thus, other conventional
cTnT assays (also called third-generation cTnTs, from 0,001
eGFR tertiles
1
2
3
0,001
0,01
0,1
1
10
eGFR tertiles
cTnT µg/L
1
2
3
AMI
0
1
***
***
***
0.007
0.004
0.003
0.241
0.034
0.225
b) Figure 2 Boxplots for cTnI (A) and HSTnT (B) values as a function
of AMI and according to eGFR tertiles. ***P < 0.001 versus AMI
patients in the same eGFR tertile. Tertile 1 (eGFR < 67.2 mL-1 minute-1
1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 mL-1 minute-1 1.73 m-2) and
tertile 3 (eGFR ≥86.9 mL-1 minute-1 1.73 m-2). Medians are indicated
for each box. Page 7 of 9 Page 7 of 9 Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Roche Diagnostics) that could be used in studies as
comparators for HSTnT have been reported to have
excellent AUCs. Collinson et al. [24] found that at 6
hours postpain, the AUC of cTnT was 0.989 (95% CI,
0.966 to 1.0). However, although the comparison of
AUCs remains the most popular metric by which to
capture discrimination, it appears that for models con-
taining clinical risk and possessing reasonably good dis-
crimination, very important associations between the
biomarker and the end point are required to provide
significantly different AUCs. In other words, compari-
sons of AUCs might be considered powerless in identi-
fying biomarkers of interest in such situations [20]. To
address this problem, new ways of evaluating the useful-
ness of biomarkers have been described, but they are
used very rarely in studies evaluating diagnostic tests or
biomarkers [14,22]. Discussion
h In the present study, reclassification,
for example, NRI, demonstrated that the use of HsTnT
with a clinical assessment (including ECG findings) only
slightly improved the discriminative power and perfor-
mance in predicting AMI [14,22,25]. As described in
previous studies, we have demonstrated a worsening of
specificity and lower PPV of HsTnT measurement com-
pared to those of conventional cTn; that is, we observed
an increase in false-positive findings. Last, the present
study is the first to investigate the impact of kidney
function on HsTnT levels. We found no significant dif-
ference in the AUCs of HsTnT regarding eGFR tertiles. Only in tertile 1 was the optimal threshold value of
HsTnT increased (0.036 μg/ml compared to 0.014 μg/L). cannot translate into a real clinical improvement. A NPV
of 99% can be interpreted as excellent, but this slight gain
from that of cTnI is not sufficient to change the conven-
tional method of chest pain investigation in our ED, even
in low to moderate PTP patients. This subgroup is the one
of most interest in our study, as high PTP patients (and
even more so for STEMI patients) are not to be promptly
discharged and will more easily undergo further investiga-
tions and care. To rapidly and reliably rule out AMI, the answer may
be assessment of a combination of different biomarkers,
as suggested by Reichlin et al. [26] in their study, where
they found that with a copeptin level < 14 pmol/L and a
TnT level < 0.01 μg/L, AMI was excluded with 99.7%
NPV in an unselected population of chest pain patients. References
1
T k F 1. Task Force for Diagnosis and Treatment of Non-ST-Segment Elevation
Acute Coronary Syndromes of European Society of Cardiology, Bassand JP,
Hamm CW, Ardissino D, Boersma E, Budaj A, Fernández-Avilés F, Fox KA,
Hasdai D, Ohman EM, Wallentin L, Wijns W: Guidelines for the diagnosis
and treatment of non-ST-segment elevation acute coronary syndromes. Eur Heart J 2007, 28:1598-1660. 1. Task Force for Diagnosis and Treatment of Non-ST-Segment Elevation
Acute Coronary Syndromes of European Society of Cardiology, Bassand JP,
Hamm CW, Ardissino D, Boersma E, Budaj A, Fernández-Avilés F, Fox KA,
Hasdai D, Ohman EM, Wallentin L, Wijns W: Guidelines for the diagnosis
and treatment of non-ST-segment elevation acute coronary syndromes. Eur Heart J 2007, 28:1598-1660. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care
Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L,
Goldmann B, Katus HA: The prognostic value of serum troponin T in
unstable angina. N Engl J Med 1992, 327:146-150. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care
Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care
Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L,
Goldmann B, Katus HA: The prognostic value of serum troponin T in
unstable angina. N Engl J Med 1992, 327:146-150. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L,
Goldmann B, Katus HA: The prognostic value of serum troponin T in
unstable angina. N Engl J Med 1992, 327:146-150. Competing interests
CCG PR
d BR
i CCG, PR and BR received honoraria from Thermo Fisher Scientific B.R.A.H.M.S. (Hennigsdorf, Germany). PR received an honorarium from bioMérieux, Roche
Diagnostics France (Lyon, France). Limitations Another limitation of
our study is that different conventional Tn assays have
been used at the two study sites with different threshold
values and CVs. These assays were used because they
were both local and well-understood methods at the time
of the study. The emergency medicine field would greatly benefit from
a new biomarker that eases and hastens the triage of non-
cardiac chest pain patients. The main incremental value
that could have provided a new highly sensitive assay for
Tn would have allowed emergency physicians to rule out
AMI and discharge patients with a normal Tn value. This
study suggests that even when considering only low to
moderate PTP patients, the better sensitivity of HsTnT Third, we used two different assays for the comparator
(that is, conventional TnI): a Siemens cTnI assay in two
centres (CCH and PSL) and a Beckman Coulter assay in Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Page 8 of 9 Page 8 of 9 Huchard, F-75018, Paris, France. 5Department of Biochemistry, Hôpital Bicêtre,
APHP, 78 rue du Général Leclerc 94270, Le Kremlin-Bicêtre, France. 6INSERM
UMRS 956, UPMC, 91 Boulevard de l’Hôpital, F-75013 Paris, France. Huchard, F-75018, Paris, France. 5Department of Biochemistry, Hôpital Bicêtre,
APHP, 78 rue du Général Leclerc 94270, Le Kremlin-Bicêtre, France. 6INSERM
UMRS 956, UPMC, 91 Boulevard de l’Hôpital, F-75013 Paris, France. the third centre (BCT). The ROC curve for the cTnI is,
then, a combined ROC curve of two different assays,
making it imprecise. However, the two different ROC
curves (for each assay) have similar AUCs. Conclusions We have confirmed that HsTnT is accurate for diagno-
sis of AMI, with a sensitivity slightly higher than that of
conventional cTnI, regardless of PTP of AMI in patients
with chest pain presenting to an ED. However, we did
not show a better NPV. Intervention studies are clearly
warranted to support the use of HsTnT to help ED phy-
sicians achieve clinical improvement in treating patients
with chest pain and providing them with an early, safe
discharge from the hospital. Received: 1 February 2011 Revised: 19 April 2011
Accepted: 10 June 2011 Published: 10 June 2011 Received: 1 February 2011 Revised: 19 April 2011
Accepted: 10 June 2011 Published: 10 June 2011 Received: 1 February 2011 Revised: 19 April 2011
Accepted: 10 June 2011 Published: 10 June 2011 Abbreviations y
7. Eggers KM, Jaffe AS, Lind L, Venge P, Lindahl B: Value of cardiac troponin I
cutoff concentrations below the 99th percentile for clinical decision-
making. Clin Chem 2009, 55:85-92. 7. Eggers KM, Jaffe AS, Lind L, Venge P, Lindahl B: Value of cardiac troponin I
cutoff concentrations below the 99th percentile for clinical decision-
making. Clin Chem 2009, 55:85-92. ACS: acute coronary syndrome; AMI: acute myocardial infarction; AUC: area
under the curve; cTn: conventional troponin; CV: coefficient of variation; ED:
emergency department; HsTn: high-sensitivity troponin; LR: likelihood ratio;
NPV: negative predictive value; NRI: net reclassification improvement;
NSTEMI: non-ST elevation myocardial infarction; PPV: positive predictive
value; PTP: pretest probability; ROC: receiver operating characteristic; SD:
standard deviation; STEMI: ST elevation myocardial infarction. ACS: acute coronary syndrome; AMI: acute myocardial infarction; AUC: area
under the curve; cTn: conventional troponin; CV: coefficient of variation; ED:
emergency department; HsTn: high-sensitivity troponin; LR: likelihood ratio;
NPV: negative predictive value; NRI: net reclassification improvement; 8. Apple FS, Pearce LA, Smith SW, Kaczmarek JM, Murakami MM: Role of
monitoring changes in sensitive cardiac troponin I assay results for early
diagnosis of myocardial infarction and prediction of risk of adverse
events. Clin Chem 2009, 55:930-937. 9. Apple FS, Smith SW, Pearce LA, Ler R, Murakami MM: Use of the Centaur
TnI-Ultra assay for detection of myocardial infarction and adverse events
in patients presenting with symptoms suggestive of acute coronary
syndrome. Clin Chem 2008, 54:723-728. Authors’ contributions CCG, BR and PR designed the study. PB, YEC, JCA, BD, FL and CC helped in
collecting the data. CC and YF carried out the statistical analyses and the
biochemical assays. YF, CCG, BR and PR wrote the paper. All authors read
and approved the final manuscript. CCG, BR and PR designed the study. PB, YEC, JCA, BD, FL and CC helped in
collecting the data. CC and YF carried out the statistical analyses and the
biochemical assays. YF, CCG, BR and PR wrote the paper. All authors read
and approved the final manuscript. Last, this study was underpowered to find any signifi-
cant change in the detection of AMI in the low to mod-
erate PTP patients. However, as the NPV is not perfect
in our patient population, we expect that this would
remain the case with a larger sample. Acknowledgements We thank Roche Diagnostics France (Meylan, France) for providing free
reagents and kits for HsTnT assays. The tests and kits for the HsTnT assays
were provided free of charge by Roche Diagnostics France. Other sources of
support were provided solely from departmental sources. We also thank Dr DJ Baker (Department of Anaesthesiology, CHU Necker-
Enfants Malades, Assistance Publique des Hôpitaux de Paris (AP-HP), Paris,
France) for reviewing the manuscript. This study was partially presented at
the research forum of the 2010 scientific assembly of the American College
of Emergency Physicians, Las Vegas, NV, USA, 29 September 2010. 10. Eggers KM, Lagerqvist B, Venge P, Wallentin L, Lindahl B: Persistent cardiac
troponin I elevation in stabilized patients after an episode of acute
coronary syndrome predicts long-term mortality. Circulation 2007,
116:1907-1914. 11. James SK, Lindahl B, Armstrong P, Califf R, Simoons ML, Venge P,
Wallentin L: A rapid troponin I assay is not optimal for determination of
troponin status and prediction of subsequent cardiac events at
suspicion of unstable coronary syndromes. Int J Cardiol 2004, 93:113-120. 12. Venge P, Lagerqvist B, Diderholm E, Lindahl B, Wallentin L: Clinical
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89:1035-1041. Key messages • Fast and reliable detection of ACS remains a great
concern in the ED. g
g
4. Lindahl B, Toss H, Siegbahn A, Venge P, Wallentin L, for the FRISC Study
Group: Markers of myocardial damage and inflammation in relation to
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2000, 343:1139-1147. • Novel assays for troponin have been developed and
tested recently. 5. Antman EM, Tanasijevic MJ, Thompson B, Schactman M, McCabe CH,
Cannon CP, Fischer GA, Fung AY, Thompson C, Wybenga D, Braunwald E:
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335:1342-1349. • HsTnT is more sensitive than cTn. • In this study, the weak gains realised by measuring
HsTnT rather than cTn in terms of NPV is not suffi-
cient to change daily clinical practice. • In this study, the weak gains realised by measuring
HsTnT rather than cTn in terms of NPV is not suffi-
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Warnholtz A, Fröhlich M, Sinning CR, Eleftheriadis MS, Wild PS, Schnabel RB,
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Chem 2010, 56:642-650. doi:10.1186/cc10270
Cite this article as: Freund et al.: High-sensitivity versus conventional
troponin in the emergency department for the diagnosis of acute
myocardial infarction. Critical Care 2011 15:R147. Author details
1
f 1Department of Emergency Medicine and Surgery, Hôpital Pitié-Salpétrière,
Assistance Publique-Hôpitaux de Paris (APHP), Université Pierre et Marie
Curie-Paris 6 (UPMC), 47-83 boulevard de l’hôpital, F-75651 Paris cedex 13,
France. 2Department of Biochemistry, Hôpital Cochin-Hôtel Dieu, APHP, 27
rue du Faubourg Saint-Jacques, F-75679 Paris cedex 14, France. 3Department
of Emergency Medicine, Hôpital Cochin-Hôtel Dieu, APHP, Université Paris
Descartes-Paris 5, 27 rue du Faubourg Saint-Jacques, F-75679 Paris cedex 14,
France. 4Department of Emergency, Hôpital Bichat, APHP, 46 rue Henri 13. Morrow DA, Cannon CP, Rifai N, Frey MJ, Vicari R, Lakkis N, Robertson DH,
Hille DA, DeLucca PT, DiBattiste PM, Demopoulos LA, Weintraub WS,
Braunwald E: Ability of minor elevations of troponins I and T to predict
benefit from an early invasive strategy in patients with unstable angina
and non-ST elevation myocardial infarction: results from a randomized
trial. JAMA 2001, 286:2405-2412. Page 9 of 9 Page 9 of 9 Freund et al. Critical Care 2011, 15:R147
http://ccforum.com/content/15/3/R147 Freund et al. Critical Care 2011, 15:R147
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test probability to rule out pulmonary embolism: a systematic review of
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Cite this article as: Freund et al.: High-sensitivity versus conventional
troponin in the emergency department for the diagnosis of acute
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https://openalex.org/W3016480775 | http://irep.ntu.ac.uk/id/eprint/46736/1/1568112_Sher.pdf | English | null | Kinetic and thermodynamic evaluation of effective combined promoters for CO2 hydrate formation | Journal of natural gas science and engineering | 2,020 | cc-by | 18,167 | *Corresponding author:
E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 1
Kinetic and thermodynamic evaluation of effective combined
1
promoters for CO2 hydrate formation
2
3
4
Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf,
5
Colin E. Snapea
6
7
a. Department of Chemical and Environmental Engineering, University of Nottingham, University
8
Park, Nottingham NG7 2RD, UK
9
b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai,
10
71800 Nilai, Negeri Sembilan, Malaysia
11
c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering,
12
Environmental and Computing, Coventry University, Coventry CV1 2JH, UK
13
d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
14
e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra
15
Malaysia, 43400 UPM Serdang, Selangor, Malaysia
16
f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10
17
9FE, UK
18
19
20
Abstract
21
The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature.
22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24
required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been
25
explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC)
26
conditions. The formation of hydrate was experimentally investigated in an isochoric system with
27
high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental
28
*Corresponding author:
E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 1
Kinetic and thermodynamic evaluation of effective combined
1
promoters for CO2 hydrate formation
2
3
4
Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf,
5
Colin E. Snapea
6
7
a. Department of Chemical and Environmental Engineering, University of Nottingham, University
8
Park, Nottingham NG7 2RD, UK
9
b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai,
10
71800 Nilai, Negeri Sembilan, Malaysia
11
c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering,
12
Environmental and Computing, Coventry University, Coventry CV1 2JH, UK
13
d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
14
e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra
15
Malaysia, 43400 UPM Serdang, Selangor, Malaysia
16
f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10
17
9FE, UK
18
19
20
Abstract
21
The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24
required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been
25
explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC)
26
conditions. The formation of hydrate was experimentally investigated in an isochoric system with
27
high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental
28
*Corresponding author:
E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 Kinetic and thermodynamic evaluation of effective combined
1
promoters for CO2 hydrate formation
2
3
4
Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf,
5
Colin E. Snapea
6
7
a. Department of Chemical and Environmental Engineering, University of Nottingham, University
8
Park, Nottingham NG7 2RD, UK
9
b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai,
10
71800 Nilai, Negeri Sembilan, Malaysia
11
c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering,
12
Environmental and Computing, Coventry University, Coventry CV1 2JH, UK
13
d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
14
e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra
15
Malaysia, 43400 UPM Serdang, Selangor, Malaysia
16
f. 1
Kinetic and thermodynamic evaluation of effective combined
1
promoters for CO2 hydrate formation
2
3
4
Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf,
5
Colin E. Snapea
6
7
a. Department of Chemical and Environmental Engineering, University of Nottingham, University
8
Park, Nottingham NG7 2RD, UK
9
b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai,
10
71800 Nilai, Negeri Sembilan, Malaysia
11
c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering,
12
Environmental and Computing, Coventry University, Coventry CV1 2JH, UK
13
d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
14
e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra
15
Malaysia, 43400 UPM Serdang, Selangor, Malaysia
16
f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10
17
9FE, UK
18
19
20
Abstract
21
The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature.
22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24
required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been
25
explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC)
26
conditions. The formation of hydrate was experimentally investigated in an isochoric system with
27
high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental
28
*Corresponding author:
E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10
17
9FE, UK
18
19
20
Abstract
21
The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24 *Corresponding author: Abstract
21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24
required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been
25
explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC)
26
conditions. The formation of hydrate was experimentally investigated in an isochoric system with
27
high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental
28 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22
CO2 emissions are closely related to human induced activities such as burning of fossil fuels and
23
deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is
24
required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been
25
explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC)
26
conditions. The formation of hydrate was experimentally investigated in an isochoric system with
27
high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental
28 1 pressure–time (P-t) curves were analyzed to determine the formation of hydrate. Additionally, the
29
effect of newly synthesized combined promoters and various driving forces were evaluated. The
30
experimental results demonstrated that the CO2 uptake expanded as ∆P expanded and designated
31
combined promoters type T1-5 and type T3-2 were the two best, acquiring a uptake of 5.95 and
32
5.57 mmol of CO2 per g of H2O separately. Ethylene glycol mono-ethyl ether (EGME) was
33
demonstrated to be a good option to THF when linked with SDS, with a CO2 uptake of 5.45 mmol
34
for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoured
35
through hydrate development maximize as the measure of water inside mesoporous silica
36
increased. All results of the studied parameters confirmed the reliability of experiments and
37
successful implementation. 38 pressure–time (P-t) curves were analyzed to determine the formation of hydrate. Additionally, the
29
effect of newly synthesized combined promoters and various driving forces were evaluated. Abstract
21 The
30
experimental results demonstrated that the CO2 uptake expanded as ∆P expanded and designated
31
combined promoters type T1-5 and type T3-2 were the two best, acquiring a uptake of 5.95 and
32
5.57 mmol of CO2 per g of H2O separately. Ethylene glycol mono-ethyl ether (EGME) was
33
demonstrated to be a good option to THF when linked with SDS, with a CO2 uptake of 5.45 mmol
34
for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoured
35
through hydrate development maximize as the measure of water inside mesoporous silica
36
increased. All results of the studied parameters confirmed the reliability of experiments and
37
successful implementation. 38 g
p
,
2 p
for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoure
35
through hydrate development maximize as the measure of water inside mesoporous silic
36
increased. All results of the studied parameters confirmed the reliability of experiments an
37
successful implementation. 38
39
Keywords: Global warming; Gas hydrate; CO2 capture and storage (CCS); HPVA; combine
40
promoters, thermodynamics and kinetics. 41
42
1 Introduction
43
The energy demands of the globe have increased very rapidly. Energy consumption rises day b
44
day globally by increasing industries, electric automobiles and developing economic demand
45
According to recent scenario, the energy consumption demand will increase by one third over nex
46
25 years and will become more than double in 2060 [1]. The increased demands of energy als
47
caused a high level of greenhouse gas (GHG) emissions in the environment, therefore as a resu
48
increased global warming [2]. Due to increased global warming, the European Union (EU) set th
49
reduction target of CO2 emission at least by 80% until 2050 [3]. According to the Internationa
50
Plant Protection Convention (IPPC) fifth assessment report, the leading issue of global warmin
51 39
Keywords: Global warming; Gas hydrate; CO2 capture and storage (CCS); HPVA; combined
40
promoters, thermodynamics and kinetics. 41 promoters, thermodynamics and kinetics. 41 1 Introduction
43 The energy demands of the globe have increased very rapidly. Energy consumption rises day by
44
day globally by increasing industries, electric automobiles and developing economic demands. 45
According to recent scenario, the energy consumption demand will increase by one third over next
46
25 years and will become more than double in 2060 [1]. The increased demands of energy also
47
caused a high level of greenhouse gas (GHG) emissions in the environment, therefore as a result
48
increased global warming [2]. Due to increased global warming, the European Union (EU) set the
49
reduction target of CO2 emission at least by 80% until 2050 [3]. According to the International
50
Plant Protection Convention (IPPC) fifth assessment report, the leading issue of global warming
51 2 2 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 52
Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power
53
plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes
54
have gained increasing concern. 55
56
Different schemes were used in the past to reduce global warming specifically carbon emissions
57
in which renewable energy technologies are very important [5, 7]. The process called carbon
58
capture and storage (CCS) emerged as the most important technology to capture and store CO2
59
emitting directly from power and chemical plants [8, 9]. This technology mainly involves
60
separation, conditioning, transportation and storage of CO2. This four-step technology first
61
captures the contents with rich CO2 from any industrial sources, then condense and liquefies CO2
62
before transporting it to the storage site usually through a pipeline and geologically stored it in the
63
formation site of deep saline [10]. Among the whole process, the separation step of CO2 is the one
64
with high energy taking pathway that accounts for about 75–80% of the total cost of CCS [11]. 65
Still, CCS is being recognized as a vital technology with the least cost against climate change
66
mitigation that will be able to limit global warming below 2 °C [12]. 67
68
There are several new strategies developed in the past that can physically and chemically capture
69 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 1 Introduction
43 52
Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power
53
plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes
54
have gained increasing concern. 55 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 52
Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power
53
plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes
54
have gained increasing concern. 55 56
Different schemes were used in the past to reduce global warming specifically carbon emissions
57
in which renewable energy technologies are very important [5, 7]. The process called carbon
58
capture and storage (CCS) emerged as the most important technology to capture and store CO2
59
emitting directly from power and chemical plants [8, 9]. This technology mainly involves
60
separation, conditioning, transportation and storage of CO2. This four-step technology first
61
captures the contents with rich CO2 from any industrial sources, then condense and liquefies CO2
62
before transporting it to the storage site usually through a pipeline and geologically stored it in the
63
formation site of deep saline [10]. Among the whole process, the separation step of CO2 is the one
64
with high energy taking pathway that accounts for about 75–80% of the total cost of CCS [11]. 65
Still, CCS is being recognized as a vital technology with the least cost against climate change
66
mitigation that will be able to limit global warming below 2 °C [12]. 67 There are several new strategies developed in the past that can physically and chemically capture
69
CO2 using blended solution [13, 14], nanostructured membranes of polymers, zeolites and various
70
carbon or inorganic nanocomposites [15], adsorption media, cryogenic systems [16], integrated
71
gasification combined cycle (IGCC) [17], hydrate based gas separation (HBGS) [18] and chemical
72
looping combustion [19]. In IGCC technology, synthetic gas is reformed from fossil fuels (coal,
73
oil and nature gas). In spite of IGCC promising utilization, it faces a major challenge of high
74 3 3 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive
75
technologies are required to capture CO2 efficiently. 1 Introduction
43 Among all of the above mentioned strategies
76
hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2
77
with relatively low consumption of energy [21]. HBGS can be used for both pre and post-
78
combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more
79
appropriate for pre-combustion of CO2 capture. This is because of the partial pressure of fuel gas
80
(consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting
81
of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82
83
Therefore, in this study HBGS has been chosen because of the continuous operation property of
84
CO2 hydrate formation which enables the treatment of large volumes of gaseous stream, less
85
operating cost and recuperative ability of CO2 capture about 99 mol% from the flue gas [23]. 86
Recently Zheng et al. [24] stated that even at ambient temperature carbon dioxide molecules could
87
be arrested and stored by using HBGS improved properties, it provides the leeway for industrialists
88
to use this pathway for further industrial applications. The process of HBGS relies on the ability
89
of gas hydrate formation that is formed by water molecules and CO2, N2, O2, H2 or natural gas
90
component (methane or ethane) at low temperature (near about 237 K) and at elevated pressure of
91
about 10–70 bar [25, 26]. CO2 hydrate is formed in case of pure CO2 gaseous system at a pressure
92
range of 12.70–45 bar and temperature range of 273.20–283 K [27]. 93
94 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive
75
technologies are required to capture CO2 efficiently. Among all of the above mentioned strategies
76
hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2
77
with relatively low consumption of energy [21]. HBGS can be used for both pre and post-
78
combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more
79
appropriate for pre-combustion of CO2 capture. 1 Introduction
43 This is because of the partial pressure of fuel gas
80
(consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting
81
of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive
75
technologies are required to capture CO2 efficiently. Among all of the above mentioned strategies
76
hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2
77
with relatively low consumption of energy [21]. HBGS can be used for both pre and post-
78
combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more
79
appropriate for pre-combustion of CO2 capture. This is because of the partial pressure of fuel gas
80
(consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting
81
of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82 Therefore, in this study HBGS has been chosen because of the continuous operation property of
84
CO2 hydrate formation which enables the treatment of large volumes of gaseous stream, less
85
operating cost and recuperative ability of CO2 capture about 99 mol% from the flue gas [23]. 86
Recently Zheng et al. [24] stated that even at ambient temperature carbon dioxide molecules could
87
be arrested and stored by using HBGS improved properties, it provides the leeway for industrialists
88
to use this pathway for further industrial applications. The process of HBGS relies on the ability
89
of gas hydrate formation that is formed by water molecules and CO2, N2, O2, H2 or natural gas
90
component (methane or ethane) at low temperature (near about 237 K) and at elevated pressure of
91
about 10–70 bar [25, 26]. CO2 hydrate is formed in case of pure CO2 gaseous system at a pressure
92
range of 12.70–45 bar and temperature range of 273.20–283 K [27]. 93 In the past, numerous parameters have been scrutinized to improve the efficiency of CO2 uptake,
95
less operational cost and ease of hydrate formation. The parameters used for the increased
96
efficiency of CO2 capture are mainly promoters, types of silica, experimental dynamic force,
97 4 4 height of the bed and amount of moisture content. 1 Introduction
43 These parameters were investigated by
98
employing a solid adsorbent approach in HBGS, which is most preferred method in the industry
99
for CCS [18, 28, 29]. Nambiar et al. [30] worked with the biodegradable porous materials that
100
enabled almost double rate of hydrates formation with only 50% water saturation level. While Park
101
et al. [31] used only porous silica gel which increased the gas uptake due to high availability of
102
surface area to increase water and gas contact. Li et al., [32] employed nano-sized Al2O3 and found
103
that gas separation efficiency was improved by approximately 43.62% due to micro-sized
104
particles. 105
106
In spite of the remarkable advancements in HBGS technology, however, this technology still
107
requires a large amount of energy for compression and extraction of CO2 and decrease in optimum
108
conditions of temperature and pressure. Thus, different thermodynamic promoters were used in
109
the past to optimize the conditions of hydrate formation. These promoters include Cyclopentane
110
(CP) [33], Tetra-n-butyl ammonium Chloride (TBAC) [34], Tetra-n-butyl ammonium bromide
111
(TBAB) [35], Tetra-n-butyl ammonium fluoride (TBAF) [29] and Tetrahydrofuran (THF) [36]. 112
However, despite the usage of these promoters, still the time taking for process of hydrate
113
formation and limited gaseous solubility in water restrict the successful application of CO2 capture
114
schemes. That is why more investigation regarding the definite solution of this problem is required. 115
Therefore, the present study investigates two parameters i.e. best type of silica and novel combined
116
type promoters to evaluate their effect for hydrate formation. The main focus was to evaluate the
117
optimum hydrate based separation in the operating conditions of an integrated gasification
118
combined cycle. Herein, the fact is highlight that hydrate formation is possible in integrated
119
gasification combined cycle conditions. Furthermore, the hydrate formation driving force and non-
120 height of the bed and amount of moisture content. These parameters were investigated by
98
employing a solid adsorbent approach in HBGS, which is most preferred method in the industry
99
for CCS [18, 28, 29]. Nambiar et al. [30] worked with the biodegradable porous materials that
100
enabled almost double rate of hydrates formation with only 50% water saturation level. While Park
101
et al. 2.1 Materials
124 Tetrahydrofuran (THF), Ethylene glycol mono-ethyl ether (EGME), sodium dodecyl sulfate (SDS)
125
and tetrabutylammonium bromide (TBAB) promoters with the purity of 99.70, 99.60, 99.90 and
126
97.50% respectively were purchased from Fisher Scientific. Silica gel with standard particle size
127
of 200–500 μm, pore volume of 0.630 cm3/g, surface area of 499 m2/g and mean pore size of 5.14
128
nm were purchased from Fisher Scientific. Antifreeze was provided by ASDA. A member of Linde
129
group i.e. BOC supplied Helium and Nitrogen gas for cleaning and controlling the valve of high
130
pressure volumetric analyzer (HPVA). 131 1 Introduction
43 [31] used only porous silica gel which increased the gas uptake due to high availability of
102
surface area to increase water and gas contact. Li et al., [32] employed nano-sized Al2O3 and found
103
that gas separation efficiency was improved by approximately 43.62% due to micro-sized
104
particles. 105 In spite of the remarkable advancements in HBGS technology, however, this technology still
107
requires a large amount of energy for compression and extraction of CO2 and decrease in optimum
108
conditions of temperature and pressure. Thus, different thermodynamic promoters were used in
109
the past to optimize the conditions of hydrate formation. These promoters include Cyclopentane
110
(CP) [33], Tetra-n-butyl ammonium Chloride (TBAC) [34], Tetra-n-butyl ammonium bromide
111
(TBAB) [35], Tetra-n-butyl ammonium fluoride (TBAF) [29] and Tetrahydrofuran (THF) [36]. 112
However, despite the usage of these promoters, still the time taking for process of hydrate
113
formation and limited gaseous solubility in water restrict the successful application of CO2 capture
114
schemes. That is why more investigation regarding the definite solution of this problem is required. 115
Therefore, the present study investigates two parameters i.e. best type of silica and novel combined
116
type promoters to evaluate their effect for hydrate formation. The main focus was to evaluate the
117
optimum hydrate based separation in the operating conditions of an integrated gasification
118
combined cycle. Herein, the fact is highlight that hydrate formation is possible in integrated
119
gasification combined cycle conditions. Furthermore, the hydrate formation driving force and non-
120 5 5 hydrate forming conditions especially in IGCC conditions were investigated with the employment
121
of pure CO2 gas. 122 2.2 Sample preparation
132 Then promoter-water solution equal to 47.50 g was
156
added to make the total mass of dry silica gel-promoter-water mixture equal to 50 g. These samples
157
were prepared by implementing the highest rates of stirring. The degassing unit was used to
158
calculate an exact amount of moisture content residing inside the pores of silica gel. The amount
159
of water content was necessary to calculate the final conversion of water to CO2 hydrate. 160 2.2 Sample preparation
132 149 water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender
144
for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached
145
equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from
146
dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each
147
promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol%
148
concentration of THF [39]. 149
150
The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2
151
(0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were
152
used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A-
153
2) in this work could provide more options for HBGS research field in future. 154 150
The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2
151
(0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were
152
used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A-
153
2) in this work could provide more options for HBGS research field in future. 154
Table 1 summarizes the concentration required for each combined-promoter employed. 2.50 g of
155
silica gel was used to prepare each sample. Then promoter-water solution equal to 47.50 g was
156
added to make the total mass of dry silica gel-promoter-water mixture equal to 50 g. These samples
157
were prepared by implementing the highest rates of stirring. The degassing unit was used to
158
calculate an exact amount of moisture content residing inside the pores of silica gel. The amount
159
of water content was necessary to calculate the final conversion of water to CO2 hydrate. 160 The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2
151
(0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were
152
used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A-
153
2) in this work could provide more options for HBGS research field in future. 154 Table 1 summarizes the concentration required for each combined-promoter employed. 2.50 g of
155
silica gel was used to prepare each sample. 2.2 Sample preparation
132 The adsorbent employed was standard because silica gel due its high porosity and reproducibility
133
can supply a large amount of contact area between water and gas molecules in a short time. Thus,
134
it increases the kinetics of hydrate formation and enhances the CO2 uptake as compared to other
135
adsorbents. Furthermore, it was noted that silica gel with chosen specific properties, as a solid
136
adsorbent can effectively overcome the gas/water contact limitation where in the gas phase will
137
have better contact with water dispersed in pores of silica gel [37]. Four methods were used for
138
the preparation of wet silica gel, the method with the best result was reported in this study. For
139
preparation, silica gel was initially dried inside the oven for one night at 200 oC, before the
140
commencement of the experiment. Oven with the model of AX30 manufactured by Carbolite was
141
used. Dry silica gel (0.50 g) was placed inside blender and water was added in excess (19 times
142 6 6 the mass of dry silica gel) so that the total mass of the mixture became 50 g. The silica gel and
143
water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender
144
for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached
145
equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from
146
dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each
147
promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol%
148
concentration of THF [39]. 149 the mass of dry silica gel) so that the total mass of the mixture became 50 g. The silica gel and
143
water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender
144
for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached
145
equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from
146
dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each
147
promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol%
148
concentration of THF [39]. 2.3 Experimental procedure
161 The pneumatic valves of HPVA were also controlled by the gas chambers. Prior to the
169
initiation of analysis, to clean the line from any sort of polluting influences, physical cleaning of
170
the system was done by gas. 171 172
The working conditions, such as; analyze time, examination gas port, working weight, and
173
temperature were pre-characterized. From that point forward, the cells valve was firstly closed and
174
sample cell was accused with silica gel having a sufficient amount of water that was placed inside
175
the water bath. During the experimental work, the desired working temperature was built up
176
through a steady temperature bath and simultaneously the required pressure was built up through
177
a supply vessel. The cells valve was directed to completely open, after the maintenance of
178
operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was
179
diminished to barometrical pressure at the equivalent working temperature for hydrate
180
disintegration. After that, the sample cell was removed from HPVA and the cells valve was
181
allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected
182
by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183 The working conditions, such as; analyze time, examination gas port, working weight, and
173
temperature were pre-characterized. From that point forward, the cells valve was firstly closed and
174
sample cell was accused with silica gel having a sufficient amount of water that was placed inside
175
the water bath. During the experimental work, the desired working temperature was built up
176
through a steady temperature bath and simultaneously the required pressure was built up through
177
a supply vessel. The cells valve was directed to completely open, after the maintenance of
178
operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was
179
diminished to barometrical pressure at the equivalent working temperature for hydrate
180
disintegration. After that, the sample cell was removed from HPVA and the cells valve was
181
allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected
182
by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183 2.3 Experimental procedure
161 Fig. 1 shows the work station for hydrate formation experiments consisting of a high-pressure
162
volumetric analyzer (model HPVA-100, manufactured by Micromeritics). It contains a computer
163
unit, a constant temperature bath, gas cylinders and a vacuum pump. The mixture of 70 vol% water
164
+ 30 vol% antifreeze was used to avoid the formation of ice inside the temperature control vessel
165 7 7 and to make sure that the water mixture was consistently circulated throughout the process. Gas
166
chambers were important to give an investigation of gas with 99.99% purity having 103 bar
167
pressure and Helium gas with the same purity having 34.40 bar pressure for expelling and cleaning
168
purposes. The pneumatic valves of HPVA were also controlled by the gas chambers. Prior to the
169
initiation of analysis, to clean the line from any sort of polluting influences, physical cleaning of
170
the system was done by gas. 171
172
The working conditions, such as; analyze time, examination gas port, working weight, and
173
temperature were pre-characterized. From that point forward, the cells valve was firstly closed and
174
sample cell was accused with silica gel having a sufficient amount of water that was placed inside
175
the water bath. During the experimental work, the desired working temperature was built up
176
through a steady temperature bath and simultaneously the required pressure was built up through
177
a supply vessel. The cells valve was directed to completely open, after the maintenance of
178
operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was
179
diminished to barometrical pressure at the equivalent working temperature for hydrate
180
disintegration. After that, the sample cell was removed from HPVA and the cells valve was
181
allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected
182
by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183
2.3.1 Uncertainty analysis
184
All prepared samples were used to investigate hydrate formation in the HPVA by using pure CO2
185 and to make sure that the water mixture was consistently circulated throughout the process. Gas
166
chambers were important to give an investigation of gas with 99.99% purity having 103 bar
167
pressure and Helium gas with the same purity having 34.40 bar pressure for expelling and cleaning
168
purposes. 2.3.1 Uncertainty analysis
184 However, the average
196
differences, standard deviation and estimation of the uncertainty of mean maximum water
197
conversion to hydrate and mean maximum CO2 uptake data through the estimation of 90%
198
confidence intervals (CI) calculated with the help online statistics calculator to verify the reported
199
results. 200 2.3.1 Uncertainty analysis
184 All prepared samples were used to investigate hydrate formation in the HPVA by using pure CO2
185
gas (99.99% purity). The P-t curve for all experiments that exhibited hydrate formation either in
186
pure CO2 or fuel gas mixture showed a similar trend. In this study, the P-t (Pressure-time) curves
187
obtained were determined through the formation of hydrate together with the study of CO2
188 8 dissolution in water according to Henry’s Law and then followed by the analysis of water
189
conversion to hydrate, CO2 uptake and rate of hydrate formation. All experiments were conducted
190
for 1200 minutes to obtain maximum water conversion to hydrate and maximum CO2 uptake. For
191
accurate measurement, the rate of hydrate formation was reported every 30 minutes because the
192
data was very large. The sampling time for data acquisition of pressure and temperature were taken
193
every 5 s by HPVA. Thus, the rate for every 30 minutes helps for proper visualization of the rate
194
change during 1200 minutes. Furthermore, to ensure the accuracy and statistical validity of the
195
reported results two runs for each sample promoters were performed. However, the average
196
differences, standard deviation and estimation of the uncertainty of mean maximum water
197
conversion to hydrate and mean maximum CO2 uptake data through the estimation of 90%
198
confidence intervals (CI) calculated with the help online statistics calculator to verify the reported
199
results. 200 dissolution in water according to Henry’s Law and then followed by the analysis of water
189
conversion to hydrate, CO2 uptake and rate of hydrate formation. All experiments were conducted
190
for 1200 minutes to obtain maximum water conversion to hydrate and maximum CO2 uptake. For
191
accurate measurement, the rate of hydrate formation was reported every 30 minutes because the
192
data was very large. The sampling time for data acquisition of pressure and temperature were taken
193
every 5 s by HPVA. Thus, the rate for every 30 minutes helps for proper visualization of the rate
194
change during 1200 minutes. Furthermore, to ensure the accuracy and statistical validity of the
195
reported results two runs for each sample promoters were performed. 3 Results and discussion
201 [41]
226
described the time from point a-c as an induction time for hydrate formation. Moreover, the fast
227
induction time observed in this work was almost less than 10 minutes by employing FBR this
228
agrees with the one reported in the literature [18, 43, 44]. Then, the second stage of pressure drop
229
was observed immediately after point c and this significant pressure drop is known as the hydrate
230
growth stage. From point c-d sudden decrease in pressure was observed which is expected due to
231
the availability of enough driving force required for the growth of hydrate. Thus, the significant
232
two-stage pressure drop observed in the initial stage (the first 20 minutes) before being followed
233
by the second small pressure drop (until 100 minutes) until almost no more drop in pressure was
234 According to Tang et al. [41], there must be at least a two-stage pressure drop upon completion of
213
the experiment to ensure the formation of hydrate. The first stage of pressure drop indicates the
214
dissolution of CO2 in water and the subsequent stages indicate hydrate growth. This trend was
215
observed for baseline experiment during the hydrate formation experiment at the constant
216
temperature of 275 K (Fig. 2), where the total pressure drop achieved after 1200 minutes was
217
around 2 bar. The complete dissolution of CO2 in water inside silica gel pores was observed after
218
the pressure dropped approximately to 33.8 bar. As seen in Fig. 2, the first 120 minutes showed
219
two stages of pressure drop. Point a-c is considered the first stage of pressure drop. Initially, a
220
pressure drop from point a-b indicates that the dissolution of CO2 in water happened around 5
221
minutes in which Sloan and Koh [42] stated that upon dissolution of gas in water, labile clusters
222
form immediately. Concurrently, labile clusters started to agglomerate by sharing faces, thus
223
increasing disorder which explained the little rise in pressure from point b-c. This process
224
continued until the size of the cluster agglomerate reached a critical value at point c, wherein Sloan
225
and Koh [42] said this was the point where primary nucleation happens. Also, Tang et al. [41]
226
described the time from point a-c as an induction time for hydrate formation. 3 Results and discussion
201 The prepared samples T1-5, T3-2, T1A-2 and standard silica gel with water (baseline experiment)
202
was used to investigate hydrate formation in HPVA at 275–293 K and 22–36 bar by using pure
203
CO2 gas (99.99% purity). All experiments were conducted for 1200 minutes to obtain maximum
204
CO2 uptake. The P-t curve obtained was firstly used to justify the successful formation of hydrate
205
together with the study of CO2 dissolution in water and then followed by the analysis of CO2 uptake
206
and rate of hydrate formation. Due to the limitation of crystallizer in which the formation of
207
hydrate could not be seen directly by the eyes, there was a necessity to justify the formation of
208
hydrate. Subsequently, two methodologies were utilized to analyze the formation of hydrate;
209
examination of P-t bends and investigation of CO2 disintegration in the water suggested by Servio
210
and Englezos, [40]. 211 9 9 212 According to Tang et al. [41], there must be at least a two-stage pressure drop upon completion of
213
the experiment to ensure the formation of hydrate. The first stage of pressure drop indicates the
214
dissolution of CO2 in water and the subsequent stages indicate hydrate growth. This trend was
215
observed for baseline experiment during the hydrate formation experiment at the constant
216
temperature of 275 K (Fig. 2), where the total pressure drop achieved after 1200 minutes was
217
around 2 bar. The complete dissolution of CO2 in water inside silica gel pores was observed after
218
the pressure dropped approximately to 33.8 bar. As seen in Fig. 2, the first 120 minutes showed
219
two stages of pressure drop. Point a-c is considered the first stage of pressure drop. Initially, a
220
pressure drop from point a-b indicates that the dissolution of CO2 in water happened around 5
221
minutes in which Sloan and Koh [42] stated that upon dissolution of gas in water, labile clusters
222
form immediately. Concurrently, labile clusters started to agglomerate by sharing faces, thus
223
increasing disorder which explained the little rise in pressure from point b-c. This process
224
continued until the size of the cluster agglomerate reached a critical value at point c, wherein Sloan
225
and Koh [42] said this was the point where primary nucleation happens. Also, Tang et al. 3 Results and discussion
201 Moreover, the fast
227
induction time observed in this work was almost less than 10 minutes by employing FBR this
228
agrees with the one reported in the literature [18, 43, 44]. Then, the second stage of pressure drop
229
was observed immediately after point c and this significant pressure drop is known as the hydrate
230
growth stage. From point c-d sudden decrease in pressure was observed which is expected due to
231
the availability of enough driving force required for the growth of hydrate. Thus, the significant
232
two-stage pressure drop observed in the initial stage (the first 20 minutes) before being followed
233
by the second small pressure drop (until 100 minutes) until almost no more drop in pressure was
234 10 observed in batch FBR as indicated by point e, could be a basic guideline to determine the
235
formation of CO2 hydrate and CO2 dissolution in water. After point e, several stages of pressure
236
drop were observed for the sample before it became a plateau. For the sample prepared by the
237
highest rates of stirring, the pressure became constant approximately after 700 minutes. Moreover,
238
the growth of hydrate and the fast induction time around 5–10 minutes for hydrate formation
239
validates by different studies conducted in the literature [18, 40, 41]. Since the formation of hydrate
240
was justified, next to the study on final water to hydrate conversion, CO2 uptake and rate of hydrate
241
formation are presented in the next section. 242 observed in batch FBR as indicated by point e, could be a basic guideline to determine the
235
formation of CO2 hydrate and CO2 dissolution in water. After point e, several stages of pressure
236
drop were observed for the sample before it became a plateau. For the sample prepared by the
237
highest rates of stirring, the pressure became constant approximately after 700 minutes. Moreover,
238
the growth of hydrate and the fast induction time around 5–10 minutes for hydrate formation
239
validates by different studies conducted in the literature [18, 40, 41]. Since the formation of hydrate
240
was justified, next to the study on final water to hydrate conversion, CO2 uptake and rate of hydrate
241
formation are presented in the next section. 242 3.2 Integrated gasification combined cycle (IGCC) process
264 Generally, most of the literature has investigated CO2 hydrate formation from fuel gas mixture in
265
non-IGCC operating conditions whereas experiments performed in this work used the IGCC
266
conditions. Mostly, the operating conditions of the IGCC are in the range of 283–290 K and 20–
267
70 bar (fuel gas mixture) and are outside the hydrate forming conditions. The minimum pressure
268
required for CO2 hydrate to form at 283 K is 30 bar (pure CO2) as discovered by Servio and
269
Englezos, [40]. Nevertheless, the initial investigation on the implementation of promoters directed
270
our attention to the hydrate formation in non-hydrate forming conditions. Therefore, the focus of
271
the study was to obtain optimum hydrate formation in the IGCC operating conditions. Hence,
272
additional experimental parameters were investigated and reported which indicated that hydrate
273
formation is possible in IGCC conditions. The experimental parameters that were studied include
274
hydrate formation driving force (∆P) and various non-hydrate forming conditions (temperature
275
and pressure), especially in the IGCC conditions. 276 3.1 Hydrate formation analysis
243 In contrast, the solubility of CO2
260
in water reduced as the temperature increased in non-hydrate forming region. This trend was
261
comparable to the equilibrium mole fraction of CO2 in water as shown in the literature [46] which
262
explains the non-existence of hydrate at elevated temperature. 263 3.1 Hydrate formation analysis
243 Hydrate formation experiments were investigated in the HPVA by using a prepared sample with
244
approximately 0.50 g of wet silica. The hydration number of 5.75 [45] was used to calculate the
245
water conversion to hydrate as 6 water molecules are needed to form CO2 hydrate (CO2.6H2O). 246
The sample prepared by the highest rates of stirring had the maximum water conversion to hydrate
247
with a value of 40.50 ± 2.28 mol%. The amount of gas uptake was directly related to the amount
248
of water conversion to hydrate. Hence, the gas uptake obtained for the prepared sample was the
249
highest amount of CO2 molecules with a value of 0.29 mmol. Additionally, it was observed that
250
the sample with the greater equilibrium moisture contents yielded the maximum water conversion
251
to hydrate. 252 Hydrate formation experiments were investigated in the HPVA by using a prepared sample with
244
approximately 0.50 g of wet silica. The hydration number of 5.75 [45] was used to calculate the
245
water conversion to hydrate as 6 water molecules are needed to form CO2 hydrate (CO2.6H2O). 246
The sample prepared by the highest rates of stirring had the maximum water conversion to hydrate
247
with a value of 40.50 ± 2.28 mol%. The amount of gas uptake was directly related to the amount
248
of water conversion to hydrate. Hence, the gas uptake obtained for the prepared sample was the
249
highest amount of CO2 molecules with a value of 0.29 mmol. Additionally, it was observed that
250
the sample with the greater equilibrium moisture contents yielded the maximum water conversion
251
to hydrate. 252
253
Moreover, the sample prepared by the highest rates of stirring demonstrated the fastest kinetics in
254
which the initial rate of hydrate formation was more than 0.05 mmol of CO2/g of H2O/min. Overall,
255
the silica contacted with water from vigorous stirring showed the best results and reproducibility. 256
Thus, the silica contacted with water was used as a baseline result for comparison purposes. 257 11 Additionally, in the hydrate forming region, the equilibrium mole fraction of CO2 in water was
258
reduced as temperature decreased [40]. Thus, highest solubility of CO2 observed in the water at
259
lowest temperature that was due to the existence of CO2 hydrate. 3.3 Effect of driving forces in hydrate forming region
277 [48] studied the formation of hydrate in pure CO2 by using STR with SDS and
301 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability
281
achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5
282
and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the
283
investigations were performed in HPVA for 1200 minutes. Then, the results were compared with
284
the baseline experiment at various driving forces. 285 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability
281
achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5
282
and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the
283
investigations were performed in HPVA for 1200 minutes. Then, the results were compared with
284
the baseline experiment at various driving forces. 285 The comparison of hydrate formation at various driving forces is illustrated in Fig. 3 and Fig. 4. 287
Fig. 3 (a) and Fig. 3(b) shows that T3-2 had a highest water conversion to hydrate and CO2 uptake
288
at 275 K and 30 bar respectively followed by T1-5 and the baseline experiment. However, T1-5
289
demonstrated the best results at 275 K and 22 bar as shown in Fig. 4(a) and Fig. 4(b) with T3-2
290
and baseline experiment obtaining almost identical results. Table 2 summarizes the gas uptake
291
obtained by each sample at various operating pressures. Generally, the gas uptake for all samples
292
increased as the driving force (∆P) increased from 5 to 19 bar with T1-5 demonstrating the best
293
result at all driving force except at ∆P = 5 bar. Combined-promoters designated type T1-5 gives
294
the maximum value of CO2 uptake up to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased
295
from 5 to 19 bar at constant temperature (275 K) that is in accord with the results reported in the
296
literature [47]. Even though the gas uptake of T3-2 was the highest at this driving force which was
297
almost 0.50 mmol of CO2 per g of H2O higher than T1-5. The total CO2 molecules captured by
298
T1-5 was the highest (0.17 mmol) which was 0.03 mmol higher than T3-2. 3.3 Effect of driving forces in hydrate forming region
277 A study was performed to investigate the effect of driving force (∆P) on hydrate formation. Various
278
operating pressures (36, 30 and 22 bar) in pure CO2 gas were investigated at 275 K by employing
279
silica contacted with different combined-promoters. T1-5 and T3-2 (0.01 mol% SDS + 0.10 mol%
280 12 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability
281
achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5
282
and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the
283
investigations were performed in HPVA for 1200 minutes. Then, the results were compared with
284
the baseline experiment at various driving forces. 285
286
The comparison of hydrate formation at various driving forces is illustrated in Fig. 3 and Fig. 4. 287
Fig. 3 (a) and Fig. 3(b) shows that T3-2 had a highest water conversion to hydrate and CO2 uptake
288
at 275 K and 30 bar respectively followed by T1-5 and the baseline experiment. However, T1-5
289
demonstrated the best results at 275 K and 22 bar as shown in Fig. 4(a) and Fig. 4(b) with T3-2
290
and baseline experiment obtaining almost identical results. Table 2 summarizes the gas uptake
291
obtained by each sample at various operating pressures. Generally, the gas uptake for all samples
292
increased as the driving force (∆P) increased from 5 to 19 bar with T1-5 demonstrating the best
293
result at all driving force except at ∆P = 5 bar. Combined-promoters designated type T1-5 gives
294
the maximum value of CO2 uptake up to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased
295
from 5 to 19 bar at constant temperature (275 K) that is in accord with the results reported in the
296
literature [47]. Even though the gas uptake of T3-2 was the highest at this driving force which was
297
almost 0.50 mmol of CO2 per g of H2O higher than T1-5. The total CO2 molecules captured by
298
T1-5 was the highest (0.17 mmol) which was 0.03 mmol higher than T3-2. This is expected due
299
to the higher amount of available water molecules attained by T1-5, 1.30 mmol higher than T3-2. 300
In past, Silva et al. 3.3 Effect of driving forces in hydrate forming region
277 Hence, the results showed that
316
high operating pressure enhanced the formation of hydrate due to greater driving force (∆P). In
317
addition, different samples had diverse effects on hydrate formation at different driving forces. In
318
past, Kobayashi et al. [49] said a batch system is assumed to instantaneously keep itself in
319
thermodynamic equilibrium and Mori et al. [50] referenced that the change in gas phase
320
arrangement in batch mode is unavoidably convoyed by a change in the guest molecule
321
composition in an instantaneously formed hydrate. These can be associated with a decrease in
322
driving force in batch mode upon hydrate growth wherein in a pure CO2 system, this effect was
323
only observed when the initial operating pressure was below 30 bar. At high initial operating
324
pressure (36 bar), a massive ratio of CO2 to water molecules was expected to provide an extra
325
driving force, which explained the high CO2 uptake, obtained. 326 In contrast to T1-5, the total CO2 molecules captured by the baseline experiment were lower at all
312
driving forces even though the amount of water molecules available for hydrate formation was
313
higher than T1-5 by almost 0.50 mmol. However, the CO2 molecules captured by the baseline
314
experiment were higher than T3-2 at all driving forces except at ∆P = 13 bar. In addition, at this
315
medium driving force, T3-2 exhibited the closest result to T1-5. Hence, the results showed that
316
high operating pressure enhanced the formation of hydrate due to greater driving force (∆P). In
317
addition, different samples had diverse effects on hydrate formation at different driving forces. In
318
past, Kobayashi et al. [49] said a batch system is assumed to instantaneously keep itself in
319
thermodynamic equilibrium and Mori et al. [50] referenced that the change in gas phase
320
arrangement in batch mode is unavoidably convoyed by a change in the guest molecule
321
composition in an instantaneously formed hydrate. These can be associated with a decrease in
322
driving force in batch mode upon hydrate growth wherein in a pure CO2 system, this effect was
323
only observed when the initial operating pressure was below 30 bar. At high initial operating
324
pressure (36 bar), a massive ratio of CO2 to water molecules was expected to provide an extra
325
driving force, which explained the high CO2 uptake, obtained. 3.3 Effect of driving forces in hydrate forming region
277 This is expected due
299
to the higher amount of available water molecules attained by T1-5, 1.30 mmol higher than T3-2. 300
In past, Silva et al. [48] studied the formation of hydrate in pure CO2 by using STR with SDS and
301
THF as promoters. They inferred that if just SDS was utilized, clathrate hydrate was formed in a
302
traditional manner yet when THF was combined with SDS in an ideal extent, it was possible to
303 13 13 observe crystals of THF hydrate which stabilized the framework and acted as a promoter of CO2
304
hydrate. Moreover, Yang et al. [39] performed a study on phase equilibrium for the THF-CO2-
305
H2O system which showed a drastic decrease in pressure in the presence of 3.00 mol% THF and
306
SDS (at all concentrations). Also, the highest equilibrium temperature obtained was 291.55 K at
307
30 bar in the presence of 3.0 mol% THF and 0 mg/L SDS respectively. The experiments on hydrate
308
formation have indicated that CO2 hydrate forms rapidly at all experimental pressures when the
309
SDS concentration is 1000 ppm which indicates that SDS enhances the hydrate formation rate. 310
311 observe crystals of THF hydrate which stabilized the framework and acted as a promoter of CO2
304
hydrate. Moreover, Yang et al. [39] performed a study on phase equilibrium for the THF-CO2-
305
H2O system which showed a drastic decrease in pressure in the presence of 3.00 mol% THF and
306
SDS (at all concentrations). Also, the highest equilibrium temperature obtained was 291.55 K at
307
30 bar in the presence of 3.0 mol% THF and 0 mg/L SDS respectively. The experiments on hydrate
308
formation have indicated that CO2 hydrate forms rapidly at all experimental pressures when the
309
SDS concentration is 1000 ppm which indicates that SDS enhances the hydrate formation rate. 310
311
In contrast to T1-5, the total CO2 molecules captured by the baseline experiment were lower at all
312
driving forces even though the amount of water molecules available for hydrate formation was
313
higher than T1-5 by almost 0.50 mmol. However, the CO2 molecules captured by the baseline
314
experiment were higher than T3-2 at all driving forces except at ∆P = 13 bar. In addition, at this
315
medium driving force, T3-2 exhibited the closest result to T1-5. 3.3 Effect of driving forces in hydrate forming region
277 326 14 3.3.1 Kinetic additives effect of hydrate formation
327 3.3.1 Kinetic additives effect of hydrate formation
327
Generally, an increase in the driving force increases the gas uptake and kinetic rate of hydrate
328
formation. Fig. 5 illustrates that the initial rate of clathrate formation of T3-2 at 275 K and 30 bar
329
was the fastest that was 13% greater than T1-5 and almost 70% faster than the baseline experiment. 330
However, the initial rate of clathrate formation at 275 K and 22 bar as shown in Fig. 6 was the
331
fastest for T1-5 with the value of 0.012 mmol of CO2 per g of H2O per min followed by T3-2
332
(0.005 mmol of CO2 per g of H2O per min) and baseline experiment (0.004 mmol of CO2 per g of
333
H2O per min). TBAB inhibit the hydrate formation but the combining promoter SDS used in the
334
formation of T3-2 mitigate the inhibition effect of TBAB on hydrate formation only to some extent. 335
Therefore, the rate of hydrate formation and CO2 uptake of T3-2 is lower than that of T1-5. In view
336
of these observations, it was inferred that THF displayed the quickest kinetics when it is joined
337
with SDS of 0.01 mol%, practically more than half (50%) a solitary promoter alone at a similar
338
concentration. In this way, it was affirmed that 0.01 mol% of SDS joined with THF gave the most
339
maximum rate of clathrate formation and also CO2 uptake due to reinforcing combined effect of
340
promoters. Hence, T1-5 was proved to be the best option for hydrate formation at low driving
341
force. These findings are in concurrence with the consequences of Kang et al. [51] who
342
investigated the formation of hydrate in bulk water (cluster of water molecules) at different
343
pressure and found that CO2 uptakes increase as the operating pressure increased. In contrast,
344
Zheng et al. [29] studied CO2 semi clathrate formation under various concentration of promoters
345
in HBGS at a driving temperature and reported that the CO2 uptakes increase as the operating
346
temperature sets up to 4.1 K. Thus, as ∆P increases or as ∆T decreases, the driving force also
347
increases that indicates the successful formation of CO2 hydrate. 348 Generally, an increase in the driving force increases the gas uptake and kinetic rate of hydrate
328
formation. Fig. 3.4 Enhanced hydrate formation in non-hydrate forming region
349 3.4 Enhanced hydrate formation in non-hydrate forming region
349
The use of promoters could enhance hydrate formation as the baseline experiment did not show
350
any hydrate formation at 288 K and 36 bar. Each promoter was extensively investigated by
351
previous researchers where SDS [41] can avoid the development of obstructing hydrate film whilst
352
TBAB [35] and THF [43] can form semi-clathrate and sII hydrates respectively. Both types of
353
hydrate are said to entrap more CO2 molecules in the small cage of sII hydrate and semi-clathrate
354
hydrate cavities correspondingly [52]. Moreover, several researchers [53, 54] have investigated
355
the effect of combining SDS and THF on CO2 hydrate formation and they discovered that the
356
synergic effect improves hydrate formation. 357
358
However, the synergic effect of combining SDS and TBAB has not yet been reported in the
359
literature. Herein, the hydrate formation is investigated in non-hydrate forming region at 36 bar
360
and various operating temperatures by employing pure CO2 gas and novel combined-promoters. 361
Yang et al. [39] plotted the phase equilibrium of hydrate formation in pure CO2 gas system and
362
showed that at 36 bar, the equilibrium temperature was 280 K. In this study, the operating
363
temperature of 288 K led to the driving force of ∆T = 8 K and for 293 K, ∆T = 13 K. Unlike ∆P,
364
the highest value of ∆T was equivalent to the lowest driving force available for the system because
365
the operating conditions could be shifted to the right-hand side of phase equilibrium, also known
366
as the non-hydrate forming region. This study was then used as a basis for the investigation of
367
hydrate formation at IGCC plant operating conditions. 368
3.4.1 Combined promoters effect at various driving forces
369
Further investigation was performed by employing three combined-promoters (T1-5, T3-2 and
370 The use of promoters could enhance hydrate formation as the baseline experiment did not show
350
any hydrate formation at 288 K and 36 bar. Each promoter was extensively investigated by
351
previous researchers where SDS [41] can avoid the development of obstructing hydrate film whilst
352
TBAB [35] and THF [43] can form semi-clathrate and sII hydrates respectively. Both types of
353
hydrate are said to entrap more CO2 molecules in the small cage of sII hydrate and semi-clathrate
354
hydrate cavities correspondingly [52]. 3.4 Enhanced hydrate formation in non-hydrate forming region
349 Moreover, several researchers [53, 54] have investigated
355
the effect of combining SDS and THF on CO2 hydrate formation and they discovered that the
356
synergic effect improves hydrate formation. 357 However, the synergic effect of combining SDS and TBAB has not yet been reported in the
359
literature. Herein, the hydrate formation is investigated in non-hydrate forming region at 36 bar
360
and various operating temperatures by employing pure CO2 gas and novel combined-promoters. 361
Yang et al. [39] plotted the phase equilibrium of hydrate formation in pure CO2 gas system and
362
showed that at 36 bar, the equilibrium temperature was 280 K. In this study, the operating
363
temperature of 288 K led to the driving force of ∆T = 8 K and for 293 K, ∆T = 13 K. Unlike ∆P,
364
the highest value of ∆T was equivalent to the lowest driving force available for the system because
365
the operating conditions could be shifted to the right-hand side of phase equilibrium, also known
366
as the non-hydrate forming region. This study was then used as a basis for the investigation of
367
hydrate formation at IGCC plant operating conditions. 368 3.3.1 Kinetic additives effect of hydrate formation
327 5 illustrates that the initial rate of clathrate formation of T3-2 at 275 K and 30 bar
329
was the fastest that was 13% greater than T1-5 and almost 70% faster than the baseline experiment. 330
However, the initial rate of clathrate formation at 275 K and 22 bar as shown in Fig. 6 was the
331
fastest for T1-5 with the value of 0.012 mmol of CO2 per g of H2O per min followed by T3-2
332
(0.005 mmol of CO2 per g of H2O per min) and baseline experiment (0.004 mmol of CO2 per g of
333
H2O per min). TBAB inhibit the hydrate formation but the combining promoter SDS used in the
334
formation of T3-2 mitigate the inhibition effect of TBAB on hydrate formation only to some extent. 335
Therefore, the rate of hydrate formation and CO2 uptake of T3-2 is lower than that of T1-5. In view
336
of these observations, it was inferred that THF displayed the quickest kinetics when it is joined
337
with SDS of 0.01 mol%, practically more than half (50%) a solitary promoter alone at a similar
338
concentration. In this way, it was affirmed that 0.01 mol% of SDS joined with THF gave the most
339
maximum rate of clathrate formation and also CO2 uptake due to reinforcing combined effect of
340
promoters. Hence, T1-5 was proved to be the best option for hydrate formation at low driving
341
force. These findings are in concurrence with the consequences of Kang et al. [51] who
342
investigated the formation of hydrate in bulk water (cluster of water molecules) at different
343
pressure and found that CO2 uptakes increase as the operating pressure increased. In contrast,
344
Zheng et al. [29] studied CO2 semi clathrate formation under various concentration of promoters
345
in HBGS at a driving temperature and reported that the CO2 uptakes increase as the operating
346
temperature sets up to 4.1 K. Thus, as ∆P increases or as ∆T decreases, the driving force also
347
increases that indicates the successful formation of CO2 hydrate. 348 15 3.4.1 Combined promoters effect at various driving forces
369 Further investigation was performed by employing three combined-promoters (T1-5, T3-2 and
370
T1A-2) at the 288 K and 36 bar operating conditions. Then, T1-5 and T3-2 were employed for the
371 16 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of
372
silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the
373
conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result
374
with around 10 mol% conversion. This was followed by T1-5 and THF with both having a
375
conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both
376
conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported
377
here are in accordance with the results reported in the literature [47]. Fig. 7 (b) and Table 3 show
378
that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of
379
H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O),
380
T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381
382
The results showed that by adding THF, TBAB and EGME to SDS, water conversion to the
383
clathrate formation and the maximum gas uptake was increased accordingly. Significant
384
improvement was observed when 5.60 mol% THF was added to 0.01 mol% SDS with almost
385
double gas uptake obtained as compared to SDS (0.01 mol%) alone. In addition, during the study
386
of hydrate phase equilibria of mixed hydrates having CO2 and N2, the gas uptake for 3 mol% THF
387
alone was almost comparable to T1-5 which showed that THF was a very good promoter for
388
hydrate formation at high temperature [55]. The same trend was observed for T3-2 in which 0.10
389
mol% TBAB was added to 0.01 mol% SDS. However, 0.1 mol% EGME only showed a minimal
390
effect on hydrate formation when it was added to 0.01 mol% SDS. Based on the results obtained
391
at these operating conditions, T1-5 and T3-2 were further investigated at 293 K and 36 bar. Fig. 3.4.1 Combined promoters effect at various driving forces
369 8
392
(a) also demonstrates that T3-2 had the best water conversion to water entrapped clathrate with a
393
conversion of around 6 mol% at temperature of 293 K and pressure of 36 bar. This was followed
394 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of
372
silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the
373
conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result
374
with around 10 mol% conversion. This was followed by T1-5 and THF with both having a
375
conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both
376
conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported
377
here are in accordance with the results reported in the literature [47]. Fig. 7 (b) and Table 3 show
378
that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of
379
H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O),
380
T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of
372
silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the
373
conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result
374
with around 10 mol% conversion. This was followed by T1-5 and THF with both having a
375
conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both
376
conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported
377
here are in accordance with the results reported in the literature [47]. Fig. 3.4.1 Combined promoters effect at various driving forces
369 As
402
a result, fewer CO2 molecules were consumed in hydrate formation at 288 K for T3-2, which was
403
0.02 mmol less than T1-5. Moreover, slightly high error bars for T3-2 observed at these operating
404
conditions, were due to regeneration experiment performed by reusing the same sample. However,
405
other regeneration experiments demonstrated quite high regeneration values as shown in Table 3. 406
Finally, the CO2 molecules captured at 293 K were comparable for both samples which showed
407
that THF and TBAB demonstrated the same effect at this operating temperature. 408 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03
395
CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396
However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows
397
consistency within the estimated uncertainties of reported results. 398 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03
395
CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396
However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows
397
consistency within the estimated uncertainties of reported results. 398 The same trend was observed at both operating temperatures due to high equilibrium moisture
400
content in T1-5 which was 50% higher than T3-2. Thus, T3-2 demonstrated the highest water
401
conversion to hydrate as compared to T1-5 due to lower water presence inside silica gel pores. As
402
a result, fewer CO2 molecules were consumed in hydrate formation at 288 K for T3-2, which was
403
0.02 mmol less than T1-5. Moreover, slightly high error bars for T3-2 observed at these operating
404
conditions, were due to regeneration experiment performed by reusing the same sample. However,
405
other regeneration experiments demonstrated quite high regeneration values as shown in Table 3. 406
Finally, the CO2 molecules captured at 293 K were comparable for both samples which showed
407
that THF and TBAB demonstrated the same effect at this operating temperature. 408 3.4.1 Combined promoters effect at various driving forces
369 7 (b) and Table 3 show
378
that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of
379
H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O),
380
T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381 The results showed that by adding THF, TBAB and EGME to SDS, water conversion to the
383
clathrate formation and the maximum gas uptake was increased accordingly. Significant
384
improvement was observed when 5.60 mol% THF was added to 0.01 mol% SDS with almost
385
double gas uptake obtained as compared to SDS (0.01 mol%) alone. In addition, during the study
386
of hydrate phase equilibria of mixed hydrates having CO2 and N2, the gas uptake for 3 mol% THF
387
alone was almost comparable to T1-5 which showed that THF was a very good promoter for
388
hydrate formation at high temperature [55]. The same trend was observed for T3-2 in which 0.10
389
mol% TBAB was added to 0.01 mol% SDS. However, 0.1 mol% EGME only showed a minimal
390
effect on hydrate formation when it was added to 0.01 mol% SDS. Based on the results obtained
391
at these operating conditions, T1-5 and T3-2 were further investigated at 293 K and 36 bar. Fig. 8
392
(a) also demonstrates that T3-2 had the best water conversion to water entrapped clathrate with a
393
conversion of around 6 mol% at temperature of 293 K and pressure of 36 bar. This was followed
394 17 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03
395
CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396
However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows
397
consistency within the estimated uncertainties of reported results. 398
399
The same trend was observed at both operating temperatures due to high equilibrium moisture
400
content in T1-5 which was 50% higher than T3-2. Thus, T3-2 demonstrated the highest water
401
conversion to hydrate as compared to T1-5 due to lower water presence inside silica gel pores. 3.4.2 Kinetic additives effect of hydrate formation
409 The
432
effect of promoters in mitigating hydrate phase equilibria to the hydrate forming region was
433
explained earlier in which THF and TBAB are known as thermodynamic promoters due to their
434
ability to form sII and semi-clathrate hydrates respectively that attracted more CO2 molecules to
435
get involved in hydrate formation. Thus, this was the reason CO2 uptake was almost 2 mmol of
436
CO2 per g of H2O when T1-5 and T3-2 combined-promoters were employed in FBR. Therefore,
437
at 293 K temperature and pressure condition of 36 bar, T1-5 and T3-2 demonstrated almost
438
comparable rates of hydrate formation as illustrated in Fig. 10. This indicated that at high
439
temperature, TBAB was the best alternative to THF to be employed together with SDS. 440 CO2 molecules for occupancy in small cages. The role of TBAB in T3-2 combined-promoter
418
provided more cavities for the occupancy of CO2 molecules by forming semi-clathrate hydrate. 419
Moreover, the ability of TBAB to readily form semi-clathrate hydrate in hydrate forming
420
conditions caused TBA+ to occupy large cage leaving the small cages empty/partially empty which
421
reduced the formation of CO2 hydrate to 0.29 mol% of TBAB. Another EGME promoter was
422
considered as an alternative to THF due to the ability of EGME molecules to act as structure maker
423
solutes when dissolved in water. However, the gas uptake of EGME containing T1A-2 sample was
424
just 9% lower than T1-5 and the total CO2 molecules consumed was only 0.05 mmol lower. 425
Therefore the initial kinetics of the sample that employed THF alone were faster than T3-2 and
426
T1A-2 and slightly slower than T1-5 which showed that THF was the best promoter to be
427
combined with SDS for enhancing clathrate formation. Even though the hydrate phase equilibrium
428
mitigated the hydrate forming region with the presence of combined-promoters, it significantly
429
affects CO2 uptake and hydrate formation if temperature and pressure conditions changed below
430
or above to their respective optimum range. The hydrate phase equilibria promoting the lower
431
pressure and high temperature regions when the thermodynamic promoters were introduced. 3.4.2 Kinetic additives effect of hydrate formation
409 Fig. 9 illustrates the rate of clathrate formation at 288 K and 36 bar where the addition of 5.60
410
mol% THF to form T1-5 significantly increased the initial kinetics of silica contacted with single
411
SDS (0.01 mol%) from 0.005 to 0.015 mmol of CO2 per g of H2O per min. Moreover, the addition
412
of 0.10 mol% TBAB and 0.10 mol% EGME in 0.01 mol% SDS also doubled the initial rate of
413
hydrate formation for single SDS as illustrated by T3-2 and T1A-2 respectively. These indicated
414
that the combination of other promoters with SDS enhanced the kinetics of hydrate formation
415
known as a synergic effect. The synergic effect of T1-5 was obtained from SDS which avoided
416
the development of obstructing hydrate film whilst THF formed sII hydrate which attracted more
417 18 CO2 molecules for occupancy in small cages. The role of TBAB in T3-2 combined-promoter
418
provided more cavities for the occupancy of CO2 molecules by forming semi-clathrate hydrate. 419
Moreover, the ability of TBAB to readily form semi-clathrate hydrate in hydrate forming
420
conditions caused TBA+ to occupy large cage leaving the small cages empty/partially empty which
421
reduced the formation of CO2 hydrate to 0.29 mol% of TBAB. Another EGME promoter was
422
considered as an alternative to THF due to the ability of EGME molecules to act as structure maker
423
solutes when dissolved in water. However, the gas uptake of EGME containing T1A-2 sample was
424
just 9% lower than T1-5 and the total CO2 molecules consumed was only 0.05 mmol lower. 425
Therefore the initial kinetics of the sample that employed THF alone were faster than T3-2 and
426
T1A-2 and slightly slower than T1-5 which showed that THF was the best promoter to be
427
combined with SDS for enhancing clathrate formation. Even though the hydrate phase equilibrium
428
mitigated the hydrate forming region with the presence of combined-promoters, it significantly
429
affects CO2 uptake and hydrate formation if temperature and pressure conditions changed below
430
or above to their respective optimum range. The hydrate phase equilibria promoting the lower
431
pressure and high temperature regions when the thermodynamic promoters were introduced. 3.4.2 Kinetic additives effect of hydrate formation
409 The
432
effect of promoters in mitigating hydrate phase equilibria to the hydrate forming region was
433
explained earlier in which THF and TBAB are known as thermodynamic promoters due to their
434
ability to form sII and semi-clathrate hydrates respectively that attracted more CO2 molecules to
435
get involved in hydrate formation. Thus, this was the reason CO2 uptake was almost 2 mmol of
436
CO2 per g of H2O when T1-5 and T3-2 combined-promoters were employed in FBR. Therefore,
437
at 293 K temperature and pressure condition of 36 bar, T1-5 and T3-2 demonstrated almost
438
comparable rates of hydrate formation as illustrated in Fig. 10. This indicated that at high
439
temperature, TBAB was the best alternative to THF to be employed together with SDS. 440 19 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC
441
conditions
442
One of the most important findings in this work was the ability of combined-promoters to shift the
443
hydrate phase equilibrium to a higher operating temperature. Fig. 11 demonstrates the hydrate
444
phase equilibrium for pure CO2. As the use of solid adsorbent for hydrate formation will lead to
445
the use of a fluidized bed reactor (FBR). Previously, some works on the application of FBR by
446
using pure CO2 gas were performed by Yang et al. [39, 52], Mekala et al. [56] and Kumar et al. 447
[37]. Kumar et al. [37] and Mekala et al. [56] investigated FBR (also known as HPVA) in which
448
0.25 mm silica gel and 0.46 mm silica sand (particle sizes) were employed respectively with no
449
improvement in hydrate phase equilibrium compared to bulk water [57] as shown in Fig. 11. 450
451 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC
441
conditions
442
One of the most important findings in this work was the ability of combined-promoters to shift the
443
hydrate phase equilibrium to a higher operating temperature. Fig. 11 demonstrates the hydrate
444
phase equilibrium for pure CO2. As the use of solid adsorbent for hydrate formation will lead to
445
the use of a fluidized bed reactor (FBR). Previously, some works on the application of FBR by
446
using pure CO2 gas were performed by Yang et al. [39, 52], Mekala et al. [56] and Kumar et al. 447
[37]. Kumar et al. [37] and Mekala et al. 3.4.2 Kinetic additives effect of hydrate formation
409 [56] investigated FBR (also known as HPVA) in which
448
0.25 mm silica gel and 0.46 mm silica sand (particle sizes) were employed respectively with no
449
improvement in hydrate phase equilibrium compared to bulk water [57] as shown in Fig. 11. 450
451 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC
441
conditions
442 However, Yang et al. [39, 52] managed to prove that the application of combined-promoters at
452
optimum concentrations with 3 mol% of THF + 0.01 mol% SDS and equivalent concentration of
453
THF + TBAB inside glass bead pores shifted the phase equilibrium to a higher temperature region
454
(290 and 291 K respectively). In addition, Yang et al. [52] also discovered that both THF and
455
TBAB showed the same role in thermodynamically shifting the phase equilibrium to a higher
456
temperature region. At the same concentration of TBAB (5 mol%), the temperature increased from
457
286 to 291 K at operating pressure of 35 bar as the concentration of THF increased from 0–5
458
mol%. Also, at the same concentration of THF (5 mol%) and 35 bar, the temperature was observed
459
to increase from 289 to 291 K as the concentration of TBAB increased from 0–5 mol%. 460 Moreover, Joshi et al. [58] reported that the addition of SDS did not mitigate the phase equilibrium
462
of CO2 -TBAB-H2O system while Yang et al. [52] mentioned that SDS is known as a kinetic
463
additive which can change the kinetic properties and has no influence on the hydrate phase
464 Moreover, Joshi et al. [58] reported that the addition of SDS did not mitigate the phase equilibrium
462
of CO2 -TBAB-H2O system while Yang et al. [52] mentioned that SDS is known as a kinetic
463
additive which can change the kinetic properties and has no influence on the hydrate phase
464 20 equilibrium [59]. Thus, the presence of thermodynamic promoters i.e. THF and TBAB in
465
combined type promoters T1-5 and T3-2 respectively inside silica gel in this work (Table 1)
466
promoted the phase equilibrium to 293 K and not the existence of 0.01 mol% SDS. Furthermore,
467
the R square value of this study, interpreting from the fitness of data set, shows more goodness of
468
fit with the value of 0.96 in comparison to the studies reported in the literature (Fig. 11). 469 4 Additives effect for CO2 hydrate formation
470 In past, massive efforts have been done to enhance the driving forces and gas uptake of CO2
471
hydrate formation by adding different thermodynamic and kinetic additives such as THF, SDS,
472
tetra-butyl ammonium salts and Cyclopentane so that it can readily be applied for pre-combustion
473
capture. THF and SDS can be effectively used to mitigate hydrate formation conditions, promote
474
hydrate growth rate and improve separation efficiency. Ricaurte et al. [54] studied the effect of
475
several additives on CO2 hydrate formation in which SDS was paired with one of the
476
thermodynamic promoters (THF, 1,3-dioxolane, 2-methyl-THF and CP) and THF was paired with
477
one of the kinetic promoters (SDS, SDBS and DATCI). The results highlight that the combination
478
of SDS and THF was the best for the formation of CO2 hydrate from natural gas. However, Torre
479
et al. [53] mentioned that the combination of THF and SDS compared to the single promoter was
480
very advantageous in accelerating hydrate. Herslund et al. [60] presented new equilibrium data for
481
the quaternary system H2O-THF-CP-CO2 which lowers equilibrium pressure of the system by 25-
482
30% due to the formation of CP and THF hydrates simultaneously. Li et al. [61] discovered that
483
the addition of CP into a TBAB solution remarkably enhanced the CO2 separation and speed up
484
the hydrate nucleation rate. While Yang et al. [52] performed a hydrate phase equilibrium
485
investigation on various combinations of THF and TBAB concentrations in pure CO2 gas system
486
and found that the THF-TBAB system greatly shifted the hydrate phase equilibrium to the higher
487 21 temperature region around 291 K at an operating pressure of 42 bar. In spite of great advancement
488
in the study of additives, the investigations are limited to the application inside stirred tank reactor. 489
Therefore, some works must have been done to investigate the synergic effect of additives so that
490
the system can readily be applied in IGCC conditions and this study successfully finds a solution
491
and a way forward to utilize novel T1A-2 and T3-2 promoters in IGCC condition. 492
493 5 Conclusions
494 Three novel combined promoters namely T1-5, T3-2 and T1A-2 were investigated. The effect of
495
these combined promoters and various driving forces on the formation of CO2 hydrates were
496
successfully investigated in IGCC conditions. Overall, the gas uptake for all samples in hydrate
497
forming conditions increased as the driving force (∆P) of the pure CO2 system increased. 498
Combined-promoters designated type T1-5 demonstrated the best result with the value of CO2
499
uptake increasing from 0.86 ± 0.09 to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased
500
from 5 to 19 bar at constant temperature (275 K). In contrast, the gas uptake was reduced from
501
5.95 ± 0.21 to 0.45 ± 0.07 mmol of CO2 per g of H2O as ∆T increased from -5 to 13 K at constant
502
pressure (36 bar). In general, the amount of available water inside silica gel pores determined total
503
number of CO2 molecules captured through hydrate formation. Combined-promoters designated
504
type T3-2 captured the fewest CO2 molecules at all driving forces due to the lowest amount of
505
available moisture content. However, T3-2 achieved an optimum result at CO2 partial pressure of
506
30 bar (identical to the IGCC operating pressure of 70 bar) where the total number of CO2
507
molecules captured were 0.01 mmol higher than the baseline experiment (0.13 mmol) due to
508
synergic effect. Thus, the study on non-hydrate forming region by employing pure CO2 gas led to
509
the selection of 283 K and 36 bar as the operating conditions in IGCC by employing pure CO2
510 22 wherein combined-promoters designated types T3-2 were chosen as an adsorbent to enhance CO2
511
capture by HBGS technique. Conclusively these results recommend that several improvements
512
can be considered to improve hydrate formation in the IGCC conditions by considering different
513
factors that were discussed in this work. In future, the study on the selectivity of CO2 gas molecules
514
towards hydrate formation in fuel gas mixture by gas chromatography (GC) analysis and the
515
improvement of reactor configuration by employing macroporous or mesoporous silicas (silica
516
sand or gel) with combined-promoters are suggested. 517 wherein combined-promoters designated types T3-2 were chosen as an adsorbent to enhance CO2
511
capture by HBGS technique. References
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494 Conclusively these results recommend that several improvements
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513
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514
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improvement of reactor configuration by employing macroporous or mesoporous silicas (silica
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674
energy, 37 (2012) 720-727. 675 27 27 List of Tables List of Tables Table 1. The amount of promoters used to prepare each combined-promoter (brief description of each code
T1-5, T3-2 and T1A-2). Table 1. The amount of promoters used to prepare each combined-promoter (brief description of each code
T1-5, T3-2 and T1A-2). No. Type of
combined-
promoter
Concentration and mass of promoter
Mass of
water
(g)
THF
SDS
TBAB
EGME
mol%
g
mol%
g
mol%
g
mol%
g
1
T1-5
5.60
9.11
0.01
0.07
-
-
-
-
38.39
2
T3-2
-
-
0.01
0.08
0.10
0.84
-
-
46.66
3
T1A-2
-
-
0.01
0.08
-
-
0.10
0.23
47.26 Table 1. The amount of promoters used to prepare each combined-promoter (brief descripti
T1-5, T3-2 and T1A-2). nt of promoters used to prepare each combined-promoter (brief description of each code
A-2) 28 28 Table 2. Comparison of gas uptake for T1-5, T3-2 and baseline experiment at 275 K and 36, 30 and 22 bar in 1200 minutes. Operating
conditions
Sample
Exp. No. No. r regeneration experiment References
519 of
moles of
water
(mmol)
CO2
formed in
hydrate
(mmol)
Mean CO2
formed in
hydrate
(mmol)
CO2 uptake
(mmol of
CO2/g of
H2O)
Mean CO2
uptake (mmol of
CO2/g of H2O)
(90% CI)
SD
275 K and 36
bar
T1-5
1
3.70
0.39
0.40
5.82
5.95 ± 0.21
0.18
2
3.70
0.41
6.08
T3-2
1
2.40
0.23
0.24
5.36
5.57 ± 0.34
0.29
2
2.40
0.25
5.77
SiG-
H2O
1
4.10
0.29
0.31
3.93
4.04 ± 0.17
0.15
2
4.30
0.32
4.14
275 K and 30
bar
T1-5
1
3.70
0.15
0.17
2.62
2.81 ± 0.30
0.26
2
3.70
0.18
2.99
T3-2
1
2.40
0.13
0.14
3.09
3.28 ± 0.31
0.27
2
2.40
0.15
3.47
SiG-
H2O
1
4.20
0.14
0.13
1.82
1.71 ± 0.19
0.16
2
4.10
0.12
1.60
275 K and 22
bar
T1-5
1
3.70
0.05
0.05
0.91
0.86 ± 0.09
0.08
2
3.70
0.04
0.80
T3-2
1
2.40
0.01
0.01
0.35
0.30 ± 0.09
0.08
2
2.40
0.01
0.24
SiG-
H2O
1
4.10
0.02
0.03
0.28
0.32 ± 0.06
0.05
2
4.20
0.03
0.35 1-5, T3-2 and baseline experiment at 275 K and 36, 30 and 22 bar in 1200 minutes. 29 Table 3. The comparison of gas uptake at 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. Operating
conditions
Sample
Exp. No. No. of
moles of
water
(mmol)
CO2
formed in
hydrate
(mmol)
Mean CO2
formed in
hydrate (mmol)
Water
conversion
to hydrate
(mol%)
Mean water
conversion
to hydrate
(mol%)
CO2 uptake
(mmol of
CO2/g of
H2O)
Mean CO2
uptake
(mmol of
CO2/g of
H2O)
(90% CI)
SD
288 K and
36 bar
T1-5
1
3.70
0.07
0.07
1.26
1.25 ± 0.01
0.01
2 r
3.70
0.07
1.24
T3-2
1
2.40
0.05
0.05
1.12
1.00 ± 0.20
0.17
2r
2.40
0.04
0.88
T1A-2
1
3.50
0.05
0.05
0.76
0.68 ± 0.13
0.11
2 r
3.50
0.04
0.60
SiG-
THF
1
3.50
0.06
0.07
1.17
1.15 ± 0.03
0.03
2
3.50
0.07
1.13
SiG-
SDS
1
3.70
0.04
0.04
0.62
0.66 ± 0.06
0.05
2
3.60
0.04
0.69
293 K and
36 bar
T1-5
1
3.70
0.02
0.02
0.41
0.45 ± 0.07
0.06
2 r
3.70
0.02
0.49
T3-2
1
2.40
0.02
0.03
0.41
0.42 ± 0.01
0.01
2
2.30
0.03
0.42
r
ti
i
t Table 3. References
519 The comparison of gas uptake at 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. 30 List of Figures Fig. 1. Schematic representation of HPVA for hydrate formation. Fig. 1. Schematic representation of HPVA for hydrate formation. 31 Fig. 2. P-t curves show 2-stage pressure drop in 1200 min for standard silica gel sample. Fig. 2. P-t curves show 2-stage pressure drop in 1200 min for standard silica gel sample. 32 32 32 Fig. 3. Comparison of experiments at 275 K and 30 bar in 1200 min; (a) Water convers
hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. Fig. 3. Comparison of experiments at 275 K and 30 bar in 1200 min; (a) Water conversion to
hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. 33 Fig. 4. Comparison of experiments at 275 K and 22 bar in 1200 min; (a) Water conversion
hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. Fig. 4. Comparison of experiments at 275 K and 22 bar in 1200 min; (a) Water conversion to
hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. 34 Fig. 5. Rate of hydrate formation at 275 K and 30 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2 and baseline experiment). Fig. 5. Rate of hydrate formation at 275 K and 30 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2 and baseline experiment). 35 35 35 Fig. 6. Rate of hydrate formation at 275 K and 22 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2 and baseline experiment). Fig. 6. Rate of hydrate formation at 275 K and 22 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2 and baseline experiment). 36 Fig. 7. The comparison of experiments at 288 K and 36 bar in 1200 min; (a) Water conversion
hydrate, (b) Gas uptake for T1-5, T3-2, T1-A and baseline. Fig. 7. The comparison of experiments at 288 K and 36 bar in 1200 min; (a) Water conversion to
hydrate, (b) Gas uptake for T1-5, T3-2, T1-A and baseline. 37 Fig. 8. The comparison of experiments at 293 K and 36 bar in 1200 min; (a) Water convers
hydrate, (b) Gas uptake for T1-5 and T3-2. Fig. 8. References
519 The comparison of experiments at 293 K and 36 bar in 1200 min; (a) Water conversion to
hydrate, (b) Gas uptake for T1-5 and T3-2. 38 Fig. 9. Rate of hydrate formation at 288 K and 36 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2, T1A-2 and baseline experiments). Fig. 9. Rate of hydrate formation at 288 K and 36 bar for 1200 minutes and inset for the first 150
minutes (T1-5, T3-2, T1A-2 and baseline experiments). 39 39 Fig. 10. Rate of hydrate formation at 293 K and 36 bar for 1200 minutes and inset for the first 500
minutes (T1-5 and T3-2). Fig. 10. Rate of hydrate formation at 293 K and 36 bar for 1200 minutes and inset for the first 500
minutes (T1-5 and T3-2). 40 Fig. 11. Comparison of hydrate phase equilibrium of pure CO2 gas of this study with Yang et al. [52], Yang et al. [39], Kumar et al. [37], Mekala et al. [56] and Carrol work [57]. Fig. 11. Comparison of hydrate phase equilibrium of pure CO2 gas of this study with Yang et al. [52], Yang et al. [39], Kumar et al. [37], Mekala et al. [56] and Carrol work [57]. 41 41 |
W264471300.txt | https://journals.iucr.org/e/issues/2009/02/00/at2706/at2706.pdf | en | 2-(2-Thienyl)-4,5-dihydro-1<i>H</i>-imidazole | Acta crystallographica. Section E | 2,009 | cc-by | 3,436 | addenda and errata
Acta Crystallographica Section E
Data collection
Structure Reports
Online
Bruker SMART APEXII CCD
area-detector diffractometer
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
Tmin = 0.825, Tmax = 0.922
ISSN 1600-5368
2-(2-Thienyl)-4,5-dihydro-1H-imidazole.
Corrigendum
Reza Kia,a‡ Hoong-Kun Funa*§ and Hadi Kargarb
28316 measured reflections
3100 independent reflections
3040 reflections with I > 2(I)
Rint = 0.021
Refinement
R[F 2 > 2(F 2)] = 0.027
wR(F 2) = 0.080
S = 1.15
3100 reflections
96 parameters
H atoms treated by a mixture of
independent and constrained
refinement
max = 0.52 e Å3
min = 0.24 e Å3
a
X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800
USM, Penang, Malaysia, and bDepartment of Chemistry, School of Science, Payame
Noor University (PNU), Ardakan, Yazd, Iran
Correspondence e-mail: hkfun@usm.my
Received 5 May 2009; accepted 18 May 2009
Key indicators: single-crystal X-ray study; T = 100 K; mean (C–C) = 0.001 Å;
R factor = 0.027; wR factor = 0.080; data-to-parameter ratio = 32.3.
Table 1
Hydrogen-bond geometry (Å, ).
D—H A
D—H
H A
D A
D—H A
N1—H1 N2i
C3—H3A N2i
0.857 (16)
0.95
2.130 (16)
2.59
2.9803 (10)
3.4815 (11)
171.5 (16)
156
Symmetry code: (i) x; y þ 12; z þ 12.
Consideration of a previous unrecognized twinning of the
original investigated crystal of the title compound [Kia et al.
(2009). Acta Cryst. E65, o301] led to improved reliability
factors and to a slightly higher precision for all geometric
parameters. The crystal under investigation was twinned by
pseudo-merohedry with [100, 010, 001] as the twin matrix and
a refined twin domain fraction of 0.9610 (5):0.0390 (5). The
results of the new crystal structure refinement are given here.
Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT
(Bruker, 2005); data reduction: SAINT; program(s) used to solve
structure: SHELXTL (Sheldrick, 2008); program(s) used to refine
structure: SHELXTL (Sheldrick, 2008); molecular graphics:
SHELXTL (Sheldrick, 2008); software used to prepare material for
publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek,
2009).
Supplementary data and figures for this paper are available from the
IUCr electronic archives (Reference: WM2233).
Experimental
References
Crystal data
C7H8N2S
Mr = 152.21
Monoclinic, P21 =c
a = 6.1321 (2) Å
b = 11.5663 (3) Å
c = 10.0098 (3) Å
= 90.154 (1)
V = 709.95 (4) Å3
Z=4
Mo K radiation
= 0.37 mm1
T = 100 K
0.54 0.28 0.22 mm
Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc. Madison,
Wisconsin, USA.
Kia, R., Fun, H.-K. & Kargar, H. (2009). Acta Cryst. E65, o301.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
Spek, A. L. (2009). Acta Cryst. D65, 148–155.
‡ Thomson Reuters ResearcherID: A-5471-2009.
§ Thomson Reuters ResearcherID: A-3561-2009.
Acta Cryst. (2009). E65, e15
doi:10.1107/S1600536809018790
Kia et al.
e15
supporting information
supporting information
Acta Cryst. (2009). E65, e15
[https://doi.org/10.1107/S1600536809018790]
2-(2-Thienyl)-4,5-dihydro-1H-imidazole. Corrigendum
Reza Kia, Hoong-Kun Fun and Hadi Kargar
2-(2-Thienyl)-4,5-dihydro-1H-imidazole
Crystal data
C7H8N2S
Mr = 152.21
Monoclinic, P21/c
Hall symbol: -P 2ybc
a = 6.1321 (2) Å
b = 11.5663 (3) Å
c = 10.0098 (3) Å
β = 90.154 (1)°
V = 709.95 (4) Å3
Z=4
F(000) = 320
Dx = 1.424 Mg m−3
Mo Kα radiation, λ = 0.71073 Å
Cell parameters from 9869 reflections
θ = 2.5–34.3°
µ = 0.37 mm−1
T = 100 K
Block, colourless
0.54 × 0.28 × 0.22 mm
Data collection
Bruker SMART APEXII CCD area-detector
diffractometer
Radiation source: fine-focus sealed tube
Graphite monochromator
φ and ω scans
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
Tmin = 0.825, Tmax = 0.922
28316 measured reflections
3100 independent reflections
3040 reflections with I > 2σ(I)
Rint = 0.021
θmax = 35.0°, θmin = 1.8°
h = −9→9
k = −18→17
l = −15→15
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.027
wR(F2) = 0.080
S = 1.15
3100 reflections
96 parameters
0 restraints
Primary atom site location: structure-invariant
direct methods
Acta Cryst. (2009). E65, e15
Secondary atom site location: difference Fourier
map
Hydrogen site location: inferred from
neighbouring sites
H atoms treated by a mixture of independent
and constrained refinement
w = 1/[σ2(Fo2) + (0.0391P)2 + 0.2148P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max = 0.001
Δρmax = 0.52 e Å−3
Δρmin = −0.24 e Å−3
sup-1
supporting information
Special details
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat
(Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full
covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and
torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry.
An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2,
conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used
only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2
are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
S1
N2
N1
C1
H1A
C2
H2A
C3
H3A
C4
C5
C6
H6A
H6B
C7
H7A
H7B
H1
x
y
z
Uiso*/Ueq
0.46976 (3)
0.06708 (11)
0.04589 (11)
0.63940 (14)
0.7552
0.58842 (14)
0.6646
0.40890 (13)
0.3524
0.32621 (12)
0.14267 (12)
−0.15422 (13)
−0.1723
−0.2848
−0.11001 (13)
−0.2425
−0.0643
0.058 (3)
0.141639 (18)
0.29657 (6)
0.30384 (6)
0.05379 (8)
0.0101
0.05399 (7)
0.0100
0.12729 (7)
0.1382
0.18073 (6)
0.26046 (6)
0.36275 (7)
0.4380
0.3144
0.37870 (7)
0.3611
0.4591
0.2686 (14)
0.59512 (2)
0.61145 (7)
0.83752 (7)
0.68566 (9)
0.6480
0.81867 (9)
0.8839
0.84861 (8)
0.9360
0.73587 (7)
0.72548 (7)
0.79460 (8)
0.8404
0.8103
0.64400 (8)
0.5911
0.6248
0.9125 (16)
0.01527 (6)
0.01355 (11)
0.01323 (11)
0.01780 (15)
0.021*
0.01659 (14)
0.020*
0.01337 (13)
0.016*
0.01149 (12)
0.01079 (11)
0.01479 (14)
0.018*
0.018*
0.01491 (13)
0.018*
0.018*
0.025 (4)*
Atomic displacement parameters (Å2)
S1
N2
N1
C1
C2
C3
C4
C5
C6
C7
U11
U22
U33
U12
U13
U23
0.01701 (9)
0.0150 (3)
0.0146 (3)
0.0174 (3)
0.0188 (3)
0.0164 (3)
0.0132 (3)
0.0119 (3)
0.0138 (3)
0.0147 (3)
0.01822 (10)
0.0168 (3)
0.0166 (3)
0.0179 (3)
0.0151 (3)
0.0128 (3)
0.0117 (3)
0.0114 (3)
0.0178 (3)
0.0179 (3)
0.01059 (9)
0.0088 (2)
0.0084 (2)
0.0181 (4)
0.0159 (3)
0.0109 (3)
0.0096 (3)
0.0090 (3)
0.0127 (3)
0.0121 (3)
0.00444 (6)
0.0027 (2)
0.0032 (2)
0.0052 (3)
0.0033 (3)
0.0005 (2)
0.0006 (2)
−0.0006 (2)
0.0027 (2)
0.0035 (2)
0.00195 (6)
−0.0001 (2)
0.0013 (2)
0.0000 (3)
−0.0028 (3)
−0.0005 (2)
0.0003 (2)
0.0006 (2)
0.0021 (2)
0.0001 (2)
−0.00027 (6)
0.0007 (2)
0.0004 (2)
−0.0017 (3)
0.0004 (2)
0.0004 (2)
−0.0002 (2)
−0.0005 (2)
0.0005 (2)
0.0020 (2)
Acta Cryst. (2009). E65, e15
sup-2
supporting information
Geometric parameters (Å, º)
S1—C1
S1—C4
N2—C5
N2—C7
N1—C5
N1—C6
N1—H1
C1—C2
C1—H1A
C2—C3
1.7120 (9)
1.7236 (8)
1.2996 (10)
1.4798 (11)
1.3657 (10)
1.4669 (11)
0.858 (16)
1.3684 (13)
0.9500
1.4221 (12)
C2—H2A
C3—C4
C3—H3A
C4—C5
C6—C7
C6—H6A
C6—H6B
C7—H7A
C7—H7B
0.9500
1.3819 (11)
0.9500
1.4586 (10)
1.5435 (12)
0.9900
0.9900
0.9900
0.9900
C1—S1—C4
C5—N2—C7
C5—N1—C6
C5—N1—H1
C6—N1—H1
C2—C1—S1
C2—C1—H1A
S1—C1—H1A
C1—C2—C3
C1—C2—H2A
C3—C2—H2A
C4—C3—C2
C4—C3—H3A
C2—C3—H3A
C3—C4—C5
C3—C4—S1
91.94 (4)
105.85 (6)
107.17 (6)
120.4 (11)
123.3 (11)
111.96 (6)
124.0
124.0
112.65 (7)
123.7
123.7
112.15 (7)
123.9
123.9
128.49 (7)
111.29 (6)
C5—C4—S1
N2—C5—N1
N2—C5—C4
N1—C5—C4
N1—C6—C7
N1—C6—H6A
C7—C6—H6A
N1—C6—H6B
C7—C6—H6B
H6A—C6—H6B
N2—C7—C6
N2—C7—H7A
C6—C7—H7A
N2—C7—H7B
C6—C7—H7B
H7A—C7—H7B
120.21 (5)
116.64 (7)
122.62 (7)
120.71 (6)
101.10 (6)
111.6
111.6
111.6
111.6
109.4
105.62 (6)
110.6
110.6
110.6
110.6
108.7
C4—S1—C1—C2
S1—C1—C2—C3
C1—C2—C3—C4
C2—C3—C4—C5
C2—C3—C4—S1
C1—S1—C4—C3
C1—S1—C4—C5
C7—N2—C5—N1
C7—N2—C5—C4
0.09 (7)
−0.35 (10)
0.50 (11)
179.29 (8)
−0.43 (9)
0.20 (7)
−179.55 (7)
0.30 (9)
−177.67 (7)
C6—N1—C5—N2
C6—N1—C5—C4
C3—C4—C5—N2
S1—C4—C5—N2
C3—C4—C5—N1
S1—C4—C5—N1
C5—N1—C6—C7
C5—N2—C7—C6
N1—C6—C7—N2
12.15 (9)
−169.84 (7)
−173.20 (8)
6.50 (10)
8.92 (12)
−171.38 (6)
−17.77 (8)
−11.91 (9)
17.89 (8)
Hydrogen-bond geometry (Å, º)
D—H···A
i
N1—H1···N2
C3—H3A···N2i
D—H
H···A
D···A
D—H···A
0.857 (16)
0.95
2.130 (16)
2.59
2.9803 (10)
3.4815 (11)
171.5 (16)
156
Symmetry code: (i) x, −y+1/2, z+1/2.
Acta Cryst. (2009). E65, e15
sup-3
organic compounds
Acta Crystallographica Section E
Data collection
Structure Reports
Online
Bruker SMART APEXII CCD
area-detector diffractometer
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
Tmin = 0.825, Tmax = 0.922
ISSN 1600-5368
2-(2-Thienyl)-4,5-dihydro-1H-imidazole
Refinement
Reza Kia,a Hoong-Kun Funa* and Hadi Kargarb
R[F 2 > 2(F 2)] = 0.050
wR(F 2) = 0.128
S = 1.24
3100 reflections
a
X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800
USM, Penang, Malaysia, and bDepartment of Chemistry, School of Science, Payame
Noor University (PNU), Ardakan, Yazd, Iran
Correspondence e-mail: hkfun@usm.my
27675 measured reflections
3100 independent reflections
3040 reflections with I > 2(I)
Rint = 0.021
91 parameters
H-atom parameters constrained
max = 0.62 e Å3
min = 0.39 e Å3
Table 1
Hydrogen-bond geometry (Å, ).
Received 8 January 2009; accepted 9 January 2009
D—H A
D—H
H A
D A
D—H A
0.75
0.95
0.99
0.99
2.23
2.60
2.89
2.83
2.977
3.482
3.539
3.691
171
155
124
146
Key indicators: single-crystal X-ray study; T = 100 K; mean (C–C) = 0.002 Å;
R factor = 0.050; wR factor = 0.128; data-to-parameter ratio = 34.1.
N1—H1N1 N2
C3—H3A N2i
C6—H6A Cg1ii
C6—H6B Cg1iii
In title compound, C7H8N2S, the five-membered rings are
twisted by a dihedral angle of 5.17 (10) . Two intermolecular
N—H N and C—H N hydrogen bonds to the same
acceptor N atom form seven-membered rings, producing
R12(7) ring motifs. These interactions link neighbouring
molecules into one-dimensional chains extended along the c
axis. The crystal structure is further stabilized by weak
intermolecular C—H interactions.
Symmetry codes: (i) x; y þ 12; z þ 12; (ii) x; y þ 12; z þ 32; (iii) x 1; y; z. Cg1 is the
centroid of the S1/C1–C4 (thiophen) ring.
Related literature
For reference geometrical data, see: Allen et al. (1987). For
details of hydrogen-bond motifs, see: Bernstein et al. (1995).
For a related structure and the synthesis, see, Kia et al. (2008);
Stibrany et al. (2004). For the applications of imidazoline
derivatives, see, for example: Blancafort (1978); Chan (1993);
Vizi (1986); Li et al. (1996); Ueno et al. (1995); Corey &
Grogan (1999).
i
(2)
(2)
(2)
(2)
Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT
(Bruker, 2005); data reduction: SAINT; program(s) used to solve
structure: SHELXTL (Sheldrick, 2008); program(s) used to refine
structure: SHELXTL; molecular graphics: SHELXTL; software used
to prepare material for publication: SHELXTL and PLATON (Spek,
2003).
HKF and RK thanks the Malaysian Government and
Universiti Sains Malaysia for the Science Fund grant No. 305/
PFIZIK/613312. RK thanks Universiti Sains Malaysia for a
post-doctoral research fellowship. HK thanks PNU for the
financial support. HKF also thanks Universiti Sains Malaysia
for the Research University Golden Goose grant No. 1001/
PFIZIK/811012.
Supplementary data and figures for this paper are available from the
IUCr electronic archives (Reference: AT2706).
References
Experimental
Crystal data
C7H8N2S
Mr = 152.21
Monoclinic, P21 =c
a = 6.1321 (2) Å
b = 11.5663 (3) Å
c = 10.0098 (3) Å
= 90.154 (1)
Acta Cryst. (2009). E65, o301
V = 709.95 (4) Å3
Z=4
Mo K radiation
= 0.37 mm1
T = 100.0 (1) K
0.54 0.28 0.22 mm
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor,
R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555–1573.
Blancafort, P. (1978). Drugs Future, 3, 592–592.
Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison,
Wisconsin, USA.
Chan, S. (1993). Clin. Sci. 85, 671–677.
Corey, E. J. & Grogan, M. J. (1999). Org. Lett. 1, 157–160.
Kia, R., Fun, H.-K. & Kargar, H. (2008). Acta Cryst. E64, o2406.
Li, H. Y., Drummond, S., De Lucca, I. & Boswell, G. A. (1996). Tetrahedron,
52, 11153–11162.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.
Stibrany, R. T., Schugar, H. J. & Potenza, J. A. (2004). Acta Cryst. E60, o527–
o529.
Ueno, M., Imaizumi, K., Sugita, T., Takata, I. & Takeshita, M. (1995). Int. J.
Immunopharmacol. 17, 597–603.
Vizi, E. S. (1986). Med. Res. Rev. 6, 431–449.
doi:10.1107/S1600536809001068
Kia et al.
o301
supporting information
supporting information
Acta Cryst. (2009). E65, o301
[doi:10.1107/S1600536809001068]
2-(2-Thienyl)-4,5-dihydro-1H-imidazole
Reza Kia, Hoong-Kun Fun and Hadi Kargar
S1. Comment
Imidazoline derivatives are of great importance because they exhibit significant biological and pharmacological activities
including antihypertensive (Blancafort 1978), antihyperglycemic (Chan 1993), antidepressive (Vizi 1986),
antihypercholesterolemic (Li et al., 1996) and antiinflammatory properties (Ueno et al., 1995). These compounds are also
used as catalysts and synthetic intermediates in some organic reactions (Corey & Grogan 1999). Due to these important
applications of imidazolines, here we report the crystal structure of the title compound (I).
In the title compound (I) (Fig. 1), bond lengths (Allen et al. 1987) and angles are within the normal ranges and are
comparable with the related structures (Stibrany et al. 2004; Kia et al., 2008). The two five-membered rings are not
coplanar to each other and twisted by a dihedral angle of 5.17 (10)°. Two intermolecular N—H···N and C—H···N
hydrogen bonds involving a nitrogen atom as an acceptor form seven-membered rings, producing, R12(7) ring motifs
(Table 1). These interactions link neighbouring molecules into 1-D extended chains along the c axis (, Fig. 2). The crystal
structure is further stabilized by weak intermolecular C—H···π interactions [C6—H6A···Cg1i and C6—H6B···Cg1ii: (i) -x,
1/2 + y, 3/2 - z, (ii) -1 + x, y, z; Cg1 is the centroid of the S1/C1–C4 thiophene ring.
S2. Experimental
The synthetic method was based on the previous work (Stibrany et al. 2004), except that 10 mmol of 2-cyano-thiophene
and 40 mmol of ethylenediamine was used. Single crystals suitable for X-ray diffraction were obtained by evaporation of
a toluene solution at room temperature.
S3. Refinement
The hydrogen atom bound to N1 was located from the difference Fourier map and constrained to refine with the
respective parent atom, see Table 1. The rest of the hydrogen atoms were positioned gemetrically and refined in a riding
model approximation with C—H = 0.95–0.99 Å and Uiso (H) = 1.2 Ueq (C).
Acta Cryst. (2009). E65, o301
sup-1
supporting information
Figure 1
The molecular structure of (I) with atom labels and 50% probability ellipsoids for non-H atoms.
Figure 2
The crystal packing of (I), viewed down the b-axis showing 1-D infinite chain along the c-axis by intermolecular N—
H···N and C—H···N interactions. The intermolecular interactions are shown as dashed lines.
2-(2-Thienyl)-4,5-dihydro-1H-imidazole
Crystal data
C7H8N2S
Mr = 152.21
Monoclinic, P21/c
Hall symbol: -P 2ybc
a = 6.1321 (2) Å
b = 11.5663 (3) Å
c = 10.0098 (3) Å
β = 90.154 (1)°
V = 709.95 (4) Å3
Z=4
Acta Cryst. (2009). E65, o301
F(000) = 320
Dx = 1.424 Mg m−3
Mo Kα radiation, λ = 0.71073 Å
Cell parameters from 9869 reflections
θ = 2.5–34.3°
µ = 0.37 mm−1
T = 100 K
Block, colourless
0.54 × 0.28 × 0.22 mm
sup-2
supporting information
Data collection
Bruker SMART APEXII CCD area-detector
diffractometer
Radiation source: fine-focus sealed tube
Graphite monochromator
φ and ω scans
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
Tmin = 0.825, Tmax = 0.922
27675 measured reflections
3100 independent reflections
3040 reflections with I > 2σ(I)
Rint = 0.021
θmax = 35.0°, θmin = 2.7°
h = −9→9
k = −18→17
l = −15→15
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.050
wR(F2) = 0.128
S = 1.24
3100 reflections
91 parameters
0 restraints
Primary atom site location: structure-invariant
direct methods
Secondary atom site location: difference Fourier
map
Hydrogen site location: inferred from
neighbouring sites
H-atom parameters constrained
w = 1/[σ2(Fo2) + 1.7551P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max < 0.001
Δρmax = 0.62 e Å−3
Δρmin = −0.39 e Å−3
Special details
Experimental. The low-temperature data was collected with the Oxford Cyrosystem Cobra low-temperature attachment.
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full
covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and
torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry.
An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2,
conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used
only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2
are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
S1
N2
N1
H1N1
C1
H1A
C2
H2A
C3
H3A
C4
C5
C6
H6A
H6B
x
y
z
Uiso*/Ueq
0.46967 (8)
0.0669 (2)
0.0460 (2)
0.0584
0.6387 (3)
0.7542
0.5888 (3)
0.6655
0.4092 (3)
0.3530
0.3260 (3)
0.1427 (3)
−0.1543 (3)
−0.1724
−0.2849
0.14161 (4)
0.29635 (14)
0.30376 (14)
0.2724
0.05389 (17)
0.0100
0.05418 (16)
0.0103
0.12742 (15)
0.1385
0.18060 (14)
0.26052 (14)
0.36276 (17)
0.4380
0.3144
0.59514 (4)
0.61122 (15)
0.83746 (14)
0.9026
0.6858 (2)
0.6482
0.81838 (19)
0.8835
0.84860 (17)
0.9360
0.73589 (16)
0.72556 (16)
0.79447 (17)
0.8403
0.8101
0.01548 (10)
0.0137 (2)
0.0133 (2)
0.016*
0.0180 (3)
0.022*
0.0169 (3)
0.020*
0.0136 (3)
0.016*
0.0117 (3)
0.0109 (3)
0.0154 (3)
0.018*
0.018*
Acta Cryst. (2009). E65, o301
sup-3
supporting information
C7
H7A
H7B
−0.1097 (3)
−0.2423
−0.0634
0.37874 (16)
0.3615
0.4591
0.64419 (17)
0.5912
0.6252
0.0151 (3)
0.018*
0.018*
Atomic displacement parameters (Å2)
S1
N2
N1
C1
C2
C3
C4
C5
C6
C7
U11
U22
U33
U12
U13
U23
0.01727 (19)
0.0153 (6)
0.0148 (6)
0.0166 (7)
0.0186 (7)
0.0164 (7)
0.0131 (6)
0.0120 (6)
0.0143 (7)
0.0152 (7)
0.01847 (19)
0.0161 (6)
0.0170 (6)
0.0181 (8)
0.0155 (7)
0.0129 (7)
0.0120 (6)
0.0113 (6)
0.0186 (7)
0.0181 (7)
0.01071 (17)
0.0098 (6)
0.0080 (5)
0.0192 (8)
0.0167 (7)
0.0113 (6)
0.0100 (6)
0.0094 (6)
0.0132 (7)
0.0120 (7)
0.00446 (15)
0.0027 (5)
0.0029 (5)
0.0057 (6)
0.0029 (6)
−0.0001 (5)
0.0005 (5)
−0.0011 (5)
0.0030 (6)
0.0035 (6)
0.00185 (13)
0.0003 (4)
0.0016 (4)
−0.0001 (6)
−0.0034 (6)
−0.0002 (5)
−0.0003 (5)
0.0005 (5)
0.0019 (5)
0.0000 (5)
−0.00026 (14)
0.0009 (5)
0.0004 (5)
−0.0015 (6)
0.0009 (6)
0.0004 (5)
−0.0005 (5)
−0.0004 (5)
0.0007 (6)
0.0018 (5)
Geometric parameters (Å, º)
S1—C1
S1—C4
N2—C5
N2—C7
N1—C5
N1—C6
N1—H1N1
C1—C2
C1—H1A
C2—C3
1.7099 (19)
1.7239 (17)
1.302 (2)
1.480 (2)
1.364 (2)
1.468 (2)
0.7501
1.362 (3)
0.9500
1.423 (3)
C2—H2A
C3—C4
C3—H3A
C4—C5
C6—C7
C6—H6A
C6—H6B
C7—H7A
C7—H7B
0.9500
1.381 (2)
0.9500
1.459 (2)
1.541 (2)
0.9900
0.9900
0.9900
0.9900
C1—S1—C4
C5—N2—C7
C5—N1—C6
C5—N1—H1N1
C6—N1—H1N1
C2—C1—S1
C2—C1—H1A
S1—C1—H1A
C1—C2—C3
C1—C2—H2A
C3—C2—H2A
C4—C3—C2
C4—C3—H3A
C2—C3—H3A
C3—C4—C5
C3—C4—S1
91.82 (9)
105.57 (14)
107.14 (14)
119.6
124.2
112.21 (14)
123.9
123.9
112.63 (16)
123.7
123.7
112.08 (15)
124.0
124.0
128.52 (15)
111.26 (13)
C5—C4—S1
N2—C5—N1
N2—C5—C4
N1—C5—C4
N1—C6—C7
N1—C6—H6A
C7—C6—H6A
N1—C6—H6B
C7—C6—H6B
H6A—C6—H6B
N2—C7—C6
N2—C7—H7A
C6—C7—H7A
N2—C7—H7B
C6—C7—H7B
H7A—C7—H7B
120.22 (12)
116.78 (15)
122.49 (15)
120.71 (14)
101.03 (13)
111.6
111.6
111.6
111.6
109.4
105.80 (14)
110.6
110.6
110.6
110.6
108.7
Acta Cryst. (2009). E65, o301
sup-4
supporting information
C4—S1—C1—C2
S1—C1—C2—C3
C1—C2—C3—C4
C2—C3—C4—C5
C2—C3—C4—S1
C1—S1—C4—C3
C1—S1—C4—C5
C7—N2—C5—N1
C7—N2—C5—C4
−0.16 (16)
−0.2 (2)
0.5 (2)
179.52 (17)
−0.60 (19)
0.44 (14)
−179.67 (15)
0.6 (2)
−177.67 (15)
C6—N1—C5—N2
C6—N1—C5—C4
C3—C4—C5—N2
S1—C4—C5—N2
C3—C4—C5—N1
S1—C4—C5—N1
C5—N1—C6—C7
C5—N2—C7—C6
N1—C6—C7—N2
11.9 (2)
−169.73 (15)
−173.27 (18)
6.9 (2)
8.5 (3)
−171.36 (13)
−17.79 (18)
−12.26 (19)
18.12 (18)
Hydrogen-bond geometry (Å, º)
D—H···A
i
N1—H1N1···N2
C3—H3A···N2i
C6—H6A···Cg1ii
C6—H6B···Cg1iii
D—H
H···A
D···A
D—H···A
0.75
0.95
0.99
0.99
2.23
2.60
2.89
2.83
2.977 (2)
3.482 (2)
3.539 (2)
3.691 (2)
171
155
124
146
Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x, y+1/2, −z+3/2; (iii) x−1, y, z.
Acta Cryst. (2009). E65, o301
sup-5
| |
https://openalex.org/W2162735961 | https://lipidworld.biomedcentral.com/counter/pdf/10.1186/1476-511X-13-61 | English | null | A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus | Lipids in health and disease | 2,014 | cc-by | 5,577 | Abstract Background: Fatty acid-binding protein 2 (FABP2) is an intracellular protein expressed exclusively in the enterocytes
of proximal small intestine. FABP2 has a high affinity for saturated and unsaturated long-chain fatty acids and is
believed to be involved in the absorption and transport of dietary fatty acids. Methods: This is a case–control study conceded in 438 T2DM cases and 460 subjects with normal glucose levels
and non-obese considered as healthy controls. Allelic discrimination was performed using TaqMan single-
nucleotide polymorphism was carried out by real time-polymerase chain reaction (RT-PCR) assays using purified
DNA. Results: Clinical data and anthropometric measurements except age, glucose levels and lipid profile of the patients
were significantly different from those of the controls (p < 0.05). Statistical analyses failed to show any type of
significant association of the polymorphism between cases and controls. However logistic regression analyses
was suggests that the TT genotype is significantly associated with male patients (p = 0.001). None of the allele or
genotypes of FABP2 A54T was associated with T2DM cases versus the controls (AT genotype, OR = 0.85
(0.64-1.12), p = 0.25; TT genotype, OR = 0.66 (0.39-1.11), p = 0.11; T allele, 0.82 (0.67-1.02), p = 0.08). Conclusion: In conclusion, this study suggests that the above named variant in FABP2 gene is not potential
contributor to the risk of T2DM and related traits in a Saudi population. However TT genotype is a risk factor for the
disease in males. Keywords: A54T polymorphism, FABP2 gene, Type 2 diabetes mellitus, Saudi population © 2014 Alharbi et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain
Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,
unless otherwise stated. Open Access A54T polymorphism in the fatty acid binding
protein 2 studies in a Saudi population with type
2 diabetes mellitus Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 A54T polymorphism in the fatty acid binding
protein 2 studies in a Saudi population with type
2 diabetes mellitus Khalid Khalaf Alharbi1†, Imran Ali Khan1*†, Mohammad D Bazzi2†, Nasser M Al-Daghri3, Tarique N Hasan4†,
May Salem Alnbaheen5,6, Fawiziah Khalaf Alharbi7, Yazeed A Al-Sheikh1, Rabbani Syed1
and Mourad AM Aboul-Soud1 * Correspondence: imkhan@ksu.edu.sa
†Equal contributors
1Department of Clinical Laboratory Sciences, College of Applied Medical
Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of
Saudi Arabia
Full list of author information is available at the end of the article Introduction relatives of T2DM patients is 3.62 times that in the com-
mon population, so the researchers of various countries
make great efforts to explore the T2DM susceptible
genes. Once the T2DM susceptible genes are sought
out, it means that the T2DM prevention clues have been
found. It is an effective measure to screen the T2DM
susceptible population and prevent T2DM progress. It
is now generally considered that T2DM is not a sole
disorder, but a multigenic disorder with extensive her-
edity heterogeneous, categorized by high levels of glu-
cose and metabolic disorders [3,4]. Obesity is one of the
complication for T2DM and the leading cause of pre-
ventable deaths and a serious health complications in
the Saudi Arabia [5]. Type 2 diabetes mellitus (T2DM) is a chronic degenerative
disease, phenotypically and genetically characterized by in-
sulin resistance (IR) in insulin-target tissues, and impaired
insulin secretion from pancreatic β-cells [1]. T2DM affects
nearly 31.6% individuals in the Kingdom of Saudi Arabia
[2]. The interaction of genetic and environmental factors
is universally acknowledged as the primary underlying
T2DM mechanism. The T2DM risk in the first degree * Correspondence: imkhan@ksu.edu.sa
†Equal contributors
1Department of Clinical Laboratory Sciences, College of Applied Medical
Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of
Saudi Arabia
Full list of author information is available at the end of the article Page 2 of 6 Page 2 of 6 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 samples were stored at −80°C. The rs1799883 polymorph-
ism was genotyped using a TaqMan® SNP genotyping
assay (Assay ID: C_2834835_10) on a 7300HT sequence
detection system (Applied Biosystems, USA). Primers and
probes were obtained from Applied Biosystems as Assays-
by-Design™. Cases and controls were ensured to have even
treatment during the assay procedure, and each plate
included negative controls (with no DNA). Plates were
read on the ABI Prism 7300 using the Sequence Detection
Software (Applied Biosystems) using 40 PCR cycles (92°C
denaturation for 15 seconds, 60°C annealing/extension
for 60 seconds). Measurements were repeated for samples
with failed genotypes. Assays that did not show >95%
concordance were discarded and replaced with alterna-
tive assays with the same tagging properties. Genome Wide Association Studies (GWAS) are power-
ful tools to identify genetic variants that are associated
with common diseases. So far, GWAS identified at least
50–52 genetic loci robustly associated with T2DM [6]. Statistical analysis
ll
l
l All statistical analysis was carried out using the statistical
program i.e. statistical package for social sciences (IBM
SPSS 19.0 SPSS Inc., Chicago, USA). The difference of
mean age of patients and controls were significantly differ-
ent (Table 1). Hence in order to overcome the significance
difference of mean age, logistic regression was performed
and it was found that patients with ages 35 (1 patient), 72
(2 patients), 77 (2 patients), 84 (2 patients), 85 (2 patients)
and 86 (2 patients) years were redundant whereas rest all
the patient ages were significantly not different from those The aim of the present study was to investigate the
contribution of A54T genetic polymorphism identified by
Baier et al [12] in the FABP2 variants to risk of T2DM in a
Saudi population, since this polymorphism results in a
functionally altered FABP2 protein which confers suscepti-
bility to metabolic disorders like T2DM, thereby to con-
tribute to the personalized prevention of this condition
and A54T polymorphism has been associated with T2DM
disease in many but not all studies. Table 1 Demographic characteristics of the study
population
Controls
(n = 460)
T2DM
(n = 438)
p
Age (Years)
45.99 ± 7.77
53.5 ± 10.78
<0.0001
Weight (kg)
76.61 ± 14.52
77.37 ± 13.55
0.41
Height (cm)
161.25 ± 8.79
161.10 ± 9.30
0.80
Body mass index (kg/m2)
29.22 ± 5.58
29.9 ± 5.89
0.95
Sex: Male/Female
(52.6%)/(47.4%)
(56.8%)/(43.2%)
0.0002
SBP (mmHg)
114.80 ± 8.04
125.83 ± 9.96
<0.0001
DBP (mmHg)
75.81 ± 6.20
81.25 ± 4.82
0.0001
Waist (cms)
89.75 ± 14.19
95.3 ± 18.96
<0.0001
Hips (cms)
101.75 ± 14.72
99.64 ± 16.52
0.61
FBS (mmol/L)
5.23 ± 0.61
12.92 ± 4.60
<0.0001
Triglycerides (mmol/L)
1.62 ± 0.86
2.24 ± 1.62
<0.0001
Cholesterol (mmol/L )
5.04 ± 0.96
5.61 ± 1.26
<0.0001
HDL-C (mmol/L )
0.64 ± 0.23
0.84 ± 0.37
<0.0001
LDL-C (mmol/L)
3.66 ± 0.85
3.76 ± 1.05
0.0008
Glucose (mmol/L)
5.7 ± 1.2
9.4 ± 1.5
0.0002
Insulin (μU/mL)
12.5 ± 1.8
16.2 ± 2.2
0.0002
HOMA-IR
3.15 ± 1.9
6.8 ± 2.4
0.00008
Note: Data represented as mean ± SD for continuous variables, pValues for
independent t-test are given. A p-value significant at <0.05. NA, Not Analyzed/
Not Applicable. Table 1 Demographic characteristics of the study
population Introduction Several genetic markers have now been implicated for
T2DM development pathways involved in the disease
[7,8]. Fatty acid binding protein 2 (FABP2) has been stud-
ied as one of the marker, due to its role in the uptake,
intracellular metabolism and excretion of long chain fatty
acids. This gene is located on 4q28-q31 chromosomal re-
gion, consist of approximately 3.4 kbs. Many polymor-
phisms in FABP2 gene have already linked with metabolic
phenotypes. The most extensively studies polymorphism
was Alanine54threnonine (A54T) substitution at codon 54
of exon 2 that results from G to A nucleotide substitution
and affects primary protein structure [9,10]. This change
affects the ability of the protein to transport dietary fatty
acids, which may elevate saturated fatty acids level in the
serum which might induce endothelial dysfunction leading
to increased cardiovascular mortality [11]. Materials and methods
Selection of subjects This is a case–control study carried out in King Saud
University, Riyadh, Saudi Arabia. In this study we have
collected in about 900 subjects; 438 T2DM cases and
460 healthy controls from the capital city. All the normal
controls were selected from the general population
based on normal glucose values and non-obese subjects. The details of the collection of patients, inclusion and
exclusion criteria were described in the prior publication
[1]. Ethical approval for the study was achieved from the
ethics committee, King Saud University. Written informed
consent was obtained from each patient. Anthropometric
and biochemical measurements of the patients involved in
this study has been described in the prior publication [1]. DNA extraction and genotyping 5 mL of the venous blood was collected into plain (coagu-
lated) and EDTA (anticoaggulated) tubes. Plain vacutainer
consist of 3 mL of the serum sample was used to analyze
the biochemical parameters and 2 mL of the EDTA sam-
ple was used for molecular analysis. Genomic DNA was
extracted from peripheral blood leukocytes using Norgen
DNA extraction kit (Norgen Biotek corp, Canada). DNA Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Page 3 of 6 Table 2 Distribution of FABP2 A54T genotypes and alleles of this study
Genotype
Patients’ n (%)
Controls n (%)
OR (CI = 95%)
P value
χ2
1 d. f. AA
220 (51.52)
260 (56.52)
1 (reference)
1 (reference)
AT
170 (39.81)
171 (37.17)
0.85 (0.64-1.12)
0.25
1.12
TT
37 (8.66)
29 (6.30)
0.66 ( 0.39-1.11)
0.11
2.43
A
610 (71.42)
691 (75.10)
1 (reference)
1 (reference)
T
224 (28.57)
229 (24.89)
0.82 (0.67-1.02)
0.08
3.06
AA + AT vs TT
0.7 (0.42-1.17)
0.18
1.79
TT + AT vs AA
1.22 (0.93-1.59)
0.13
2.22
The genotypic and allelic frequencies and dominant as recessive models of patients are significantly not different from controls. Table 2 Distribution of FABP2 A54T genotypes and alleles of this study The genotypic and allelic frequencies and dominant as recessive models of patients are significantly not different from controls. 0.82 (95% CI = 0.67-1.02); p = 0.08). There were no signifi-
cant differences in both the genotypic and allelic frequen-
cies between the cases as well as controls. However upon
multiple logistic regression analysis TT genotype was
found to be associated with male patients (OR = 1.24 95%
CI = 0.09-0.60, p = 0.001) (Tables 3 and 4). FABP2 geno-
typic frequencies of A54A, A54T, and T54T were 56.5%,
37.2%, and 6.3% in the control group, 51.52%, 39.81% and
8.66% in the T2DM group; allelic frequencies of Ala and
Thr were 0.75 and 0.25 for the control group, 0.71 and
0.29 for the T2DM group. The odds ratio for any genotype
of A54T SNP was not significantly related with the risk
of developing T2DM in this studied population (for
AA + AT vs TT; OR-0.7 (95% CI = 0.42-1.17); p = 0.12
and for TT + AT vs AA; OR-1.22 (95% CI = 0.93-1.59);
p = 0.25) from the Saudi population. of controls. Hence those patients were excluded from
the further calculations if genotypic and allelic analyses. DNA extraction and genotyping The sex ratio of patients and controls were also differ-
ent significantly. So, separate multiple analyses after
logistic regressions were performed for patient and con-
trols. The allele and genotype frequencies of FABP2
gene in patients were compared to controls by chi-square
analysis. The distribution of the genotypes deviates from
Hardy-Weinberg equilibrium (HWE). Clinical characteris-
tics of all the subjects were expressed as mean ± SD. Con-
tinuous variables were compared between the groups
using two-tailed student t-test. Odds ratios (ORs) and 95%
CI, with adjustment for age, sex and BMI were calculated
using multiple logistic regression analysis. All tests were
conducted at the p < 0.05 level of significance. Clinical characteristics
h
l FABP2 is an intracellular protein expressed in the villus
tips of the small intestine, has a high affinity for saturated
and unsaturated long-chain fatty acids and is believed to
be involved in the absorption and transport of dietary fatty
acids [13]. The association between fatty acid metabolism
and IR is well known, and the FABP2 gene has been sug-
gested as a possible candidate gene in the development of
IR and T2DM [14]. A54T polymorphism in FABP2 was
investigated as a possible genetic factor associated with
T2DM and Obesity. Studies examining the association of In this case–control study, we have carried out in almost
900 subjects; 438 patients with T2DM (216 females and
244 males, 45.99±7.77 years old) and 460 normal control
subjects (200 female and 238 male, 53.5 ± 10.78 years
old). The mean age was 60 years for patients and 59 years
for the control group. Clinical and anthropometric data
are revealed in Table 1 for T2DM patients and control
subjects. The results show that T2DM subjects were
significantly older than controls but anthropometric
measurements and hip were not significant (p > 0.05). T2DM subjects appear to have higher levels of SBP,
DBP, fasting glucose, insulin, HOMA-IR and lipid profile
and waist (p < 0.05). Table 3 Genotypic distribution according to sex
Patients
AA
AT
TT
Male
122
95
31
Female
98
86
6
Total
220
181
37
Controls
Male
136
95
13
Female
124
76
16
Total
260
171
29 Table 3 Genotypic distribution according to sex Genotype frequencies Canani et al [26] showed that A54T polymorphism
confers susceptibility to renal disease in T2DM patients. There are very few reports on the association of this poly-
morphism with T2DM. Several studies from non-European
ethnic backgrounds have reported a positive association
between FABP2 variants and T2DM. A54T polymorphism
was carried out in relation to multiple diseases and the re-
ports are summarize in Table 5, which shows positive as-
sociation with T2DM and a combination of other diseases
like chronic kidney disease, Microalbminuria, postprandial
fatty acids and with the glyburide therapy. In our study,
we have examined only T2DM (n = 438) samples and that
have not examined its association with other disease. 0.5 OR, Odds ratio, 95% CI-95% confidence interval; multiple logistic regression
calculated by SPSS v.19, AA genotype was set as zero because redundancy A54T polymorphism with IR, T2DM and Obesity are
contradictory and inconclusive [10]. The product of T al-
lele of FABP2 possesses a greater affinity for long-chain
FA than the A allele [15]. In addition, individuals with the
T allele of this polymorphism were more insulin resistant
than were those with the A allele [12]. The T allele was
also shown to be associated with higher plasma levels of
LDL-C [16] and dyslipidemia (high plasma concentration
of triglycerides and low concentration of HDL-C) [17]. In
addition, the T allele of A54T polymorphism has previ-
ously been associated with atherothrombotic cerebral in-
farction in individuals with metabolic syndrome [18] and a
parental history of stroke in the Swedish population [19]. Moreover, it was associated with a 2- to 3.5- fold increase
in cardiovascular risk in dyslipidemic men with diabetes There are several studies denote no association of the
T allele with T2DM [27-29] and our study is supporting
the above mentioned studies. In some studies, subjects
were distributed in homozygous for the A allele (AA) and
T allele carriers (AT and TT), mainly because there were
only few subjects homozygous for the variant [23,30]. We
observed the association of A54T polymorphism with Table 5 Association Studies of FABP2 A54T gene polymorphism on different ethnic groups
S. Genotype frequencies Results for the genotypic distribution of FABP2 A54T
polymorphism and the frequency of A and T alleles in
patients and controls have been tabulated in Table 2. The
genotype distribution for A54T polymorphism showed no
deviation from HWE in both the case and control groups
(χ2 = 0.37, p = 0.54). Genotyping of the A54T polymorph-
ism in the FABP2 gene revealed that the allelic frequency
of T allele was 0.285 in cases and 0.248 in controls (OR- Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Page 4 of 6 Page 4 of 6 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Table 4 Calculation for the association of A54T genotypes
with T2DM patients and control in male and female sexes
OR
95% CI
P Value
Patients
Genotypes
AT
Male
1 (reference)
Female
1.1
(0.74-1.65)
0.62
TT
Male
1 (reference)
Female
1.24
(0.09-0.60)
0.001
Controls
Genotypes
AT
Male
1 (reference)
Female
0.87
(0.59-1.29)
0.5
TT
Male
Female
1.35
(0.62-2.91)
0.44
OR, Odds ratio, 95% CI-95% confidence interval; multiple logistic regression
calculated by SPSS v.19, AA genotype was set as zero because redundancy Table 4 Calculation for the association of A54T genotypes
with T2DM patients and control in male and female sexes Table 4 Calculation for the association of A54T genotypes
with T2DM patients and control in male and female sexes
OR
95% CI
P Value compared with their dyslipidemic nondiabetic counter-
parts [20]. We have now shown that A54T polymorphism
was not significantly associated with T2DM, with the minor
allele representing the risk factor for this condition. In the present study we investigated the association
of FABP2 A54T polymorphism with T2DM in a Saudi
population. To the best of our knowledge, this is the first
study investigating the association of A54T polymorphism
in a Saudi population. The frequency of T allele of A54T
polymorphism was 0.29 similar to Greek and Caucasian
population [21-23]. A54T polymorphism was identified
via linkage disequilibrium map, as a haploblock spanning
50 kb that includes 22 SNPs. However, the T54 allele is
present in only one of six possibilities among the frequent
haplotypes (>2%). It is interesting that in this haploblock,
there are no other known or putative genes except for
FABP2 [24]. Previous studies of A54T polymorphisms investigated
lipid related diseases such as coronary artery disease (CAD)
[25]. Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 T2DM according to all possible genetic models (i.e. addi-
tive, dominant and recessive). No association of A54T
polymorphism was found with T2DM according to any
genetic model used, a finding shared by other studies that
examined such an association [31]. There are limitations
to the study design as it is a case–control observational
study rather than cross sectional or prospective study. We
have chosen only one SNP (A54T) to study the T2DM
disease. with and without type 2 diabetes mellitus. Clin Med Insights Endocrinol
Diab 2014, 7:1–6. Diab 2014, 7:1 6. 3. Li YY, Wang LS, Lu XZ, Yang ZJ, Wang XM, Zhou CW, Xu J, Qian Y, Chen AL:
CDKAL1 gene rs7756992 A/G polymorphism and type 2 diabetes
mellitus: a meta-analysis of 62, 567 subjects. Sci Rep 2013, 4(3):3131. 4. Shen HB, Shen DB: An epidemiological study on genetic agent in type 2
diabetes mellitus. China Public Health 1999, 15:492–494. 5. Al-Daghri NM, Alkharfy KM, Al-Attas OS, Krishnaswamy S, Mohammed AK,
Albagha OM, Alenad AM, Chrousos GP, Alokail MS: Association between
type 2 diabetes mellitus-related SNP variants and obesity trait in a Saudi
population. Mol Bio Rep 2014, 41:1731–1740. p p
p
6. Wilson PW, Meigs JB, Sullivan X, Fox CS, Nathan DM, D’Agostino RB:
prediction of incident diabetes mellitus in middle-aged adults: the
Framingham offspring study. Arch Intern Med 2007, 167:1068–1074. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms
with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. 6. Wilson PW, Meigs JB, Sullivan X, Fox CS, Nathan DM, D’Agostino RB:
prediction of incident diabetes mellitus in middle-aged adults: the
Framingham offspring study. Arch Intern Med 2007, 167:1068–1074. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms
with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. In conclusion, the present study provides no evidence of
any association between A54T polymorphism (rs1799883)
in FABP2 gene and T2DM, suggesting that A54T poly-
morphism is not a major risk factor for the T2DM. Over-
all, this study indicates that A54T polymorphism could
not affect directly the presence of T2DM due to the differ-
ential absorption of long chain fatty acids in the presence
of the T allele. Authors’ contributions AKK and BMD were main investigator of this study. IAK has plan the
study protocol, drafted the manuscript, prepared the final version of the
manuscript and CA. ANM has confirmed the T2DM samples. HTN has
helped in the revision of the manuscript. AMS and AFK helped with the
genotyping and interpretation of the data. SR, took care about the sample
collection. AYA and AMAM has participated in the study coordination and
took part in the statistical analysis. All authors read and approved the final
manuscript. 11. Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ,
Warrington NM, Widen E, Hottenga JJ, Kaakinen M, Lange LA, Bradfield JP,
Kerkhof M, Marsh JA, Magi R, Chen CM, Lyon HN, Kirin M, Adair LS, Aulchenko
YS, Bennett AJ, Borja JB, Bouatia-Naji N, Charoen P, Coin LJ, Cousminer DL, de
Geus EJ, Deloukas P, Elliott P, Early Growth Genetics (EGG) Consortium,
McCarthy MI: Variants in ADCY5 and near CCNL1 are associated with fetal
growth and birth weight. Nat Genet 2010, 42:430–435. 11. Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ,
Warrington NM, Widen E, Hottenga JJ, Kaakinen M, Lange LA, Bradfield JP,
Kerkhof M, Marsh JA, Magi R, Chen CM, Lyon HN, Kirin M, Adair LS, Aulchenko
YS, Bennett AJ, Borja JB, Bouatia-Naji N, Charoen P, Coin LJ, Cousminer DL, de
Geus EJ, Deloukas P, Elliott P, Early Growth Genetics (EGG) Consortium,
McCarthy MI: Variants in ADCY5 and near CCNL1 are associated with fetal
growth and birth weight. Nat Genet 2010, 42:430–435. 12. Baier LJ, Sacchettini JC, Knowler WC, Eads J, Paolisso G, Tataranni PA,
Mochizuki H, Bennett PH, Bogardus C, Prochazaka M: An amino acid
substitution in the human intestinal fatty acid binding protein is
associated with increased fatty acid binding, increased fat oxidation, and
insulin resistance. J Clin Invest 1995, 95:1281–1287. Competing interest
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Christakidis D, Manolopoulos VG: Tha 54 allele of fatty acid binding protein 2
gene is associated with obesity but not type 2 diabetes mellitus in a
Caucasian population. Diabetes Res Clin Pract 2009, 84:132–137. 10. Tavridou A, Arvanitidis KI, Tiptiri-Kourpeti A, Petridis I, Ragia G, Kyroglou S,
Christakidis D, Manolopoulos VG: Tha 54 allele of fatty acid binding protein 2
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The authors declare that they have no competing interests. Acknowledgement The author would like to extend their sincere appreciation to the Deanship
of Scientific Research at King Saud University for its funding of this research
through the Research Group Project no RGP-VPP-244. 13. Albala C, Villaroel A, Santos JL, Angel B, Lera L, Liberman C, Sanchez H,
Perez-Bravo F: FABPS Ala54Thr polymorphism and diabetes in Chilean
elders. Diabetes Res Clin Pract 2007, 77:245–250. Author details
1 1Department of Clinical Laboratory Sciences, College of Applied Medical
Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of
Saudi Arabia. 2Department of Biochemistry, College of Science, King Saud
University, Riyadh 11451, Kingdom of Saudi Arabia. 3Biomarkers research
programme, Department of Biochemistry, College of Science, King Saud
University, Riyadh 11451, Kingdom of Saudi Arabia. 4Department of Food
Science and Nutrition, College of Food and Agricultural Sciences, King Saud
University, Riyadh 11451, Kingdom of Saudi Arabia. 5Stem Cell unit,
Department of Anatomy, College of Medicine, King Khalid University
Hospital, Riyadh 11461, Kingdom of Saudi Arabia. 6Prepratory Year, Saudi
Electronic University, Riyadh, Kingdom of Saudi Arabia. 7Department of
Biology Science, College of Science and Arts, Al-Qassim University, P.O. Box
1300, Buraidah 51431, Kingdom of Saudi Arabia. 14. Zhao T, Zhao J, Yang W: Association of the fatty acid-binding protein 2
gene Ala54Thr polymorphism with insulin related and blood glucose: a
meta-analysis in 13451 subjects. Diabetes Metab Res Rev 2010, 26:357–364. 15. Lowe JB, Sacchettini JC, Laposata M, McQuillan JJ, Gordon JI: Expression of
rat intestinal fatty acid-binding protein in Escherichia coli: purification
and comparison of ligand binding characteristics with that of Escherichia
coli-derived rat liver fatty acid-binding protein. J Biol Chem 1987,
262:5931–5937. 16. Yamada K, Yuan X, Ishiyama S, Koyama K, Ichikawa F, Koyanagi A, Koyama
W, Nonaka K: Association between Ala54Thr substitution of the fatty
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fat thickness in Japanese men. Diabetologia 1997, 40:706–710. 17. Galluzzi JR, Cupples LA, Otvos JD, Wilson PW, Schaefer EJ, Ordovas JM:
Association of the A/T54 polymorphism in the intestinal fatty acid
binding protein with variations in plasma lipids in the Framingham
Offspring Study. Atherosclerosis 2001, 159:417–424. Received: 15 March 2014 Accepted: 26 March 2014
Published: 1 April 2014 18. Guettier JM, Georgopoulos A, Tsai MY, Radha V, Shanthirani S, Deepa R,
Gross M, Rao G, Mohan V: Polymorphisms in the fatty acid-binding pro-
tein 2 and apolipoprotein C-III genes are associated with the metabolic
syndrome and dyslipidemia in a South Indian population. J Clin
Endocrinol Metab 2005, 90:1705–1711. Alharbi et al. Lipids in Health and Disease 2014, 13:61
http://www.lipidworld.com/content/13/1/61 This is the first study finding the interaction
between FABP2 and T2DM in Saudi population. Further
functional studies as well as well-characterized larger mo-
lecular epidemiological studies are necessary to confirm
our findings. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms
with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. 8. Perry JRB, Vought BF, Yengo L, Amin N, Dupuis J, Ganser M, Grallert H, Navarro
P, Li M, Qi L, Steinthorsdottir V, Scott RA, Almgren P, Arking DE, Aulchenko Y,
Balkau B, Benediktsson R, Bergman RN, Boerwinkle E, Bonnycastle L, Burtt NP,
Campbell H, Charpentier G, Collins FS, Gieger C, Green T, Hadjadj S, Hattersley
AT, Herder C, Hofman A: Stratifying type 2 diabetes Cases by BMI identifies
genetic risk variants in LAMA1 and enrichment for risk variants in lean
compared to obese cases. PLoS Genet 2012, 8(5):e1002741. 9. Mansego ML, Martinez F, Martinez-Larrad MT, Zabena C, Rojo G, Morcillio S,
Soriquer F, Martin-Escudero JC, Serrano-Rios M, Redon J, Chaves FJ:
Common variants of the liver fatty acid binding protein gene influences
the risk of type 2 diabetes and insulin resistance in Spanish population. PLoS One 2012, 7(3):e31853. 9. Mansego ML, Martinez F, Martinez-Larrad MT, Zabena C, Rojo G, Morcillio S,
Soriquer F, Martin-Escudero JC, Serrano-Rios M, Redon J, Chaves FJ:
Common variants of the liver fatty acid binding protein gene influences
the risk of type 2 diabetes and insulin resistance in Spanish population. PLoS One 2012, 7(3):e31853. Genotype frequencies No
Population
Cases
Controls
Association
Disease
1
Germany
-
68
No
Obesity
2
Japan
228
813
Yes
MI + chronic kidney disease
3
Japan
636
1106
Yes
Chronic kidney disease + T2DM
4
Japan
313
971
Yes
Atherothrombic cerebral infarction
5
Brazil
72
37
Yes
T2DM + microalbminuria
6
Mexico
-
131
No
Lipid metabolism
7
Brazil
513
529
Yes
Renal disease + T2DM
8
Brazil
26
529
Yes
Postprandial fatty acids + T2DM
9
Spain
108
101
Yes
Hypercholesterolemic
10
Present Study
438
460
No
T2DM Table 5 Association Studies of FABP2 A54T gene polymorphism on different ethnic groups Table 5 Association Studies of FABP2 A54T gene polymorphism on diff Page 5 of 6 Page 5 of 6 2.
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Yoshida H, Satoh K, Ichihara S, Aoyagi Y, Yasunaga A, Park H, Tanaka M, 19. Yamada Y, Kato K, Oguri M, Yoshida T, Yokoi K, Watanabe S, Metoki N,
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Cite this article as: Alharbi et al.: A54T polymorphism in the fatty acid
binding protein 2 studies in a Saudi population with type 2 diabetes
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https://openalex.org/W2217499237 | https://europepmc.org/articles/pmc4596571?pdf=render | English | null | Genetic Polymorphisms in Inflammasome-Dependent Innate Immunity among Pediatric Patients with Severe Renal Parenchymal Infections | PloS one | 2,015 | cc-by | 9,298 | RESEARCH ARTICLE Data Availability Statement: All relevant data are
within the paper and its Supporting Information files. Funding: CHC was supported by Ministry of Science
and Technology, Taiwan (MOST 103-2314-B-182-
022-MY3; NSC 98-2314-B-182A-007-MY3) and the
Chang Gung Memorial Hospital (CMRPG 4A0111,
4A0112, 4A0113) for this study. The funders had no
role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript. Background Inflammasome innate immune response activation has been demonstrated in various
inflammatory diseases and microbial infections. However, to our knowledge, no study has
examined the inflammasome-dependent pathways in patients with urinary tract infection. Defective or variant genes associated with innate immunity are believed to alter the host’s
susceptibility to microbial infection. This study investigated genetic polymorphisms in genes
encoding inflammasomes and the subsequent released cytokines in pediatric patients with
severe renal parenchymal infections. Editor: Zhanjun Jia, University of Utah School of
Medicine, UNITED STATES Medicine, UNITED STATES
Received: May 10, 2015
Accepted: September 22, 2015
Published: October 7, 2015
Copyright: © 2015 Cheng et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. Received: May 10, 2015
Accepted: September 22, 2015
Published: October 7, 2015 Copyright: © 2015 Cheng et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. OPEN ACCESS Citation: Cheng C-H, Lee Y-S, Chang C-J, Lin J-C,
Lin T-Y (2015) Genetic Polymorphisms in
Inflammasome-Dependent Innate Immunity among
Pediatric Patients with Severe Renal Parenchymal
Infections. PLoS ONE 10(10): e0140128. doi:10.1371/journal.pone.0140128 * pedneph.cheng@msa.hinet.net Chi-Hui Cheng1,2*, Yun-Shien Lee3,4, Chee-Jen Chang5, Jui-Che Lin6, Tzou-Yien Lin2,7 Chi-Hui Cheng1,2*, Yun-Shien Lee3,4, Chee-Jen Chang5, Jui-Che Lin6, Tzou-Yien Lin2,7 1 Division of Pediatric Nephrology, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung
Memorial Hospital, Taoyuan, Taiwan, 2 College of Medicine, Chang Gung University, Taoyuan, Taiwan,
3 Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan,
4 Department of Biotechnology, Ming-Chuan University, Taoyuan, Taiwan, 5 Statistical Center for Clinical
Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, 6 Institute of Oral Medicine, Department of
Chemical Engineering, National Cheng Kung University, Tainan, Taiwan, 7 Division of Pediatric Infectious
Diseases, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital,
Taoyuan, Taiwan * pedneph.cheng@msa.hinet.net Methodology This study included patients diagnosed with acute pyelonephritis (APN) and acute lobar
nephronia (ALN) who had no underlying disease or structural anomalies other than vesi-
coureteral reflux (VUR). Single nucleotide polymorphism (SNP) genotyping was performed
in the genes associated with inflammasome formation and activation (NLRP3, CARD8) and
subsequent IL–1β cytokine generation (IL–1β). Data Availability Statement: All relevant data are
within the paper and its Supporting Information files. Introduction Urinary tract infections (UTIs) are among the most prevalent bacterial infectious diseases
among pediatric patients, with morbidity risks of ~3% and ~1% in prepubertal females and
males, respectively [1]. The clinical severity of UTIs ranges from uncomplicated lower UTIs,
such as asymptomatic bacteriuria (ABU), to acute pyelonephritis (APN), acute lobar nephronia
(ALN), and renal abscess formation [2, 3]. Among these UTIs, ALN presents as a localized
non-liquefactive inflammatory renal bacterial infection. ALN has been identified as a compli-
cated form of acute renal infection, representing progression of the inflammatory process of
APN. Our previous studies suggested that ALN might represent a relatively early stage in renal
abscess development [2, 3], with a longer duration of antibiotic treatment recommended for
patients with ALN compared with those with APN [2]. Nevertheless, APN, ALN, and intrare-
nal abscess are considered the most serious forms of UTIs requiring different durations of anti-
biotic treatment. Furthermore, in some cases, additional surgical procedures are indicated for
proper treatment [2, 4]. Patients’ susceptibility to UTIs and disease severity are determined by complicated interac-
tions between the host and pathogenic microbes [4–6]. In addition to certain virulence factors
associated with uropathogenic Escherichia coli in specific UTIs [4–8], intra-individual varia-
tions play a role in clinical severity. These observations highlight the importance of host fac-
tors, such as the presence of vesicoureteral reflux (VUR) or genetic polymorphisms in innate
immunity pathway genes, in defending bacterial invasion and infection [9–11]. The innate immune system is considered the first line of defense against microbial infection. In response to microbial invasion, innate immunity is initiated or activated with expression of
extracellular or intracellular germline-encoded pattern-recognition receptors (PRRs) [12, 13]. Next, various intracellular signaling cascades are triggered, which ultimately culminate in host
defense responses to eliminate the microbial invasions. However, such host responses can also
result in various tissue injuries if the host proinflammatory responses are too robust. Previously, we studied pediatric patients with UTIs of differing clinical severity to examine
the associations with genetic variations in the innate immunity pathways that were dependent
upon Toll-like receptors (TLRs), one of the best-characterized PRRs. We demonstrated that
the AA genotype and A allele of the IL–8 SNP were related to patient susceptibility to paren-
chymal infection and were correlated with the severity of infection in pediatric patients with
APN and ALN, probably due to the upregulation of IL–8 expression [14]. Conclusions This study is the first to suggest that the inflammasome-dependent innate immunity path-
way is associated with the pathogenesis of pediatric severe renal parenchymal infections. Further investigation is warranted to clarify its pathogenic mechanism. Principal Findings A total of 40 SNPs were selected for initial genotyping. Analysis of samples from 48 patients
each and 96 controls revealed that only nine SNPs (five SNPs in NLRP3; three SNPs in
CARD8; one SNP in IL–1β) had heterozygosity rates >0.01. Hardy–Weinberg equilibrium
was satisfied for the observed genotype frequencies of these SNPs. Analysis excluding Competing Interests: The authors have declared
that no competing interests exist. 1 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs patients with VUR, a well-known risk factor for severe UTIs, revealed a lower frequency of
the CC genotype in NLRP3 (rs4612666) in patients with APN and ALN than in controls. Cor-
rection for multiple-SNP testing showed that the non-VUR subgroup of the APN+ALN com-
bined patient groups remained significantly different from the control group (P < 0.0055). PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Introduction Additionally, MAL-
DI-TOF SNP analyses revealed that the genetic variant in TLR–2 (rs3804100, T1350C) might
protect the host from severe UTIs such as ALN [15]. 2 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Similar to TLRs, the cytosolic nucleotide-binding domain–leucine-rich repeat-containing
receptors (NLRs, or NOD-like receptors) have been investigated as PRRs for microbial attacks
[13, 16, 17]. In addition to recognizing the pathogen-associated molecular patterns (PAMPs),
the highly conserved markers specific to microbes, these PRRs can also sense danger signals or
danger-associated molecular patterns (DAMPs) released after cellular damage or stress
induced by pathogen attacks [13, 16, 18]. Pathogen recognition activates the host inflamma-
some, a complex of cytosolic NLR-containing proteins, including the NLRP3 protein, protease
caspase–1, and the adaptor protein ASC (apoptosis associated speck-like protein containing a
CARD; the caspase recruitment domain). Activated caspase–1 leads to the cleavage of the pro-
IL–1β and pro-IL–18 to produce IL–1β and IL–18 cytokines, respectively, to form an inflam-
masome-dependent immune response [17, 19, 20]. Despite of inflammasome-dependent immune response has been reported to be associated
with various microbial sensing and reaction to microbial infections [13, 16, 21, 22], none has
explored its likely association with urinary tract infections, to our knowledge. Henceforth, to
exam inflammasome-dependent innate immunity pathway on pediatric patients with severe
renal parenchymal infections might provide supplementary information to our earlier findings
based on the TLR-dependent pathway [14, 15]. In this investigation, we attempted to assess the
likely variations in genes associated with the inflammasome-dependent innate immunity path-
way for pediatric patients with various severe UTIs. The genes selected for initial genotyping
involved in inflammasome formation (NLRP3, CARD8) and subsequent activation and IL–1β
cytokine generation (IL–1β). Among these, NLRP3 has been implicated to be associated with
the tubulointerstitious disease, such as renal infection [19]. These components may play a role
in various inflammatory responses and bacterial clearance in pediatric patients with UTIs of
differing clinical severity, such as APN and the clinically more severe disease ALN. Addition-
ally, as VUR is a well-known risk factor for severe parenchymal infectious disease [9, 23], a sub-
group of APN and ALN cases without VUR (non-VUR) was examined to exclude the possible
effects of VUR. Ethics statement This investigation was approved by the Institutional Review Board of Chang Gung Memorial
Hospital. Written informed consent was obtained from the parents of all participating patients
following a full explanation of the study. Introduction This investigation was part of our ongoing effort to explore the pathogenic host and bacte-
rial urovirulence factors related to pediatric APN and ALN; as such, it includes patients contin-
uously enrolled since our previous studies [5, 14, 15]. Therefore, compared with our previous
reports, this study enrolled a greater number of participants, with a total of 138 APN and 222
ALN cases and 225 controls, including those cases in our earlier investigations on SNPs in
TLR-dependent innate immunity pathway genes (113 APN and 172 ALN cases and 222 con-
trols) [14, 15]. Genotying for the genes associated with the inflammsome-dependent pathway
was commenced on the second half of year 2012, while genotyping for genes associated with
the TLR-dependent pathway presented in earlier publications [14, 15] has been completed in
2010. Study setting and patient selection criteria This study is part of our ongoing investigation of the pathogenic host and bacterial uroviru-
lence factors related to pediatric APN and ALN [5, 14, 15]. Patients were enrolled in the study
if they fulfilled the diagnostic criteria for APN and ALN caused by E. coli and lacked any of the 3 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs exclusion criteria. Participants were admitted to Chang Gung Children’s Hospital, a tertiary
medical center located near Taipei in northern Taiwan, between January 2004 and December
2008 as well as between January 2012 and December 2013. The controls consisted of patients
who visited the outpatient clinic for reasons other than a UTI or severe infection. The controls
had no history of UTI or severe infections and no positive urine culture [14, 15]. A detailed diagnostic schematic plan for patients suspected of having APN or ALN was
described previously [2, 5, 14, 15]. Briefly, all patients with a suspected UTI due to the presence
of pyuria (>5 white blood cells/high-power field) who had fever with symptoms and signs
related to UTIs (e.g., pain, dysuria, and frequent urination) or without focus underwent renal
ultrasonography on the first or second day after admission. Computed tomography (CT) was
performed immediately when the initial ultrasonographic findings showed unilateral or bilat-
eral nephromegaly or a focal renal mass. For patients who presented with borderline nephro-
megaly on ultrasonography, CT was performed when the patient remained febrile for 72 h
after starting the antibiotic therapy. ALN was diagnosed based on positive CT findings. Tech-
netium 99m-dimercaptosuccinic acid scintigraphy (99mTc-DMSA) was performed within 3–7
days of admission in patients suspected of having a febrile UTI who did not satisfy the sono-
graphic criteria for ALN. APN was defined as focal or diffuse areas of decreased 99mTc-DMSA
uptake without evidence of cortical loss. Patients were excluded from this study if they showed evidence of underlying disease such
as diabetes; immunodeficiency; or structural anomalies such as neurogenic bladder, posterior
urethral valve, urinary diversion, bladder diverticulum, ureterocele, or urinary tract obstruction
(other than VUR). PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Genotyping by matrix-assisted laser desorption/ionization time-of-flight
(MALDI-TOF)-based mini-sequencing analysis or direct DNA
sequencing Genotyping for the genes associated with inflammasome-dependent innate immunity pathway
presented here commenced on the second half of year 2012, while genotyping for genes associ-
ated with the TLR-dependent pathway presented in earlier publications [14, 15] has been com-
pleted in 2010. No further genotyping on the inflammasome-dependent pathway was planned. SNPs in the genes encoding NLRP3, CARD8, and IL–1β, as well as in their respective pro-
moter regions, were identified in the NCBI dbSNP database [24]. A total of 40 SNPs
(rs35829419, rs10754558, rs4925659, rs12239046, rs10754555, rs35829479, rs10733113,
rs1539019, rs4925648, rs4925663, rs10802501, rs2027432, rs76291085, rs4353135, rs4266924,
rs55646866, rs6672995, rs4925650, rs3806265, rs4612666, rs10733112, rs12079994,
rs12048215, rs10925019, rs4925654, rs10925026, rs12565738, and rs4378247 for NLRP3;
rs2043211, rs6509365, rs1965759, rs1062808, rs4389238, rs2288877, rs2288876, and rs1972619
for CARD8; rs1143643, rs1143634, rs1143629, and rs16944, for IL–1β) were selected for initial
genotyping based on previous studies on SNPs in inflammasome-dependent pathogenic mech-
anisms for various diseases [25–42]. Analysis of samples from 96 controls and 48 patients each
revealed that only nine SNPs had heterozygosity rates >0.01. Among these, rs4612666
(NLRP3), rs4925650 (NLRP3), rs10754558 (NLRP3), rs1965759 (CARD8), rs2043211
(CARD8), and rs1143629 (IL–1β) were analyzed by direct DNA sequencing (S1 Table). Three
other SNPs, rs1539019 (NLRP3), rs4925663 (NLRP3) and rs1972619 (CARD8), were genotyped
by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based mini-
sequencing analysis (S2 Table). Genomic DNA was extracted from peripheral blood lymphocytes using a Nucleospin
1
Blood DNA extraction kit (Macherey-Nagel, Düren, Germany) [15]. For direct DNA Genomic DNA was extracted from peripheral blood lymphocytes using a Nucleospin
1
Blood DNA extraction kit (Macherey-Nagel, Düren, Germany) [15]. For direct DNA 4 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs sequencing, polymerase chain reaction (PCR) was performed in a master mix (50 μL) contain-
ing 25 ng of DNA, 25 μL DreamTaq Green PCR Master Mix (2x) (Thermo Scientific), 0.5 μL of
each primer (5 pM, Integrated DNA Technologies, IDT) (S1 Table), and 23.5 μL distilled
deionized water (dd H2O). PCR was carried out for 35 cycles with initial denaturation at 94°C
for 2 min followed by denaturation at 94°C for 30 s, annealing for 30 s, extension at 72°C for 40
s, and final extension at 72°C for 7 min. All PCR products were analyzed on a 1.5% agarose gel
to verify the amplification reaction. Genotyping by matrix-assisted laser desorption/ionization time-of-flight
(MALDI-TOF)-based mini-sequencing analysis or direct DNA
sequencing The amplified products were then subjected to direct auto-
mated sequencing (ABI Prism 3730 DNA Analyzer). For MALDI-TOF-based mini-sequencing analysis, the SNPs were genotyped as described
previously [14, 15] using the primers listed in S2 Table. Briefly, the PCR mix (25 μL) contained
200 ng of genomic DNA, primers (25 pM each), dNTPs (0.2 mM), 1× Fast-Start PCR buffer, 1
M betaine, and 1 U of Fast-Start Taq Polymerase (Roche Diagnostics, Basel, Switzerland). The
PCR reaction was initiated at 95°C for 5 min, followed by 40 cycles at 95°C for 45 s, 50°C for 45
s, and 60°C for 45 s, with a final extension at 52°C for 10 min. Unincorporated dNTPs and
primers were removed automatically by MAPIIA (GenePure PCR Purification System; Bruker,
Bremen, Germany). The purified products were amplified further using the respective mini-
sequencing primers (S2 Table) in 20 μL of a solution containing 50 ng of the PCR product,
1 μL (10 pmol) of mini-sequencing primer, 0.5 μL of 1 mM ddNTP/dNTP mixture, 0.5 U of
Thermo Sequenase DNA Polymerase (Amersham Biosciences, Piscataway, NJ), and 2 μL of the
reaction buffer provided by the manufacturer. The reactions were carried out with initial dena-
turation at 96°C for 1 min, followed by 50 cycles of 96°C for 15 s, 50°C for 15 s, 60°C for 100 s,
and 96°C for 30 s (Thermo Hybaid, Waltham, MA). The reaction products were purified auto-
matically by MAPIIA (Single-Strand DNA Binding Beads; Bruker). The purified samples were
then mixed with 0.5 μL of matrix solution (50 mg/mL 3-hydropicolinic acid in a 4:5:1 mixture
of water, acetonitrile, and 50 mg/mL diammonium citrate) and spotted onto 384-well Teflon
sample plates (PerSeptive Biosystems, Framingham, MA). MALDI-TOF mass spectra were
acquired with a Bruker Autoflex MALDI-TOF mass spectrometer (Bruker) and AutoXecute
software (Bruker) to validate the genotype data. PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Results A total of 360 patients (182 males and 178 females) who fulfilled the enrollment criteria for
APN and ALN were included in this study. Among these, 138 patients (77 males and 61
females; 2.50 ± 2.98 years old; range, one month to 14.42 years old) were diagnosed with APN
and 222 (105 males and 117 females; 3.05 ± 2.78 years old; range, one month to 15 years old)
with ALN. The control population consisted of 225 subjects (123 males and 102 females; mean
age ± SD, 2.96 ± 3.02 years old; range, one month to 11 years old]). Although more patients
were included in this investigation as compared to those reported in earlier studies [14, 15], sta-
tistical differences in the demographic and clinical characteristics among these three groups
remained similar to those reported earlier [14, 15], with no significant differences detected in
the sex ratio and age among the three groups (control, APN and ALN). The observed genotype frequency in all groups met the requirements for HWE. The MAL-
DI-TOF mass spectra in NLRP3 (rs1539019) matched with the auto-sequencing results from
randomly selected cases (Fig 1), indicating that MALDI-TOF could be used as the direct DNA
sequencing method for analyzing the likely SNPs. Genotypic analyses of the nine SNPs revealed that NLRP3 (rs4612666) demonstrated a sig-
nificant difference in genotype frequency between the APN and control cases [OR (95% CI):
2.32 (1.66, 3.97)] as well as between the APN and ALN cases [OR (95% CI): 0.50 (0.29, 0.86)]
in the dominant model (Table 1). Additionally, NLRP3 (rs4925650), NLRP3 (rs10754558), and
CARD8 (rs1965759) showed significant differences among different groups using the recessive
model (Table 1). Nevertheless, after correction for multiple-SNP testing (nine SNPs examined),
only NLRP3 (rs4612666) showed a significant difference between the APN and control using
the dominant model (P < 0.0055). Allele frequency analyses demonstrated that NLRP3
(rs4612666) and NLRP3 (rs10754558) showed significant differences when comparing ALN
with APN [OR (95% CI): 1.42 (1.04, 1.93)] and APN with control [OR (95% CI): 1.46 (1.20,
2.01)] (Table 2). As VUR has been indicated as a significant risk factor for upper UTIs [9, 23], further analy-
ses were carried out in the subgroups of APN and ALN patients with no VUR. Statistical analysis Hardy–Weinberg equilibrium (HWE) was tested for goodness-of-fit using a χ2 test with one
degree of freedom. Comparison of genotype and allele frequencies among the control, APN,
and ALN groups were performed by χ2 analysis or two-sided Fisher’s exact test, as appropriate. The association of outcome and SNP genotype was analyzed with recessive and dominant
models [10]. For the dominant model, the genotypes of minor homozygotes and heterozygotes
were combined and compared with common homozygous genotypes. In a similar manner, the
genotypes of common homozygotes and heterozygotes were combined and compared with
minor homozygous genotype for recessive model analysis. A P-value <0.05 was considered to
indicate statistical significance. As no adjustments were made to correct for multiple compari-
sons, the chance of type I errors may have been increased. All statistical analyses were per-
formed using SPSS software (Version 17.0, IBM SPSS Statistics). At first, 96 cases (48 APN and 48 ALN) and 96 control samples were analyzed for NLRP3
(rs4612666) SNP. These 192 samples indicated that the probability of exposure among controls
is 0.25. Using the dominant model, if the true odds ratio for disease in exposed subjects relative
to unexposed subjects is 1.89 as we noted among these 192 samples, we will need to study 196
patients and 196 control patients to be able to reject the null hypothesis that this odds ratio
equals 1 with probability (power) of 0.8. The Type I error probability associated with this test
of this null hypothesis is 0.05. The samples size estimate was performed with PS Power and PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 5 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Sample Size Calculations Version 3.1.2 (http://biostat.mc.vanderbilt.edu/PowerSampleSize)
[43]. PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Results VUR was not
observed in 65 APN patients (35 males and 30 females; 2.51 ± 2.77 years old) and 133 ALN
patients (67 males and 66 females; 2.92 ± 2.63 years old).Our previous report indicated that the
number of patients with VUR in the control group needed to be determined based upon the
reported prevalence rate because voiding cystourethrography (VCUG) was not medically
advised in these control patients [15, 44]. Because the prevalence rate of VUR at the mean age
of the control group (2.96 years old) was ~0.3%, the number of patients with VUR in the 225
control cases could be assumed to be zero. Additionally, no differences were found in age and
sex ratio among the control and non-VUR subgroup of APN and ALN. Among the nine SNPs examined using the dominant model, only NLRP3 (rs4612666)
showed a significant difference in genotypic frequency between the control group and non-
VUR in the APN, ALN, and combined (APN+ALN) subgroups. In these analyses, the CC
genotype frequency of the non-VUR subgroups of APN, ALN, and APN+ALN cases were sig-
nificantly lower than that of the control (Table 3). However, with the correction for multiple-
SNP testing, only the non-VUR subgroup of the APN+ALN group remained significantly dif-
ferent from the control group (P < 0.0055). Nevertheless, allele frequency analyses showed
no significant differences between the control and non-VUR subgroups of APN and ALN
(Table 4). 6 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Discussion A concerted host innate and adaptive immune response is required for defending against bac-
terial invasion or infection. For this defense, the host must first recognize the pathogen through A concerted host innate and adaptive immune response is required for defending against bac-
terial invasion or infection. For this defense, the host must first recognize the pathogen through
Table 1. Genotypic analysis of the SNPs. SNP
Group
Genotype, n (%)
Dominant model
Recessive model
00
01
11
(01, 11 vs. 00)
(00, 01vs. Discussion 11)
CC
CT
TT
OR (95% CI)
Pa
OR (95% CI)
Pa
OR (95% CI)
Pa
OR (95% CI)
Pa
NLRP3
Control
68 (32.7)
95 (45.7)
45 (21.6)
1.00
1.00
(rs4612666)
APN
23 (17.3)
84 (63.2)
26 (19.5)
2.32 (1.66, 3.97)
0.002c
1.00
1.14 (0.66, 1.95)
0.644
1.00
ALN
61 (29.5)
116 (56.0)
30 (14.5)
1.16 (0.77, 1,76)
0.478
0.50 (0.29, 0.86)
0.011
1.63 (0.98, 2.71)
0.059
1.43 (0.81, 2.55)
0.220
Combinedb
84 (24.7)
200 (58.8)
56 (16.5)
1.48 (1.01, 2.17)
0.043
1.40 (0.90, 2.17)
0.133
GG
GA
AA
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
NLRP3
Control
66 (31.9)
97 (46.9)
44 (21.3)
1.00
1.00
(rs4925650)
APN
40 (30.5)
70 (53.4)
21 (16.0)
1.07 (0.66, 1.71)
0.794
1.00
1.41 (0.80, 2.51)
0.235
1.00
ALN
65 (30.4)
89 (41.6)
60 (28.0)
1.07 (0.71, 1.62)
0.738
1.01 (0.63, 1.62)
0.975
0.69 (0.44, 1.08)
0.107
0.49 (0.28, 0.85)
0.011
Combined
105 (30.4)
159 (46.1)
81 (23.5)
1.07 (0.74, 1.55)
0.721
0.88 (0.58, 1.33)
0.546
CC
CG
GG
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
NLRP3
Control
85 (37.9)
105 (46.9)
34 (15.2)
1.00
1.00
(rs10754558)
APN
64 (47.8)
59 (44.0)
11 (8.2)
0.67 (0.43, 1.03)
0.066
1.00
2.03 (0.99, 4.16)
0.049
1.00
ALN
86 (40.0)
102 (47.4)
27 (12.6)
0.92 (0.63, 1.35)
0.659
1.37 (0.89, 2.12)
0.151
1.25 (0.72, 2.15)
0.427
0.61 (0.29, 1.28)
0.189
Combined
150 (43.0)
161 (46.1)
38 (10.9)
0.81 (0.58, 1.14)
0.228
1.47 (0.90, 2.42)
0.124
GG
GT
TT
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
NLRP3
Control
86 (39.4)
104 (47.7)
28 (12.8)
1.00
1.00
(rs1539019)
APN
53 (40.5)
58 (44.3)
20 (15.3)
0.96 (0.62, 1.49)
0.852
1.00
0.82 (0.44, 1.52)
0.524
1.00
ALN
67 (32.2)
104 (50.0)
37 (17.8)
1.37 (0.92, 2.04)
0.120
1.43 (0.91, 2.25)
0.122
0.68 (0.40, 1.16)
0.156
0.83 (0.46, 1.51)
0.546
Combined
120 (35.4)
162 (47.8)
57 (16.8)
1.19 (0.84, 1.69)
0.334
0.73 (0.45, 1.19)
0.203
TT
TC
CC
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
NLRP3
Control
57 (28.9)
97 (49.2)
43 (21.8)
1.00
1.00
(rs4925663)
APN
29 (24.8)
60 (51.3)
28 (23.9)
1.24 (0.73, 2.08)
0.426
1.00
0.89 (0.52, 1.53)
0.666
1.00
ALN
51 (24.8)
101 (49.0)
54 (26.2)
1.24 (0.80, 1.92)
0.344
1.00 (0.59, 1.69)
0.995
0.79 (0.50, 1.24)
0.303
0.89 (0.52, 1.50)
0.651
Combined
80 (24.8)
161 (49.8)
82 (25.4)
1.24 (0.83, 1.84)
0.295
0.82 (0.54, 1.25)
0.357
CC
CT
TT
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
CARD8
Control
126 (60.6)
71 (34.1)
11 (5.3)
1.00
1.00
(rs1965759)
APN
70 (53.8)
59 (45.4)
1 (0.8)
1.32 (0.85, 2.05)
0.223
1.00
7.20 (0.92, 56.5)
0.033
1.00
ALN
116 (54.7)
87 (41.0)
9 (4.2)
1.27 (0.86, 1.87)
0.224
0.97 (0.62, 1.50)
0.875
1.26 (0.51, 3.11)
0.616
1.00 (0.02, 1.42)
0.096
Combined
186 (54.4)
146 (33.9)
10 (2.9)
1.29 (0.91, 1.83)
0.155
1.85 (0.77, 4.44)
0.161
TT
TA
AA
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
CARD8
Control
65 (29.4)
108 (48.9)
48 (21.7)
1.00
1.00
(rs2043211)
APN
37 (28.0)
72 (54.5)
23 (17.4)
1.07 (0.66, 1.73)
0.782
1.00
1.32 (0.76, 2.28)
0.330
1.00
ALN
58 (26.5)
118 (53.9)
43 (19.6)
1.16 (0.77, 1.77)
0.475
1.09 (0.67, 1.77)
0.733
1.14 (0.72, 1.81)
0.573
0.87 (0.50, 1.52)
0.622
Combined
95 (27.1)
190 (54.1)
66 (18.8)
1.13 (0.78, 1.64)
0.529
1.20 (0.79, 1.82)
0.386
GG
GA
AA
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
CARD8
Control
113 (51.6)
93 (42.5)
13 (5.9)
1.00
1.00
(rs1972619)
APN
60 (48.0)
53 (42.4)
12 (9.6)
1.16 (0.74, 1.79)
0.521
1.00
0.59 (0.26, 1.35)
0.208
1.00
ALN
93 (44.5)
97 (46.4)
19 (9.1)
1.33 (0.91, 1.95)
0.142
1.15 (0.74, 1.80)
0.534
0.63 (0.30, 1.31)
0.215
1.06 (0.50, 2.27)
0.877
Combined
153 (45.8)
150 (44.9)
31 (9.3)
1.26 (0.90, 1.77)
0.183
0.62 (0.32, 1.21)
0.155
CC
CT
TT
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
OR (95% CI)
P
IL1-β
Control
52 (23.7)
122 (55.7)
45 (20.5)
1.00
1.00
(rs1143629)
APN
24 (18.0)
71 (53.4)
38 (28.6)
1.43 (0.83, 2.45)
0.196
1.00
0.65 (0.40, 1.08)
0.093
1.00
ALN
52 (24.0)
114 (52.5)
51 (23.5)
1.00 (0.64, 1.55)
1.000
0.70 (0.41, 1.20)
0.196
0.85 (0.54, 1.34)
0.488
1.30 (0.80, 2.13)
0.287
Combined
76 (21.7)
185 (52.4)
89 (25.4)
1.14 (0.76, 1.70)
0.537
0.77 (0.51, 1.15)
0.200
a P-values <0.05 are shown in bold. SNPs in Inflammasome among Pediatric Patients with Severe UTIs b APN + ALN
c Statistically significant with correction for multiple-SNP testing (P < 0.0055) SNPs in Inflammasome among Pediatric Patients with Severe UTIs Fig 1. MALDI-TOF mass spectra from the genotyping of NLRP3 (rs1539019) PCR product and its sequencing results. (A) The SNP
by MALDI-TOF MS based on the molecular weights of the mini-sequencing products listed in S2 Table. (B) Sequencing results for each of
from the G/T, T/T, and G/G genotypes of rs1539019. The SNPs are indicated by arrows. doi:10.1371/journal.pone.0140128.g001
PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Fig 1. MALDI-TOF mass spectra from the genotyping of NLRP3 (rs1539019) PCR product and its sequencing results. (A) The SNPs were genotyped
by MALDI-TOF MS based on the molecular weights of the mini-sequencing products listed in S2 Table. (B) Sequencing results for each of the PCR products
from the G/T, T/T, and G/G genotypes of rs1539019. The SNPs are indicated by arrows. doi:10.1371/journal.pone.0140128.g001 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 7 / 15 c Statistically significant with correction for multiple-SNP testing (P < 0.0055) doi:10.1371/journal.pone.0140128.t001 b APN + ALN
c Statistically significant with correction for multiple SNP testing (P < 0 0055) b APN + ALN b APN + ALN a P-values <0.05 are shown in bold. APN
Control
APN
ALN
Combinedb
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
NLRP3, (rs4612666), C
major allele
55.53
48.87
57.49
54.12
0.77 (0.56,
1.04)
0.089
1.08 (0.82,
1.43)
0.569
0.95 (0.74,
1.21)
0.649
1.42 (1.04,
1.93)
0.028
NLRP3, (rs4925650), G
major allele
55.31
57.25
51.17
53.48
1.08 (0.79,
1.48)
0.621
0.85 (0.65,
1.11)
0.228
0.93 (0.73,
1.19)
0.553
0.78 (0.57,
1.07)
0.120
NLRP3, (rs10754558), C
major allele
61.38
69.78
63.72
66.05
1.46 (1.02,
2.01)
0.021
1.11 (0.84,
1.45)
0.475
1.23 (0.96,
1.57)
0.104
0.76 (0.55,
1.05)
0.095
NLRP3, (rs1539019), G
major allele
63.30
62.60
57.21
59.29
0.97 (0.71,
1.33)
0.851
0.78 (0.59,
1.02)
0.069
0.84 (0.66,
1.08)
0.181
0.80 (0.58,
1.10)
0.165
NLRP3, (rs4925663), T
major allele
53.55
50.43
49.27
49.69
0.88 (0.64,
1.22)
0.448
0.84 (0.64,
1.11)
0.224
0.86 (0.67,
1.10)
0.227
0.96 (0.69,
1.32)
0.778
CARD8, (rs1965759), C
major allele
77.64
76.54
75.24
75.73
0.94 (0.65,
1.36)
0.739
0.88 (0.64,
1.20)
0.411
0.90 (0.69,
1.20)
0.468
0.93 (0.65,
1.34)
0.700
CARD8, (rs2043211), T
major allele
53.84
55.30
53.42
54.13
1.06 (0.78,
1.44)
0.707
0.98 (0.75,
1.28)
0.896
1.01 (0.80,
1.29)
0.928
0.93 (0.68,
1.26)
0.625
CARD8, (rs1972619), G
major allele
72.83
69.20
67.70
68.26
0.84 (0.60,
1.18)
0.310
0.78 (0.58,
1.05)
0.101
0.80 (0.62,
1.05)
0.105
0.93 (0.67,
1.31)
0.688
IL1-β, (rs1143629), C
major allele
51.60
44.74
50.23
48.14
0.76 (0.56,
1.03)
0.078
0.95 (0.73,
1.23)
0.685
0.87 (0.69,
1.11)
0.258
1.25 (0.92,
1.69)
0.159
a P-values <0.05 are shown in bold. b APN + ALN
doi:10.1371/journal.pone.0140128.t002
g Table 2. Allele frequency analysis of the SNPs. SNP
Major allele frequency (%)
APN vs. control
ALN vs. control
Combined vs. control
ALN vs. APN
Control
APN
ALN
Combinedb
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
NLRP3, (rs4612666), C
major allele
55.53
48.87
57.49
54.12
0.77 (0.56,
1.04)
0.089
1.08 (0.82,
1.43)
0.569
0.95 (0.74,
1.21)
0.649
1.42 (1.04,
1.93)
0.028
NLRP3, (rs4925650), G
major allele
55.31
57.25
51.17
53.48
1.08 (0.79,
1.48)
0.621
0.85 (0.65,
1.11)
0.228
0.93 (0.73,
1.19)
0.553
0.78 (0.57,
1.07)
0.120
NLRP3, (rs10754558), C
major allele
61.38
69.78
63.72
66.05
1.46 (1.02,
2.01)
0.021
1.11 (0.84,
1.45)
0.475
1.23 (0.96,
1.57)
0.104
0.76 (0.55,
1.05)
0.095
NLRP3, (rs1539019), G
major allele
63.30
62.60
57.21
59.29
0.97 (0.71,
1.33)
0.851
0.78 (0.59,
1.02)
0.069
0.84 (0.66,
1.08)
0.181
0.80 (0.58,
1.10)
0.165
NLRP3, (rs4925663), T
major allele
53.55
50.43
49.27
49.69
0.88 (0.64,
1.22)
0.448
0.84 (0.64,
1.11)
0.224
0.86 (0.67,
1.10)
0.227
0.96 (0.69,
1.32)
0.778
CARD8, (rs1965759), C
major allele
77.64
76.54
75.24
75.73
0.94 (0.65,
1.36)
0.739
0.88 (0.64,
1.20)
0.411
0.90 (0.69,
1.20)
0.468
0.93 (0.65,
1.34)
0.700
CARD8, (rs2043211), T
major allele
53.84
55.30
53.42
54.13
1.06 (0.78,
1.44)
0.707
0.98 (0.75,
1.28)
0.896
1.01 (0.80,
1.29)
0.928
0.93 (0.68,
1.26)
0.625
CARD8, (rs1972619), G
major allele
72.83
69.20
67.70
68.26
0.84 (0.60,
1.18)
0.310
0.78 (0.58,
1.05)
0.101
0.80 (0.62,
1.05)
0.105
0.93 (0.67,
1.31)
0.688
IL1-β, (rs1143629), C
major allele
51.60
44.74
50.23
48.14
0.76 (0.56,
1.03)
0.078
0.95 (0.73,
1.23)
0.685
0.87 (0.69,
1.11)
0.258
1.25 (0.92,
1.69)
0.159
a P-values <0.05 are shown in bold. b APN + ALN
d i 10 1371/j
l
0140128 t002 Table 2. Allele frequency analysis of the SNPs. doi:10.1371/journal.pone.0140128.t002 the expression of various extracellular or intracellular PRRs such as the TLRs and the NOD-
like receptors (NLRs). Following this microbial sensing step, consecutive activation of intracel-
lular signaling cascades marks the initiation of the immune responses [13]. These responses
determine the host health status as well as the clinical severity [9]. Therefore, the risk of bacte-
rial infection would be influenced by the signal transmission effectiveness in the immune
response pathway. Defective signal transmission caused by a genetic polymorphism in the
receptors, adaptors, or cytokines would influence an individual’s risk for infectious diseases
[11, 14, 15, 45, 46]. NLRs have been considered important PRRs for various PAMPs, including lipopolysaccha-
ride (LPS), bacterial toxins, and viral nucleic acids [19, 22]. Discussion Table 1. Genotypic analysis of the SNPs. PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 8 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs the expression of various extracellular or intracellular PRRs such as the TLRs and the NOD-
like receptors (NLRs). Following this microbial sensing step, consecutive activation of intracel-
lular signaling cascades marks the initiation of the immune responses [13]. These responses
determine the host health status as well as the clinical severity [9]. Therefore, the risk of bacte-
rial infection would be influenced by the signal transmission effectiveness in the immune
response pathway. Defective signal transmission caused by a genetic polymorphism in the
receptors, adaptors, or cytokines would influence an individual’s risk for infectious diseases
[11, 14, 15, 45, 46]. NLRs have been considered important PRRs for various PAMPs, including lipopolysaccha-
ride (LPS), bacterial toxins, and viral nucleic acids [19, 22]. The NLRs can also sense damage-
associated molecular patterns (DAMPs) such as potassium efflux, reactive oxygen species,
urate crystals, and extracellular matrix components including hyaluronan and biglycan [13,
16–20]. Following recognition of the signal pattern, the inflammasome consisting of NLRs,
adaptor protein ASC, and caspase–1 is activated, and cytokines are released. These signal trans-
mission cascades form an inflammasome-dependent innate immunity pathway. In the present study, the most significant finding was the association between NLRP3
(rs4612666) and severe renal parenchymal infections, APN and ALN. After excluding patients
with VUR, a well-known risk factor for severe UTI, we found that patients with APN and ALN
had a lower genotype frequency of NLRP3 (rs4612666) CC than did controls. This result
implies that the CC genotype in NLRP3 (rs4612666) participates in regulating the inflamma-
tory responses for pediatric renal parenchymal infections in patients from Taiwan. Genetic variations can modify the extent or severity of disease in susceptible patients. Muta-
tions in the NLRP3 gene have been linked to several autoinflammatory disorders including
Table 2. Allele frequency analysis of the SNPs. SNP
Major allele frequency (%)
APN vs. control
ALN vs. control
Combined vs. control
ALN vs. PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoureteral reflux (non-VUR). SNP
Group
Genotype, n (%)
Dominant model
Recessive model
00
01
11
(01, 11 vs. 00)
(00, 01vs. The NLRs can also sense damage-
associated molecular patterns (DAMPs) such as potassium efflux, reactive oxygen species,
urate crystals, and extracellular matrix components including hyaluronan and biglycan [13,
16–20]. Following recognition of the signal pattern, the inflammasome consisting of NLRs,
adaptor protein ASC, and caspase–1 is activated, and cytokines are released. These signal trans-
mission cascades form an inflammasome-dependent innate immunity pathway. In the present study, the most significant finding was the association between NLRP3
(rs4612666) and severe renal parenchymal infections, APN and ALN. After excluding patients
with VUR, a well-known risk factor for severe UTI, we found that patients with APN and ALN
had a lower genotype frequency of NLRP3 (rs4612666) CC than did controls. This result
implies that the CC genotype in NLRP3 (rs4612666) participates in regulating the inflamma-
tory responses for pediatric renal parenchymal infections in patients from Taiwan. Genetic variations can modify the extent or severity of disease in susceptible patients. Muta-
tions in the NLRP3 gene have been linked to several autoinflammatory disorders including PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 9 / 15 11)
CC
CT
TT
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
NLRP3
Control
68
(32.7)
95
(45.7)
45
(21.6)
1.00
1.00
(rs4612666)
APN
12
(19.0)
40
(63.5)
11
(17.5)
2.06 (1.03,
4.13)
0.038
1.00
1.31 (0.63,
2.71)
0.473
1.00
ALN
26
(20.6)
82
(65.1)
18
(14.3)
1.87 (1.11,
3.14)
0.018
0.91 (0.42,
1.94)
0.797
1.66 (0.91,
3.01)
0.096
1.27 (0.56,
2.88)
0.568
Combinedb
38
(20.1)
122
(64.6)
29
(15.3)
1.93 (1.22,
3.05)
0.005c
1.52 (0.91,
2.55)
0.108
GG
GA
AA
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
NLRP3
Control
66
(31.9)
97
(46.9)
44
(21.3)
1.00
1.00
(rs4925650)
APN
20
(32.8)
34
(55.7)
7 (11.5)
0.96 (0.52,
1.77)
0.894
1.00
2.08 (0.89,
4.90)
0.087
1.00
ALN
43
(33.1)
59
(45.4)
28
(21.5)
0.95 (0.59,
1.51)
0.820
0.99 (0.52,
1.89)
0.968
0.98 (0.58,
1.68)
0.951
0.47 (0.19,
1.15)
0.094
Combined
63
(33.0)
93
(48.7)
35
(18.3)
0.95 (0.63,
1.45)
0.815
1.20 (0.73,
1.97)
0.464
CC
CG
GG
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
NLRP3
Control
85
(37.9)
105
(46.9)
34
(15.2)
1.00
1.00
(rs10754558)
APN
28
(45.9)
25
(41.0)
8 (13.1)
0.72 (0.41,
1.28)
0.260
1.00
1.19 (0.52,
2.71)
0.687
1.00
ALN
45
(34.9)
63
(48.8)
21
(16.3)
1.14 (0.73,
1.79)
0.566
1.58 (0.85,
2.95)
0.145
0.92 (0.51,
1.67)
0.784
0.78 (0.32,
1.87)
0.571
Combined
73
(38.4)
88
(46.3)
29
(15.3)
0.98 (0.66,
1.46)
0.921
0.99 (0.58,
1.70)
0.981
GG
GT
TT
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
NLRP3
Control
86
(39.4)
104
(47.7)
28
(12.8)
1.00
1.00
(rs1539019)
APN
20
(31.7)
33
(52.4)
10
(15.9)
1.40 (0.77,
2.54)
0.267
1.00
0.78 (0.36,
1.71)
0.682
1.00
ALN
46
(35.9)
63
(49.2)
19
(14.8)
1.16 (0.74,
1.83)
0.516
0.83 (0.44,
1.58)
0.567
0.85 (0.45,
1.59)
0.600
1.08 (0.47,
2.49)
0.852
Combined
66
(34.6)
96
(50.3)
29
(15.2)
1.23 (0.82,
1.85)
0.307
0.82 (0.47,
1.44)
0.496
TT
TC
CC
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
NLRP3
Control
57
(28.9)
97
(49.2)
43
(21.8)
1.00
1.00
(rs4925663)
APN
15
(26.8)
27
(48.2)
14
(25.0)
1.11 (0.57,
2.17)
0.753
1.00
0.84 (0.42,
1.68)
0.616
1.00
ALN
35
(27.8)
57
(45.2)
34
(27.0)
1.06 (0.64,
1.74)
0.822
0.95 (0.47,
1.93)
0.890
0.76 (0.45,
1.27)
0.289
0.90 (0.44,
1.86)
0.779
Combined
50
(27.5)
84
(46.2)
48
(26.4)
1.08 (0.69,
1.68)
0.752
0.78 (0.49,
1.25)
0.301
(Continued) Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoureteral reflux (non-VUR). Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoure PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 10 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 3. (Continued)
SNP
Group
Genotype, n (%)
Dominant model
Recessive model
00
01
11
(01, 11 vs. 00)
(00, 01vs. 11)
CC
CT
TT
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
CARD8
Control
126
(60.6)
71
(34.1)
11 (5.3)
1.00
1.00
(rs1965759)
APN
37
(60.7)
23
(37.7)
1 (1.6)
1.00 (0.56,
1.79)
0.991
1.00
3.35 (0.42,
26.5)
0.309
1.00
ALN
72
(55.8)
50
(38.8)
7 (5.4)
1.22 (0.78,
1.90)
0.388
1.22 (0.66,
2.27)
0.529
0.97 (0.37,
2.58)
0.956
0.29 (0.04,
2.44)
0.440
Combined
109
(57.4)
73
(38.4)
8 (4.2)
1.14 (0.77,
1.70)
0.516
1.27 (0.50,
3.23)
0.788
TT
TA
AA
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
CARD8
Control
65
(29.4)
108
(48.9)
48
(21.7)
1.00
1.00
(rs2043211)
APN
17
(26.6)
34
(53.1)
13
(20.3)
1.15 (0.62,
2.15)
0.657
1.00
1.09 (0.55,
2.17)
0.809
1.00
ALN
38
(29.2)
65
(50.0)
27
(20.8)
1.01 (0.63,
1.62)
0.971
0.88 (0.45,
1.71)
0.698
1.06 (0.62,
1.80)
0.834
0.97 (0.46,
2.04)
0.941
Combined
55
(28.4)
99
(51.0)
40
(20.6)
1.05 (0.69,
1.61)
0.812
1.07 (0.67,
1.71)
0.784
GG
GA
AA
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
CARD8
Control
113
(51.6)
93
(42.5)
13 (5.9)
1.00
1.00
(rs1972619)
APN
28
(50.9)
23
(41.8)
4 (7.3)
1.03 (0.57,
1.86)
0.927
1.00
0.81 (0.25,
2.57)
0.713
1.00
ALN
59
(46.8)
56
(44.4)
11 (8.7)
1.21 (0.78,
1.88)
0.393
1.18 (0.63,
2.22)
0.613
0.66 (0.29,
1.52)
0.326
0.82 (0.25,
2.70)
0.744
Combined
87
(48.1)
79
(43.6)
15 (8.3)
1.15 (0.78,
1.71)
0.482
0.70 (0.32,
1.51)
0.359
CC
CT
TT
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
OR (95%
CI)
P
IL1-β
Control
52
(23.7)
122
(55.7)
45
(20.5)
1.00
1.00
(rs1143629)
APN
12
(20.0)
34
(56.7)
14
(23.3)
1.25 (0.62,
2.52)
0.541
1.00
0.85 (0.43,
1.68)
0.640
1.00
ALN
33
(25.8)
67
(52.3)
28
(21.9)
0.90 (0.54,
1.48)
0.670
0.72 (0.34,
1.52)
0.387
0.92 (0.54,
1.57)
0.770
1.09 (0.52,
2.26)
0.823
Combined
45
(23.9)
101
(53.7)
42
(22.3)
0.99 (0.63,
1.56)
0.964
0.90 (0.56,
1.45)
0.660
a P values <0 05 are shown in bold APN + ALN
c Statistically significant with correction for multiple-SNP testing (P < 0.0055) Muckle–Wells syndrome, familial cold autoinflammatory syndrome, and chronic infantile
neurologic cutaneous and articular syndrome [17]. SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 4. Allele frequency analysis of the SNPs in the non-VUR patient subgroup. SNP
Major allele frequency (%)
APN vs. control
ALN vs. control
Combined vs. control
ALN vs. APN
Control
APN
ALN
Combinedb
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
OR (95%
CI)
Pa
NLRP3, (rs4612666), C
major allele
55.53
50.79
53.17
52.38
0.83 (0.56,
1.23)
0.350
0.91 (0.66,
1.25)
0.554
0.88 (0.67,
1.17)
0.374
1.10 (0.72,
1.69)
0.662
NLRP3, (rs4925650), G
major allele
55.31
60.66
55.77
57.33
1.25 (0.83,
1.88)
0.296
1.02 (0.75,
1.39)
0.908
1.09 (0.82,
1.44)
0.567
0.82 (0.53,
1.27)
0.368
NLRP3, (rs10754558), C
major allele
61.38
66.39
59.30
61.58
1.24 (0.82,
1.89)
0.311
0.92 (0.67,
1.25)
0.586
1.10 (0.76,
1.34)
0.954
0.74 (0.47,
1.16)
0.185
NLRP3, (rs1539019), G
major allele
63.30
57.94
60.55
59.69
0.80 (0.53,
1.20)
0.274
0.89 (0.65,
1.22)
0.470
0.86 (0.65,
1.14)
0.289
1.11 (0.72,
1.72)
0.625
NLRP3, (rs4925663), T
major allele
53.55
50.89
50.40
50.55
0.90 (0.59,
1.37)
0.619
0.88 (0.64,
1.21)
0.433
0.89 (0.67,
1.18)
0.408
0.98 (0.63,
1.53)
0.930
CARD8, (rs1965759), C
major allele
77.64
79.51
75.19
76.58
1.12 (0.68,
1.84)
0.662
0.87 (0.61,
1.26)
0.464
0.94 (0.68,
1.31)
0.721
0.78(0.46,
1.32)
0.354
CARD8, (rs2043211), T
major allele
53.84
53.13
54.23
53.87
0.97 (0.66,
1.44)
0.885
1.02 (0.75,
1.38)
0.921
1.00 (0.76,
1.32)
0.995
1.05 (0.68,
1.60)
0.837
CARD8, (rs1972619), G
major allele
72.83
71.82
69.05
69.89
0.95 (0.60,
1.51)
0.831
0.83 (0.59,
1.17)
0.89
0.87 (0.64,
1.18)
0.359
0.88 (0.53,
1.43)
0.597
IL1-β, (rs1143629), C
major allele
51.60
48.33
51.95
50.80
0.88 (0.59,
1.32)
0.526
1.01 (0.75,
1.38)
0.928
0.97 (0.74,
1.28)
0.820
1.16 (0.75,
1.78)
0.513
a P-values <0.05 are shown in bold. b APN + ALN
doi:10 1371/journal pone 0140128 t004 Table 4. Allele frequency analysis of the SNPs in the non-VUR patient subgroup. doi:10.1371/journal.pone.0140128.t004 sensing and reaction to various microbial infections [13, 16, 21, 22]. However, to our knowl-
edge, no study has reported the likely association of renal parenchymal infections and the
inflammasome-dependent innate immune pathway. This investigation suggested that the
NLRP3 polymorphisms could influence the susceptibility of pediatric patients to severe renal
parenchymal infections. NLRP3 is in the NLR family of proteins. Other NLR proteins, including NLRP1, NLRC4
and AIM2 are also involved in sensing and activation by various microbes [16, 17, 21, 22]. Additionally, NLRP3 polymorphisms have
been associated with susceptibility to a number of different diseases, such as coal workers'
pneumoconiosis, Crohn’s disease, sporadic malignant melanoma, psoriasis and many others
[27, 28, 30–32, 34, 37, 41, 42, 47]. Inflammasome activation has been associated with microbial PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 11 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 Author Contributions Conceived and designed the experiments: CHC YSL TYL. Performed the experiments: CHC
YSL. Analyzed the data: CHC YSL CJC JCL. Contributed reagents/materials/analysis tools:
CHC YSL CJC JCL. Wrote the paper: CHC JCL. Conceived and designed the experiments: CHC YSL TYL. Performed the experiments: CHC
YSL. Analyzed the data: CHC YSL CJC JCL. Contributed reagents/materials/analysis tools:
CHC YSL CJC JCL. Wrote the paper: CHC JCL. Whether polymorphisms in genes encoding other NLR proteins are linked with the severity of
pediatric renal parenchymal infections remains to be explored. Similarly, the likely roles of IL–
18 polymorphism, another cytokine indicated in inflammasome-dependent innate immunity
pathway in various kidney diseases [17–20], in pediatric renal infectious diseases would also
require further investigations. Previous study has shown the CC genotype frequency is higher in the cases with food-
induced anaphylaxis than those without [42]. In addition, the NLRP3 rs4162666 C allele has
been demonstrated to be associated with higher transcriptional activity in THP–1 cell in vitro
[42]. However, the CC genotype is significantly less in the non-VUR subgroup of cases with
APN and ALN as compared to the control. This suggests that the finding about the higher tran-
scription activity in C allele may not be feasible to explain our results here. More experimental
works are warranted to clarify about the possible biological pathway. In summary, this is the first study to show that the inflammasome-dependent innate immu-
nity pathway is likely involved in severe renal parenchymal infection. We showed that genetic
polymorphisms in NLRP3 (rs4612666) are related to the pediatric patient’s susceptibility to
APN and ALN. Further investigations of phenotypes or functional assessment of this SNP is 12 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs warranted to confirm their pathogenic roles. Additionally, as the statistical power to detect sig-
nificant associations with genetic variants is determined by sample size, a larger cohort study is
recommended to replicate and validate the associations of SNPs with the severe UTIs, includ-
ing APN and ALN. S1 File. The supplementary patient data.
(XLSX) S1 Table. Primers employed for DNA amplification by direct DNA sequencing analysis of
single nucleotide polymorphisms (SNPs). (DOCX) S2 Table. Primers used for DNA amplification and mini-sequencing analysis of the SNPs. (DOCX) PLOS ONE | DOI:10.1371/journal.pone.0140128
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20661102 5. Cheng CH, Tsau YK, Su LH, Lin CL, Lin TY. Comparison of urovirulence factors and genotypes for bac-
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susceptibility to urinary tract infections in adult women. PLoS One. 2009; 4(6):e5990. doi: 10.1371/
journal.pone.0005990 PMID: 19543401 11. Lundstedt AC, McCarthy S, Gustafsson MC, Godaly G, Jodal U, Karpman D, et al. A genetic basis of
susceptibility to acute pyelonephritis. PLoS One. 2007; 2(9):e825. PMID: 17786197 PLOS ONE | DOI:10.1371/journal.pone.0140128
October 7, 2015 13 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs 12. Franchi L, Eigenbrod T, Munoz-Planillo R, Nunez G. PLOS ONE | DOI:10.1371/journal.pone.0140128
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variation in inflammasome genes is associated with outcome in bacterial meningitis. Immunogenetics. 2013; 65(1):9–16. doi: 10.1007/s00251-012-0653-x PMID: 23053059 27. Verma D, Bivik C, Farahani E, Synnerstad I, Fredrikson M, Enerback C, et al. Inflammasome polymor-
phisms confer susceptibility to sporadic malignant melanoma. Pigment Cell & Melanoma Research. 2012; 25(4):506–13. doi: 10.1111/j.1755-148X.2012.01008.x PMID: 22524199 28. Pontillo A, Oshiro TM, Girardelli M, Kamada AJ, Crovella S, Duarte AJS. Polymorphisms in inflamma-
some' genes and susceptibility to HIV–1 infection. Journal of Acquired Immune Deficiency Syndromes:
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masome genes are involved in the predisposition to systemic lupus erythematosus. Autoimmunity. 2012; 45(4):271–8. doi: 10.3109/08916934.2011.637532 PMID: 22235789 30. Ji X, Hou Z, Wang T, Jin K, Fan J, Luo C, et al. Polymorphisms in inflammasome genes and risk of coal
workers' pneumoconiosis in a Chinese population. PLoS ONE. 2012; 7(10):e47949. doi: 10.1371/
journal.pone.0047949 PMID: 23110140 31. Carlstrom M, Ekman A-K, Petersson S, Soderkvist P, Enerback C. Genetic support for the role of the
NLRP3 inflammasome in psoriasis susceptibility. Experimental Dermatology. 2012; 21(12):932–7. doi:
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October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs 32. Blomgran R, Patcha Brodin V, Verma D, Bergstrom I, Soderkvist P, Sjowall C, et al. Common genetic
variations in the NALP3 inflammasome are associated with delayed apoptosis of human neutrophils. PLoS ONE. 2012; 7(3):e31326. doi: 10.1371/journal.pone.0031326 PMID: 22403613 33. Yang S-K, Kim H, Hong M, Lim J, Choi E, Ye BD, et al. Association of CARD8 with inflammatory bowel
disease in Koreans. Journal of Human Genetics. 2011; 56(3):217–23. doi: 10.1038/jhg.2010.170
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NALP3/NLRP3 gene and an NLRP1 haplotype are associated with celiac disease. American Journal of
Gastroenterology. 2011; 106(3):539–44. doi: 10.1038/ajg.2010.474 PMID: 21245836 35. Lewis GJ, Massey DCO, Zhang H, Bredin F, Tremelling M, Lee JC, et al. Genetic association between
NLRP3 variants and Crohn's disease does not replicate in a large UK panel. Inflammatory Bowel Dis-
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masome component, cervical mycoplasma detection and female infertility in women undergoing in vitro
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PMID: 20060594 37. Roberts RL, Topless RKG, Phipps-Green AJ, Gearry RB, Barclay ML, Merriman TR. Evidence of inter-
action of CARD8 rs2043211 with NALP3 rs35829419 in Crohn's disease. Genes & Immunity. 2010; 11
(4):351–6. doi: 10.1038/gene.2010.11 PMID: 20182451 38. Pontillo A, Brandao LA, Guimaraes RL, Segat L, Athanasakis E, Crovella S. A 3'UTR SNP in NLRP3
gene is associated with susceptibility to HIV–1 infection. Journal of Acquired Immune Deficiency Syn-
dromes: JAIDS. 2010; 54(3):236–40. doi: 10.1097/QAI.0b013e3181dd17d4 PMID: 20502346 39. Pontillo A, Brandao L, Guimaraes R, Segat L, Araujo J, Crovella S. Two SNPs in NLRP3 gene are
involved in the predisposition to type–1 diabetes and celiac disease in a pediatric population from north-
east Brazil. Autoimmunity. 2010; 43(8):583–9. doi: 10.3109/08916930903540432 PMID: 20370570 40. Kastbom A, Johansson M, Verma D, Soderkvist P, Rantapaa-Dahlqvist S. CARD8 p.C10X polymor-
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Diseases. 2010; 69(4):723–6. doi: 10.1136/ard.2008.106989 PMID: 19443463 41. Schoultz I, Verma D, Halfvarsson J, Torkvist L, Fredrikson M, Sjoqvist U, et al. Combined polymor-
phisms in genes encoding the inflammasome components NALP3 and CARD8 confer susceptibility to
Crohn's disease in Swedish men. American Journal of Gastroenterology. 2009; 104(5):1180–8. doi: 10. 1038/ajg.2009.29 PMID: 19319132 42. Hitomi Y, Ebisawa M, Tomikawa M, Imai T, Komata T, Hirota T, et al. Associations of functional NLRP3
polymorphisms with susceptibility to food-induced anaphylaxis and aspirin-induced asthma. Journal of
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19767079 43. Dupont WD, Plummer WD Jr. Power and sample size calculations for studies involving linear regres-
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infants and young children. American Academy of Pediatrics. Committee on Quality Improvement. Sub-
committee on Urinary Tract Infection. Pediatrics. 1999; 103(4 Pt 1):843–52. PMID: 10103321 45. Hawn TR, Scholes D, Wang H, Li SS, Stapleton AE, Janer M, et al. Genetic variation of the human uri-
nary tract innate immune response and asymptomatic bacteriuria in women. PLoS One. 2009; 4(12):
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October 7, 2015 References Genetics of innate immunity
and UTI susceptibility. Nat Rev Urol. 2011; 8(8):449–68. doi: 10.1038/nrurol.2011.100 PMID:
21750501 47. Verma D, Lerm M, Blomgran Julinder R, Eriksson P, Soderkvist P, Sarndahl E. Gene polymorphisms in
the NALP3 inflammasome are associated with interleukin–1 production and severe inflammation: rela-
tion to common inflammatory diseases? Arthritis & Rheumatism. 2008; 58(3):888–94. doi: 10.1002/art. 23286 PMID: 18311798 15 / 15 |
https://openalex.org/W3153787920 | https://iris.unibs.it/bitstream/11379/550083/4/Neri_2021_J._Phys.__Conf._Ser._1868_012027%20%282%29.pdf | English | null | Sustainable and low-cost solutions for thermal and acoustic refurbishment of old buildings | Journal of physics. Conference series | 2,021 | cc-by | 4,333 | Sustainable and low-cost solutions for thermal and acoustic
refurbishment of old buildings To cite this article: M Neri et al 2021 J. Phys.: Conf. Ser. 1868 012027 View the article online for updates and enhancements. This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 Journal of Physics: Conference Series Journal of Physics: Conference Series PAPER • OPEN ACCESS PAPER • OPEN ACCESS M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1
1 University of Brescia, Department of Industrial and Mechanical Engineering, via
Branze 38, Brescia, Italy 2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona
manuela.neri@unibs.it 2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona
manuela.neri@unibs.it Abstract. This paper investigates the possibility to realize solutions for buildings thermal and
acoustic refurbishment by using end-of-life household materials, such as cardboard, clothes,
and egg-boxes. These solutions can be installed to improve the indoor quality in neighborhoods
populated by people below the poverty threshold. The considered end-of-life household
materials and their combination have been analyzed from the acoustic and thermal points of
view. First of all, the sound insulation and the sound absorption properties have been
determined by means of an impedance tube. Then, the summer and the winter thermal
performances, when coupled to different wall systems, have been investigated analitically. The
results suggest that good thermal and acoustic characteristics can be achieved in a contained
thickness by coupling end-of-life household materials. Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution
of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.
Published under licence by IOP Publishing Ltd
1 This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 1868 (2021) 012027
doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Sustainable and low-cost solutions for thermal and acoustic
refurbishment of old buildings M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1
1 University of Brescia, Department of Industrial and Mechanical Engineering, via
Branze 38, Brescia, Italy
2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona
l
i@
ib it M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1
1 University of Brescia, Department of Industrial and Mechanical Engineering, via
Branze 38, Brescia, Italy 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 020)
1868 (2021) 012027
IOP Publishing
doi:10.1088/1742-6596/1868/1/012027 1868 (2021) 012027
doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series This article is part of a project that aims to develop the knowledge towards possible low-cost
improvements in thermal and acoustic comfort conditions for people living under the poverty
threshold, providing also simple and fast application solutions. However, these solutions not only aim
to solve the thermal and acoustic vulnerability, but also to become an instrument for social change and
the realization of individuals. In particular, in this paper, the acoustic and thermal performance of a
group of end-of-life household materials are investigated with the aim to identify a solution to be
installed indoor on vertical walls to guarantee an improvement of the acoustic and thermal conditions. This article is part of a project that aims to develop the knowledge towards possible low-cost
improvements in thermal and acoustic comfort conditions for people living under the poverty
threshold, providing also simple and fast application solutions. However, these solutions not only aim
to solve the thermal and acoustic vulnerability, but also to become an instrument for social change and
the realization of individuals. In particular, in this paper, the acoustic and thermal performance of a
group of end-of-life household materials are investigated with the aim to identify a solution to be
installed indoor on vertical walls to guarantee an improvement of the acoustic and thermal conditions. About acoustic comfort, the two main properties to be considered are the attitude of the material to
dissipate acoustic energy, expressed through the sound absorption coefficient α, and the sound
insulation capability, represented by the sound transmission loss TL. In this work, to determine these
parameters a four-microphone transmission tube has been used in this work. This apparatus is a double
standing wave tube equipped with four microphones. By means of this device it is possible to
determine the transfer matrix of a material. For this reason, this device is particularly suitable for the
acoustic characterization and optimization of complex layered structures [9]. Another advantage is that
it requires smaller samples if compared to the 10 m2 necessary to perform measurements in a
transmission suite. The only drawback using a transmission tube is that only the “normal incidence”
characteristics of the materials can be evaluated, while in real life applications diffuse incidence is the
actual condition. 2. Methods In this paper, a group of end-of-life household materials has been analyzed from the acoustic and the
thermal points of view. Firstly, end-of-life household materials have been tested acoustically and,
then, some of them have been analyzed thermally. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Nonetheless, with the experimental tests it has been possible to compare the acoustic
performances of several samples when subject to normal incidence. These first results will be refined
in future studies. Then, some of the tested configurations have been analyzed also from the thermal
point of view. Since the systems are designed for Italy and the Raval neighborhood, that are situated in
the Mediterranean area, both the summer and the winter conditions have been considered. Indeed,
since in these locations, summer is characterized by a wide daily temperature variation, it is necessary
to consider not only the thermal conductivity and thickness of the layers, but also their heat capacity
and their position in the wall. 1. Introduction Good structural performance but weak thermal and acoustic insulation performances characterize the
most widespread building technologies in Europe. Despite in recent years many buildings have been
refurbished from an energetic point of view, this kind of interventions is not reasonably priced for
low-income people. Consequently, in these realities, tenants are often forced to live in unhealthy
conditions because the heating system is missing, or ventilation is not adequate. This phenomenon of
social urban vulnerability is common in many developed countries. In the orbit of urban vulnerability
are found concepts such as exclusion, marginality, and poverty which, though not synonymous, may
be mutually reinforcing. The correlation between poverty and low indoor air quality (IAQ) has been
highlighted in several studies [1,2]. This problem mainly affects elderly people and people forced to
stay home for many hours, like long-term unemployed or disabled. The city of Barcelona, like many
other cities in the world, suffers strong internal vulnerabilities and inequalities because of differences
in the social composition of the population through spatial distribution. The Raval area is the one with
the highest concentration of poverty in the whole urban area of Barcelona, and it is characterized by
two population groups, that are elderly people and immigrants, both with low incomes. Nowadays,
building design embraces many aspects such as environmental, social and sustainability issues [3]. For
example, local sustainable construction materials should be chosen, and local workers should be
involved as already done in several projects [4]. For this reason, building systems must be cheap,
made of materials easy-to-be-found in the vicinity of the building site, safe and easy to be installed
during the construction phase also by non-skilled workers. From this point of view, end-of-life
household materials are cheap (or even free), easy-to-be-found, safe and, when discharged, they have
properties that can still be exploited. The possibility to reuse these materials was investigated by
several authors: properties of clothes [5], cardboards [6], and plastic containers [7] were analyzed in
several works. The reuse of these materials reduces the amount of produced waste and, consequently,
of material discharged in the environment; indeed, only a small percentage of household waste
materials is recycled. For example, in 2017, only the 14% of the textile waste was recycled and the
rest was addressed to incineration [8]. 1 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 2.1. Acoustic performances 2.1. Acoustic performances
The acoustic characterization has been carried out according to the procedure described in the ASTM
E2611 standard [9]. The procedure requires the measurements to be performed using a four-
microphone impedance tube. Such device has a loudspeaker, generating a wide-band white noise,
mounted at one end and an anechoic termination at the other end. The sample is placed in the central
section, between two microphone pairs. A multichannel analyzer measures the microphones signals
and computes the transfer functions. Such functions are then post-processed by a MATLAB script
based on the ASTM E2611 [10] standard to obtain the acoustic parameters of the sample and its
transfer matrix. The single materials and the combinations reported in Table 1 have been tested. For
each sample type, three tests have been performed and the results have been averaged. The tests have
been organized as follows: the first two sets are made of egg-boxes samples featuring single/double
layers (test 02-03-22) and egg-boxes coupled with polyester fiber (test 04-05). In some cases, a steel
sphere was embedded inside the polyester fiber and the structure closed using a cardboard layer (test
07-08-17). In order to accommodate the steel element inside the structure, a cylindrical hole was made
at the center of the cardboard disks. A third set of samples includes samples mainly made of cardboard
(test 13–14). Samples made of clothes of different fabric types represent the fourth experimental set. Several repetitions have been performed for each measurement to assess how the ability of the person
assembling the samples can affect its performances. This aspect will be further investigated in future
analysis. The fifth (and final) set of measurements has been made on samples obtained by combining
egg boxes, clothes and metal elements. In general, to improve the acoustical behavior, disks and egg- 2 020)
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doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series boxes exposed to the sound source were perforated to allow the sound to pass through the first layer. The sequences reported in Table 1 start with the material closest to the sound source. The frequency
range investigated goes from 100 Hz to 3150 Hz. boxes exposed to the sound source were perforated to allow the sound to pass through the first layer. 2.1. Acoustic performances The sequences reported in Table 1 start with the material closest to the sound source. The frequency
range investigated goes from 100 Hz to 3150 Hz. Table 1. Specimens tested in the impedance tube. The diameter of the samples is 46 mm. Table 1. Specimens tested in the impedance tube. The diameter of the samples is 46 mm. 3 3 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 1868 (2021) 012027
doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Figure 1. Walls configurations (MP, MPF, MLP) and the additional panels (Poli, CDB) considered in
the analysis. The additional panels are installed internally. Figure 1. Walls configurations (MP, MPF, MLP) and the additional panels (Poli, CDB) considered in
the analysis. The additional panels are installed internally. 3.1. Acoustic performances The absorption coefficient α and the sound transmission loss TL of the samples reported in Table 1
have been determined by means of a 4-microphone impedance tube. When dealing with the acoustic
comfort both sound absorption and sound insulation performances are influential. Yet, since the
reference walls have good sound insulation basic performances, sound absorption can be considered
more interesting. In Figure 2, for the first set of samples the most interesting sound insulation
performance is the one given by specimen 22 (reverse double pyramid) with a TL following the mass
law up to 800 Hz and then a behavior typical of double walls, with a mass-spring-mass resonance
frequency around 1800 Hz. Also the specimen 02 (single egg box) showed an acceptable performance,
with a rather flat TL of 12 dB from 100 Hz up to 2000 Hz, while specimen 03 (perforate egg box with
polyester) is not able to reach the performances of the other samples. For the same samples, with the
exception of sample 02 which is not permeable to air, α is characterized by wide peaks at given
frequencies due to holes obtained in the egg cardboard behaving like Helmholtz resonators (sample
03) or quarter wavelengths resonators (sample 22). In the case of sample 03 the peak around 700 Hz is
very wide due to the presence of sound absorbing polyester fiber inside the main volume. As concerns
the second set of samples, TL curves are all very similar as can be seen in Figure 3. This behavior can
be explained by the nature of the samples which are built with the same elements: the egg cardboard,
the polyester foam and the steel sphere. The only variables are the orientation of the samples and the
presence of a cardboard disk. The TL of samples 04 and 05 are characterized by the typical mass law
behavior due to the single egg cardboard, except a dip around 1200 Hz. The samples 07 and 08 have
higher values of TL due to the double or triple layer structure which causes an increase of the mass and
an increase of the curve slope due to multiple resonances of the layers. In particular, sample 08
exhibits very interesting performances at low frequencies and the higher TL of the group also at high
frequencies. For these samples α is characterized by multiple peaks typical of the resonators featured
in the cardboard parts. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020)
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doi:10.1088/1742-6596/1868/1/012027 3.1. Acoustic performances The breadth of the peaks depends again on the presence of polyester fibers. The
best sample is Test 08, having a rather high α also at high frequency, with a maximum of 0.95 at 2
kHz. The third set of samples shown in Figure 4 presents very similar TL curves for all the samples. The performances are very similar and TL at low frequency is the highest among the entire group of
tested materials. Such behaviour is due to the density of the stacking, which makes the samples similar
to sandwich materials featuring non compressible cores. For this reason the trend is characterised by a
linear behaviour followed by the typical coincidence dip. For samples 13 and 14, α is marked out by a
maximum around 600 Hz due to the resonance of the Helmholtz resonators featured in the cardboard. For sample 17, α is very similar to the one of sample 08 (having a very similar structure), with three
peaks reaching a value of 0.8. The fourth set considers tissues and results are shown in Figure 5. Comparing the different samples, the TL curves are all very similar and are typical for porous
materials. The better performances are reached by the thicker samples (sample 26 – 100 mm) and by
the sample having the higher density (sample 30 – high density viscose). Also, α curves have a shape
typical for porous materials, with an S shape, low values at low frequencies and values approaching 1
at high frequencies. The fifth and last set is a combination of tissues, egg boxes and metal parts. As
can be seen in Figure 6, the TL curves have very similar trends. If compared to the TL curves of the
fourth set, the values are generally higher at low frequency due to the higher mass per unit area of the
samples. Sample 36 has the best performances for this group. As concerns α, the behavior is
dominated by the Helmholtz resonator characteristic shape featuring a peak around 400 Hz followed
by an increase of the coefficient due to the presence of the tissues. As a general remark, the higher the
flow resistivity of the tissue, the lower α in the high frequency region. 3 2 Th
l
f 2.2. Thermal investigation g
The thermal effect of an insulating panel made of end-of-life household materials applied to different
walls has been investigated. The aim of the analysis is to understand if the materials at hand exhibit
promising characteristics that can justify further investigations. Three basic wall configurations called
MP103, MLP01, and MPF01 have been considered. Such configurations have been renamed MP,
MLP and MPF in the following part (Section 3.2). These basic types of walls have been extrapolated
from the UNI/TR 11552 [11] standard and represent the typical building solutions used for Italian
council estate. Since, as stated in [11], the wall thickness is variable, the largest and the smallest
thicknesses have been considered. The thermal performances of the walls have been compared with
those of the walls equipped with one of the additional insulating panels shown in Figure 1 (Poli or
CDB), these latter installed on the internal side of the wall. Indeed, the solutions considered in this
paper are designed for historical urban contexts in which the external appearance of the buildings must
be preserved and external intervention are not allowed. In the following sections, type and thickness of
each configuration are declared in the name. For example, MPmin-Poli50 represents the thinner wall
configuration MP coupled to the Poli panel. The variable layer of the Poli panel is 50 mm thick. In
particular, the periodic thermal transmittance Y12, the delay, the thermal transmittance U and the
decrement factor f have been calculated according to the UNI EN ISO 13786:1999 [12]. The periodic
thermal transmittance Y12, an important parameter for the evaluation of the summer comfort
conditions, represents the amplitude of the density of heat flow rate on one side when the temperature
amplitude on that side is zero and there is unit temperature amplitude on the other side. The decrement
factor f describes how well the wall reduces the internal temperature peak. The thermal transmittance,
instead, describes the insulating performance in stationary conditions like the ones found during the
wintertime. 4 020)
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doi:10.1088/1742-6596/1868/1/012027 3.2. Thermal performances Since clothes and cardboard have shown good acoustic performances, they have been evaluated also
from the thermal point of view. Given their limited thickness, egg-boxes have not been considered in
this section. 5 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020)
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doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Figure 2. Acoustic
properties of
samples made of
clothes (one fabric
at a time). Figure 5. Acoustic
properties of
samples made of
clothes combined
with other
household waste
materials. Figure 4. Acoustic
properties of
samples made of
egg-box coupled
with other
household waste
materials. Figure 6. Acoustic
properties of
samples made of
cardboard. Figure 3. Acoustic
properties of
samples made of
at least one egg-
box. Figure 2. Acoustic
properties of
samples made of
clothes (one fabric
at a time). Figure 2. Acoustic
properties of
samples made of
clothes (one fabric
at a time). Figure 3. Acoustic
properties of
samples made of
at least one egg-
box. Figure 3. Acoustic
properties of
samples made of
at least one egg-
box. Figure 3. Acoustic
properties of
samples made of
at least one egg-
box. Figure 4. Acoustic
properties of
samples made of
egg-box coupled
with other
household waste
materials. Figure 4. Acoustic
properties of
samples made of
egg-box coupled
with other
household waste
materials. Figure 4. Acoustic
properties of
samples made of
egg-box coupled
with other
household waste
materials. Figure 5. Acoustic
properties of
samples made of
clothes combined
with other
household waste
materials Figure 6. Acoustic
properties of
samples made of
cardboard. Figure 6. Acoustic
properties of
samples made of
cardboard. 6 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020)
Journal of Physics: Conference Series
1868 (2021) 012027
IOP Publishing
doi:10.1088/1742-6596/1868/1/012027 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) )
1868 (2021) 012027
g
doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Journal of Physics: Conference Series
1868 (2021) 012027
doi:10.1088/1742-6596/1868/1/012027
Figure 7. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the
POLI additional panels. Figure 7. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the
POLI additional panels. aracteristics of MP, MLP, MPF wall configurations coupled with the Figure 8. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the
CDB additional panels. Figure 8. 3.2. Thermal performances Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the
CDB additional panels. The thermal characteristics of MP, MLP and MPF wall configurations with and without the additional
insulating panels are shown in Figures 7 and 8. In Figure 7 it can be noted that the addition of the
panel Poli (made of clothes and cardboard), determines a reduction of Y12, f, and U, whereas the delay
of the dynamic thermal transmittance slightly increases in modulus. In particular, a significant
reduction of Y12 has been obtained with the thicker 100POLI panel. A significant reduction of U has
been obtained for MPF and MLP wall configurations. For the thicker version of the panel (100POLI),
the decrement factor f increases of about 2 hours, and for MP-max and MPF-max the addition of the
panel corresponds to a time shift of about 12 hours. Even if the increment of f is limited, the time shift
represents a good improvement because the indoor temperature peak takes place when it is possible to
cool the indoor ambient naturally, simply opening the windows. In Figure 8 it is shown how the
addition of a cardboard layer determines a decrease of Y12, f and U. As regards the time shift f of the
dynamic thermal transmittance, the variation is lower than one hour. However, with the same
thickness, better performances belong to the panel made of polyester and this is probably due to the
fact that this latter has greater density. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020)
Journal of Physics: Conference Series
1868 (2021) 012027
IOP P
doi:10.1088/1742-6596/1868/ 020)
1868 (2021) 012027
IOP Publishing
doi:10.1088/1742-6596/1868/1/012027 020)
1868 (2021) 012027
IOP Publishing
doi:10.1088/1742-6596/1868/1/012027 1868 (2021) 012027
doi:10.1088/1742-6596/1868/1/012027 and transmission loss has been obtained for samples made of cardboard, but interesting results have
been obtained also for samples made with two egg-boxes, especially in terms of transmission loss. Moreover, it has been shown that higher density clothes ensure a better acoustic performance. Due to
the practical difficulties met when manufacturing the samples, which are often non planar, further
analysis will be required to investigate how the operators manual skills affect the acoustic
performances of the specimens. From the thermal point of view, the installation of panels made of
clothes and cardboard respectively determines a reduction of the periodic thermal transmittance and
the thermal transmittance. However, due its greater density, panels made of clothes are more effective. This paper shows that end-of-life household materials have a potential for the refurbishment of old
buildings from both the acoustic and the thermal points of view. Future works will investigate how the
application of these panels can affect the hygrometric behavior of the walls. Moreover, other
configurations will be tested acoustically. Acknowledgements The authors would like thank the Department of Mechanical and Industrial Engineering for funding
the research through the MetATer PRD project. 4. Conclusions In this paper the acoustic and thermal performances of several end-of-life household materials have
been investigated. From the acoustic point of view, the best compromise between sound absorption 7 References References
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[4] Burroughs S and Růžička J. 2019 The Use of Natural Materials for Construction Projects –
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https://openalex.org/W2112161913 | https://hqlo.biomedcentral.com/counter/pdf/10.1186/1477-7525-8-46 | English | null | TMD pain: the effect on health related quality of life and the influence of pain duration | Health and quality of life outcomes | 2,010 | cc-by | 6,221 | RESEARCH Open Access BioMed Central
© 2010 Tjakkes et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. Abstract Objectives: As impact of literature concerning this subject is scarce, the objectives of this study were to assess
whether the Health Related Quality of Life (HRQoL) is decreased in patients with painful temporomandibular disorders
as compared to the HRQoL in the general population, and to evaluate to what extent pain duration affects HRQoL. Methods: Data concerning physical and mental health were retrieved from patients with painful temporomandibular
disorders. Assessment tools used were: the Mandibular Function Impairment Questionnaire (MFIQ), the Short-Form-36
(SF-36), the Hospital Anxiety and Depression Schedule (HADS), and the General Health Questionnaire (GHQ). In order to
examine the influence of the duration of pain on HRQoL, the total sample was divided into three different subgroups. Subgroup 1 consisted of patients with complaints existing less than one year. Patients with complaints from 1 to 3
years were allocated to the second group. The 3rd subgroup included patients with complaints longer than 3 years. Results: The total sample consisted of 95 patients (90 females and 5 males). On most physical and social functioning
items, groups 2 and 3 scored significantly worse than the general population. On the other hand, none of the groups
differed from the general population when comparing the mental items. Duration of pain was significantly correlated
with SF-36 subscale physical functioning and the mandibular impairment. Conclusion: Patients with TMD pain less than one year score better than compared to the population norm. With a
longer duration of pain, mental health scores and role limitations due to emotional problems do not appear to be
seriously affected by reduced physical health, while social functioning appears to be considerably affected. * Correspondence: g.h.e.tjakkes@kchir.umcg.nl
1 Department of Oral and Maxillofacial Surgery, University Medical Center
Groningen University of Groningen, Groningen, PO Box 30.001, 9700 RB, The
Netherlands
Full list of author information is available at the end of the article Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 * Correspondence: g.h.e.tjakkes@kchir.umcg.nl Background become more obvious and prominent. Even after a
decrease of the somatosensory input, suffering and pain
behaviour may continue and even increase [6]. Temporomandibular disorders (TMDs) comprise a group
of disorders that affect the temporomandibular joint
(TMJ), the masticatory muscles, or both. TMDs involve
musculoskeletal pain, disturbances in the mandibular
movement patterns, and/or impairment in functional
movement [1]. Pain is the main characteristic of most
TMDs and also the main reason for patients to seek treat-
ment [2]. Many TMDs should be considered chronic pain
conditions, since they show lot of similarities [3]. Psycho-
logical factors have been implicated in the initiation as
well in the perpetuation of several TMDs [4]. Stress,
somatic distress, and depression may be potential etiolog-
ical risk factors for TMD-related pain [5]. When the
duration of pain increases, psychological factors may It is generally accepted that quality of life is negatively
affected by chronic pain [7,8]. The impact of TMDs (and
other types of orofacial pain) on Health Related Quality
of Life (HRQoL), however, has scarcely been described. Recently, Naito et al. conducted a systematic review on
oral health status and health-related quality of life [9]. They found only one study concerning TMDs. In this
study, Reisine and Weber [10] observed a sample of 30
patients with temporomandibular disorders, during 6
months. Different aspects of HRQoL were investigated
e.g. anxiety, perceptions and social functioning. It was
found that while the pain decreased over time, oral and
functional aspects did not improve significantly within
the same period of time. This result may be due to a
slower response of other parameters to treatment in con-
trast to a relatively rapid response of pain. Furthermore,
the authors found relatively poor ratings of well-being Page 2 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 Page 2 of 8 less than one year. Patients with complaints from 1 to 3
years were allocated to the second group. The 3rd sub-
group consisted of patients with complaints longer than 3
years. Secondly, the influence of the duration of pain was
studied using results of the total sample in regression
analysis. During their first visit to the clinic, patients were
informed about the study and the content of the ques-
tionnaires. When patients were willing to participate,
they were requested to fill in an informed consent. HRQoL was measured by the following instruments
SF-36 The Medical Outcome Short Form Health Survey, a 36
item health survey, was used to assess the patients'
HRQoL [18]. It includes eight health concepts: physical
functioning (PF, measuring the physical activities), role
limitations due to physical health problems (RP, measur-
ing the effect of the physical health on work and daily
activities), bodily pain (BP), general health (GH) percep-
tions, vitality (VT, measuring energy/fatigue), social
functioning (SF), role limitations due to personal or emo-
tional problems (RE measuring the effect of the emotions
on work and daily activities) and general mental health
(MH including anxiety and depression). The scores on
every subscale range from 0-100, with higher scores indi-
cating better health states. Reference values were used to
compare the results of the group in question. The refer-
ence values were taken from a Dutch study, which con-
sisted of a random Dutch sample of 1742 persons, which
is used as the reference group [19]. In this study the mean
values for each subscale were for PF 83.0 (sd 22.8), RP
76.4 (sd 36.3), BP 74.9 (sd 23.4), GH 70.7 (sd 20.7) VT
68.8 (sd 19.3), SF 84.0 (sd 22.4), RE 82.3 (sd 32.9), MH
76.8 (sd 17.4) [19]. MFIQ Assessment and Instruments During the second visit to the clinic, patients were
instructed how to complete the questionnaires. Subse-
quently, patients were left alone to complete the ques-
tionnaires. When necessary, unclear test items could be
clarified by the interviewer. Only Dutch versions of the
questionnaires were used. It is not clear whether and, if so, how (chronic) pain
related to TMDs influences HRQoL, and whether pain
duration is of influence. It may be hypothesized that
when pain has just begun, this will mainly affect physical
factors such as physical functioning. When the pain lasts
for a longer period, and treatment so far has failed to
relieve the pain, it may start to have more impact on the
emotional behaviour, social factors and HRQoL. How-
ever, whether this is the case is yet not clear. Information
concerning the influence of pain and its persistence on
HRQoL may guide (the emphasis of) treatment in these
patients. Therefore, the aims of this study were to assess
whether the HRQoL is decreased in orofacial pain
patients as compared to the general population, and to
study the effect of duration of pain on HRQoL. Methods and materials
Sample Patients were recruited from the department of Oral and
Maxillofacial Surgery of the University Medical Center
Groningen. The group consisted of 95 patients consecu-
tively consulting the TMD/Orofacial Pain section for
their orofacial pain problems. The inclusion criteria were
age over 16 years, no language barrier, and the presence
of a painful temporomandibular disorder as classified
according to the RDC/TMD [15,16]. From the axis II
information, the duration and impact of the pain were
assessed. The influence of the duration of pain on
HRQoL was examined by two means. Firstly, the total
sample was divided into three different subgroups. Sub-
group 1 consisted of patients with complaints existing Background and high levels of anxiety, suggesting that TMD patients
are characterized by relatively negative psychological
states, and that when pain persist (even when dimin-
ished) functional aspects do not improve. Murray et al. [11] described the HRQoL, as measured
with the Oral Health Impact Profile (OHIP), of patients
referred to a craniofacial pain unit because of TMD and
facial pain. With regard to pain-related disability and
HRQoL, 29.7% of the sample reported a frequently dis-
turbed sleep as a consequence of their oral conditions,
and 36.4% reported feelings of depression. Different
researchers have found a larger impairment of the oral
HRQoL in TMD patients compared with healthy popula-
tion, using the OHIP [12,13]. Quality of life has been described by the World Health
Organisation as " ... an individual's perception of their
position in life in the context of the culture and value sys-
tem of which they live with the relation to their goals,
expectations, standards and concerns." This concept
incorporates different aspects of individuals, including
physical health, psychological state, level of indepen-
dence, social relationships, personal beliefs and their rela-
tionship to salient features of the environment [17]. LeResche et al. [14] studied the facial expression as well
as states of anxiety, depression, somatization and daily
stress in a group of TMD pain patients, subgrouped into a
chronic and non-chronic category. With regard to these
four aspects of HRQoL, no differences were found
between a group of patients that perceived pain for the
first time within the last two months (non chronic group)
and a group that suffered from pain for over 6 months
(chronic group). Sample size calculation To estimate the a priori sample size, an effect size of 0.4
was chosen. By convention this effect size is considered as
a moderate effect size. Sample was calculated on an
ANOVA with the parameters α, β, number of groups and
effect size. α was set at 5%, β at 10%, number of groups 3,
resulting in a critical F of 3.10931. The total calculated
sample was 84. To account for possible dropouts, sample
size was about 10% increased to 95. Results
Patients In total 95 patients (90 females and 5 males) provided
their consent to participate in the study. Their average
age was 40.3 yrs (sd 13.1, ranging from 17-69). According
to the RDC/TMD criteria, patients were diagnosed with a
group I diagnosis (myofascial pain), a group II diagnosis
(disc displacement) a group III (arthralgia, osteoarthritis
and osteoarthrosis). A group I diagnosis was established
in 31.9%; a group II diagnosis in 4.4% and a group III in
35.2%. A combined diagnosis was made in 28.7% of all
cases (in 7.8% group I and II, in 17.6% group I and III, and
in 3.3% group II and III were combined). Furthermore,
the participants of the 3 subgroups based on pain dura-
tion were calculated: subgroup 1 (pain present for less
than one year) consisted of 15 patients (14 females; 1
male, mean age 37.7 yrs, sd 14.4, range 17-69), subgroup 2
(1-3 years pain duration) consisted of 16 patients (13
females, 3 males; mean age 37.5 yrs, sd 14.1, range 20-68),
and subgroup 3 (more than 3 years of pain) consisted of
64 patients (63 females, 1 male; mean age 41.6 yrs, sd
12.5, range 17-67). The distribution of the diagnoses,
medication use and coinciding chronic pain diseases
among the three groups is listed in Table 1. To assess depression and anxiety in a hospital setting, the
HADS was used [21]. To screen for anxiety (HADS-A)
the odd items were used. For the screening of depression
(HADS-D), the even items of questionnaire were used. On each subscale, scores up to 7 indicate no signs of anx-
iety or depression, scores between 8 and 10 suggest prob-
able anxiety or depression, and scores over 10 indicate the
presence of anxiety or depression, respectively [21]. GHQ 28 The general health questionnaire was used to assess dif-
ferent types of psychiatric distress. It is a 28 item list
which can be divided into four different subscales:
somatic symptoms (GHQA), anxiety and insomnia
(GHQB), social dysfunction (GHQC) and severe depres-
sion (GHQD) [22]. The reference values were for GHQA
6.2, GHQB 5.8, GHQC 7.0, GHQD 1.6 and were retrieved
from a general Dutch population of 485 persons [23]. Effects of pain duration: Three groups
Results compared with reference values Table 2 shows the mean SF-36 and GHQ scores for the
three subgroups. The first ("relatively acute") subgroup
scored better on the subscale physical functioning and
worse on subscales general health and vitality than the
general population, but on the other subscales this sub-
group and the general population revealed comparable
scores. (
MFIQ The Mandibular Function Impairment Questionnaire
was used to obtain information about the function Page 3 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 analysis. Data were analyzed using SPSS 14 (SPSS Inc,
USA). The level of significance was set at 0.05. This study
was approved by the Medical Ethical Committee of the
University Medical Center Groningen. impairment of the jaw. It was developed to provide for a
tool, additional to the clinical assessment, for assessment
of function impairment in the patients own value system
[20]. It comprises 17 items, concerning mandibular func-
tions e.g. speaking and eating different types of food. A
functional impairment rating score (FIRS) can be
retrieved. This is a score ranging from 0 (no function
impairment) up to 5 (indicating severe function impair-
ment) [20]. HADS impairment of the jaw. It was developed to provide for a
tool, additional to the clinical assessment, for assessment
of function impairment in the patients own value system
[20]. It comprises 17 items, concerning mandibular func-
tions e.g. speaking and eating different types of food. A
functional impairment rating score (FIRS) can be
retrieved. This is a score ranging from 0 (no function
impairment) up to 5 (indicating severe function impair-
ment) [20]. Statistical analysis Descriptive statistics were performed to summarize sam-
ple characteristics. Data were tested for normality using
the Kolmogorov-Smirnov test. By means of one sample
T-tests, the HRQoL scores of the patients were compared
to those of a general population. To test mean differences
in HRQoL among subgroups, one-way ANOVA was car-
ried out, followed by Scheffe's post hoc multiple compari-
son test in case of a significant result. In order to study
the association between the duration of pain and the
scores on the different SF-36 subscales, HADS scores,
GHQ-28 scores, and MFIQ score, respectively, Pearson
correlation coefficients were calculated. Outlier analysis
with scatter plots was performed to look for possible dif-
ference in scores between female and male participants. Data from the total sample was analysed in a regression Compared with the general population, the second sub-
group scored worse on four subscales (bodily pain, vital-
ity, general health and social functioning) and the third
subgroup scored worse on six SF-36 subscales (bodily
pain, vitality, general health, social functioning, physical
functioning and role emotional). In the first and second group, scores on the GHQ scales
did not significantly differ from scores in the general pop-
ulation. The third group showed more impairment in
somatic symptoms and showed higher social dysfunction,
with worse scores on GHQA and the GHQC, compared
to those obtained from the general population. g
Comparisons between groups No differences were found in age between the three
groups. Statistically significant differences were found Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 Page 4 of 8 Table 1: Distribution of age, RDC diagnoses medication usage and coinciding chronic pain disorders among the three
subgroups. Group
1
2
3
Total
15
16
64
Female/male
1/14
3/13
1/63
Age (sd)
37.6 (14.4)
37.5 (14.1)
41.6 (12.5)
RDC/TMD diagnosis:
n
n
n
Group I
3
8
20
Group II
0
0
3
Group III
5
7
24
Group I + group II
0
0
4
Group I + group III
5
0
12
Group II + group III
2
1
1
Analgesic usage
Paracetamol
0
1
7
NSAID
1
0
3
Tricyclic antidepressant
1
5
6
Tricyclic antidepressant +
paracetamol
1
0
0
Tricyclic antidepressant +
NSAID
0
0
2
NSAID + opioid
0
0
2
Other chronic pain condition
Rheumatoid arthritis
0
2
1
Hernia
0
0
1
Back pain
0
0
1
Group 1: Myofascial pain
Group 2: Disc displacement
Group 3: Arthralgia/osteoarthritis/osteoarthrosis n of age, RDC diagnoses medication usage and coinciding chronic pain disorders among the three between groups 1 and 3 with regard to the SF-36 subscore
on the scales physical functioning and bodily pain (i.e. scores were better in group 1), but not between groups 2
and 3. Other SF-36 scores did not differ significantly
between the three groups. between groups 1 and 3 with regard to the SF-36 subscore
on the scales physical functioning and bodily pain (i.e. scores were better in group 1), but not between groups 2
and 3. Other SF-36 scores did not differ significantly
between the three groups. in these three subgroups (Table 2). No significant differ-
ences between the three groups were found in the FIRS. in these three subgroups (Table 2). No significant differ-
ences between the three groups were found in the FIRS. Both HADSA and HADSD scores were worse in groups
2 and 3 as compared to group 1 (Table 3). In addition, the
HADSD score in group 2 was worse than in group 3. Both HADSA and HADSD scores were worse in groups
2 and 3 as compared to group 1 (Table 3). In addition, the
HADSD score in group 2 was worse than in group 3. g
Comparisons between groups The third group showed more somatic problems as well
as a higher level of social dysfunction compared to the
first group, as GHQA and GHQC scales revealed signifi-
cant differences between these groups. Effects of pain duration: total sample The social, psychological and part of the physical mea-
sures did not show significant correlation with pain dura-
tion. Of all calculated correlations, the SF-36 subscale
bodily pain and the Function Impairment Rating Scale
(FIRS) were significantly correlated with the duration of
pain. The patients' impairment in mandibular function, as
assessed with the MFIQ and expressed in the function
impairment rating scale (FIRS), was 2.4 (sd 1.1) for the
first group, 2.6 (sd 2.0) for the second group, and 3.3 (sd
1.6) for the third group, indicating moderate impairment Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 Page 5 of 8 Table 2: SF-36 and GHQ scores in three groups of orofacial pain patients and reference values. reference
1
2
3
Scale
Mean (SD)
Mean (SD)
n = 15
Mean (SD)
n = 16
Mean (SD)
n = 64
SF-36 PFa
83.0 (22.8)
92.1 (8.1)*3
74.2 (33.1)
72.3 (25.7)*1
SF-36 RPa
76.4 (36.3)
54.2 (38.1)
71.2 (3.6) 3
41.2 (39.7)*2
SF-36 BPa
74.9 (23.4)
66.1 (20.4)3
53.2 (27.5)*
48.5 (19.7)*1
SF-36 GHa
70.7 (20.7)
53.0 (23.4)*
55.8 (18.7)*
54.4 (20.6)*
SF-36 VTa
68.8 (19.3)
52.9 (14.9)*
49.3 (21.6)*
55.2 (19.4)*
SF-36 SFa
84.0 (22.4)
74.0 (22.9)
66.0 (29.2)*
66.7 (23.4)*
SF-36 REa
82.3 (32.9)
66.7 (31.8)
81.0 (55.0)
80.9 (34.1)
SF-36 MHa
76.8 (17.4)
66.4 (12.5)
60.6 (17.9)3
73.2 (13.0)2
GHQAb
6.2
6.7 (4.1)
6.3 (4.1)
8.2 (4.0)*
GHQBb
5.8
2.8 (2.1)2
7.5 (3.6)1
5.9 (4.4)
GHQCb
7.0
6.6 (1.8) 3
8.2 (3.3)
8.3 (2.3)*1
GHQDb
1.6
0.8 (1.8)
2.7 (3.5)
1.9 (3.0)
Values in mean (standard deviation, * p < 0.05 from reference values, in superscript the group to which the value is statistically different;
reference values from a Aaronson et al.[19], b Koeter & Ormel [23]. (PF, physical functioning; RP, Role limitations physical; BP, bodily pain; GH, general health; VT, vitality; SF, social functioning; RE, role
limitations emotional; MH, mental health; SD, standard deviation; GHQA, somatic symptoms; GHQB, anxiety and insomnia; GHQC, social
dysfunction; GHQD, severe depression; P, P-value)
1. group with complaints of one year or shorter
2. group with complaints within 1 and 3 years
3. group with complaints longer than 3 years. Table 2: SF-36 and GHQ scores in three groups of orofacial pain patients and reference values. Outlier analysis revealed no differences on the sub-
scales in any of the assessed subscales between female
and male patients. Effects of pain duration: total sample patients classified into different cognitive-behavioural
profiles seem to respond differently when the same treat-
ment is offered [24]. Thus, not only the physical but also
the psychological status may influence the treatment out-
come. Discussion The duration of pain is thought to have a significant
impact on a patient's psychological status (Figure 1) [6]. To provide more insight into the effect of duration of pain
complaints, we compared patients with relatively acute
pain (less than 1 year) and patients with chronic pain (1-3
years and > 3 years, respectively). A striking finding was In this study we examined whether the duration of pain in
TMD patients seeking treatment affects the HRQoL and
psychological well-being. When managing these patients,
psychological assessment may lead the clinician to multi-
dimensional, biobehavioral therapy modalities rather
than to somatically based therapies [2]. Also, TMD Table 3: FIRS, HADSA and HADSD scores (standard deviation) for three groups. Group
1
2
3
score
FIRS (sd)
2.4 (1.1)
2.6 (2.0)
3.3 (1.6)
HADS A (sd)
3.3 (1.8)2,3
6.4 (4.1)1
5.0 (3.6)1
HADS D (sd)
1.6 (1.1)2,3
6.2 (4.2)1,3
3.5 (3.1)1,2
1.: group with complaints of one year or shorter
2.: group with complaints within 1 and 3 years
3.: group with complaints longer than 3 years. (FIRS; functional impairment rating score, HADSA; anxiety, HADSD; depression. In superscript the group to which the value is statistically
different) Table 3: FIRS, HADSA and HADSD scores (standard deviation) for three groups. Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 Page 6 of 8 Page 6 of 8 Page 6 of 8 Figure 1 The effect of duration of symptoms on psychosocial fac-
tors. From Okeson [6]. Used with permission. Between the different pain duration groups, statistically
significant differences were found only on a few scales. Comparing "better" scores from the first group with
"worse" scores from the third group, leads in the physical
functioning scale to a significant difference between those
scores. Although the HADS scores are interpreted using
cut-off points, it is striking that the depression scale
(HADSD) in group 2 is not only higher compared to
group 1, but also compared to group 3. Patients who
experience complaints for a short time may not be seri-
ously affected, but when pain persists, psychological dis-
tress will be more pronounced. Later, when patients are
used to the pain or when they are sufficiently reassured
about their health status, the psychological distress will
return to lower values again. Discussion This is in accordance with
the score on the mental health item of the SF-36, which is
better in the third group compared to the second group. Figure 1 The effect of duration of symptoms on psychosocial fac-
tors. From Okeson [6]. Used with permission. that in all three subgroups the SF-36 scores of the scales
role emotional and mental health did not differ signifi-
cantly from the reference values. It may be, that patients
with a longer experience of complaints tend to get used to
their pain and symptoms and incorporate them as a part
of their life, thereby leaving their mental health less
affected. According to our findings, it may seem that patients
with a shorter duration of pain seem to underrate their
physical impairment or at least do not consider it to be
relevantly impaired, as the scores are "better" compared
with a healthy reference group. Patients with longer last-
ing pain at least longer than one year, have more pro-
nounced physical problems. The role limitations due to
emotional problems or the mental health seem to be
hardly affected, however. It has been suggested that psy-
chological functioning is merely related to patients'
beliefs and coping strategies rather than to the physical
impairment [25]. On the other hand, the social function-
ing scale in the SF-36 as well as the GHQC score suggest
that social functioning is affected in the third group. This
may be explained by role limitations due to physical limi-
tations, which in turn may be the result of the actual dis-
order. The first group did score significantly higher ("better")
on the scale "physical functioning", compared to the pop-
ulation norm. This finding could be explained by possible
underestimation of the physical situation, when patients
visit a hospital and are allocated to a study group that
answers questions about health. Patients with pain or
function problems that have arisen within the last year,
may tend to focus on these problems in an opposite man-
ner than patients who have a longer experience with these
problems. In addition, the scale bodily pain was not sig-
nificantly different from the reference value. Because of
the relatively short existence of pain, patients may under-
estimate or underrate the consequences of their disorders
on the measured scales. Discussion They may be convinced that
(pain) symptoms will be transient and, therefore, patients
will not allow them to affect the physical items. Patients
may also feel the need to convince the doctor that the
symptoms are purely physical, and want to display that
statement in the answers of the subscales. In addition to the analysis with three subgroups, we cal-
culated Pearson correlation coefficients with data from
all patients. This revealed a significant correlation
between the whole range duration of pain with the sub-
scale physical functioning and the mandibular impair-
ment (FIRS). So with a longer duration of pain, the
somatic well-being is considered worse. It remains
unclear whether the physical discomfort has worsened
during its existence or whether the discomfort is only
rated worse due to its longer existence. Other subscales
and other scores did not show significant correlation with
duration of pain, which may be explained by a large range
of duration of pain in contrast to the smaller scale range
of the scores on other subscales and the other question-
naires. By contrast, on SF-36 physical health items ("bodily
pain", "general health" and "vitality") the second and third
group scored significantly worse than reference values. In
addition, in the third group the items physical functioning
and role physical were also worse than reference values. This physical impairment was confirmed by the FIRS
scores, indicating moderate function impairment. So the
mandibular function was lowered in all three groups. The
GHQA score, which represents the somatic general
health, is significantly lower ("worse") in the third group,
which is in accordance with the scores on the SF-36. With
significantly lower scores on the physical scales of the SF-
36, the second and third subgroup did not score signifi-
cantly lower on the mental scales. One factor that may be of influence on the results is the
age. In our sample, no difference was found between the
three groups. Besides TMD pain, other pain condition
could play a role in HRQoL. Of the studied sample totally
five had an accompanying chronic condition. In the sec- Page 7 of 8 Page 7 of 8 Tjakkes et al. References Chigago: Quintessence
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Cite this article as: Tjakkes et al., TMD pain: the effect on health related qual-
ity of life and the influence of pain duration Health and Quality of Life Out-
comes 2010, 8:46 22. Goldberg DP, Hillier VF: A scaled version of the General Health
Questionnaire. Psychol Med 1979, 9:139-145. 22. Goldberg DP, Hillier VF: A scaled version of the General Health
Questionnaire. Psychol Med 1979, 9:139-145. 23. Koeter MWJ, Ormel J: General Health Questionnaire, Nederlandse bewerking;
handleiding Lisse: Swets Test services; 1991. 23. Koeter MWJ, Ormel J: General Health Questionnaire, Nederlandse bewerking;
handleiding Lisse: Swets Test services; 1991. 24. Dahlstrom L, Widmark G, Carlsson SG: Cognitive-behavioural profiles
among different categories of orofacial pain patients: diagnostic and
treatment implications. Eur J Oral Sci 1997, 105:377-383. 25. Turner JA, Dworkin SF, Mancl L, Huggins KH, Truelove E: The roles of
beliefs, catastrophizing, and coping in the functioning of patients with
temporomandibular disorder. Pain 2001, 92:41-51. 26. LeResche L: Epidemiology of temporomandibular disorders:
implications for the investigation of etiological factors. Crit Rev Oral Biol
1997, 8:291-305. 27. Bush FM, Harkins SW, Harrington WG, Price DD: Analysis of gender
effects on pain perception and symptom presentation in
tempormandibular pain. Pain 1993, 53:73-80. 28. Turk DC, Okifuji A: Psychological factors in chronic pain: evolution and
revolution. J Consult Clin Psychol 2002, 70:678-690. Author Details 1Department of Oral and Maxillofacial Surgery, University Medical Center
Groningen University of Groningen, Groningen, PO Box 30.001, 9700 RB, The
Netherlands, 2Center for Dentistry and Oral Hygiene, Department of Oral
Health Care and Clinical Epidemiology, University Medical Center Groningen,
University of Groningen, Groningen, 9700 VB, The Netherlands, 3Research
Innovation Group in Health Care and Nursing, Hanze University Groningen, 20. Stegenga B, De Bont LG, De Leeuw R, Boering G: Assessment of
mandibular function impairment associated with temporomandibular
joint osteoarthrosis and internal derangement. J Orofac Pain 1993,
2:183-195. 21. Zigmond AS, Snaith RP: The Hospital Anxiety and Depression Scale. Acta Psychiatr Scan 1983, 67:361-370. Page 8 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46
http://www.hqlo.com/content/8/1/46 doi: 10.1186/1477-7525-8-46
Cite this article as: Tjakkes et al., TMD pain: the effect on health related qual-
ity of life and the influence of pain duration Health and Quality of Life Out-
comes 2010, 8:46 |
https://openalex.org/W3034111647 | https://europepmc.org/articles/pmc7286221?pdf=render | English | null | COVID-19: viral–host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection | Journal of translational medicine | 2,020 | cc-by | 7,404 | Messina et al. J Transl Med (2020) 18:233
https://doi.org/10.1186/s12967-020-02405-w Messina et al. J Transl Med (2020) 18:233
https://doi.org/10.1186/s12967-020-02405-w Journal of
Translational Medicine Open Access COVID‑19: viral–host interactome analyzed
by network based‑approach model to study
pathogenesis of SARS‑CoV‑2 infection Francesco Messina1†, Emanuela Giombini1†, Chiara Agrati1, Francesco Vairo1, Tommaso Ascoli Bartoli1,
Samir Al Moghazi1, Mauro Piacentini1,2, Franco Locatelli3, Gary Kobinger4, Markus Maeurer5,6,
Alimuddin Zumla7,8, Maria R. Capobianchi1* , Francesco Nicola Lauria1†, Giuseppe Ippolito1† and COVID 19
INMI Network Medicine for IDs Study Group Abstract Background: Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under
evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment
modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response
against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are there-
fore a key source of information. Methods: We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-
CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV–host interactome
was carried out in order to provide a theoretic host–pathogen interaction model for HCoV infections and in order to
translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was
compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV,
MERS-CoV, HCoV-229E and the host interactome were inferred through published protein–protein interactions (PPI)
as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. Results: Although the amino acid sequences of the S-glycoprotein were found to be different between the various
HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2,
consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV
and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and
chemokines. Conclusions: In this paper, we developed a network-based model with the aim to define molecular aspects of
pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided phar-
maceutical and diagnostic research with the prospect to identify potential new biological targets. Keywords: Coronavirus infection, Virus–host interactome, Spike glycoprotein Background
In December 2019, a novel coronavirus (SARS-CoV-2)
was first identified as a zoonotic pathogen of humans
in Wuhan, China, causing a respiratory infection
with associated bilateral interstitial pneumonia. The *Correspondence: maria.capobianchi@inmi.it
†Francesco Messina, Emanuela Giombini, Francesco Nicola Lauria and
Giuseppe Ippolito contributed equally to this work
1 National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS,
Rome, Italy © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material
in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material
is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the
permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativeco
mmons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/
zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material
in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material
is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the
permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativeco
mmons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/
zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Messina et al. J Transl Med (2020) 18:233 Messina et al. J Transl Med (2020) 18:233 Page 2 of 10 Page 2 of 10 disease caused by SARS-CoV-2 was named by the
World Health Organization as COVID-19 and it has
been classified as a global pandemic since it has spread
rapidly to all continents. As of May 20, 2020, there have
been 4.889.287 confirmed COVID-19 cases worldwide
with 322.457 deaths reported to the WHO [1]. Whilst
clinical and epidemiological data on COVID-19 have
become readily available, information on the pathogen-
esis of the SARS-CoV-2 infection has not been forth-
coming [2]. The transcriptomic and proteomic data on
host response against SARS-CoV-2 is scanty and not
effective therapeutics and vaccines for COVID-19 are
available yet.f We investigated here biologically and clinically relevant
molecular targets of three human coronaviruses (HCoV)
infections using a network based approach. A functional
analysis of HCoV–host interactome was carried out in
order to provide a theoretic host–pathogen interaction
model for HCoV infections, and to predict viable mod-
els for SARS-CoV-2 pathogenesis. Three HCoV caus-
ing respiratory diseases were used as the model targets,
namely: SARS-CoV, that shares with SARS-CoV-2 a
strong genetic similarity, including MERS-CoV, and
HCoV-229E. Comparative reconstruction of S‑glycoprotein in HCoVsh Comparative reconstruction of S‑glycoprotein in HCoVsh Comparative reconstruction of S‑glycoprotein in HCoVs
The reconstruction of virus–host interactome was car-
ried out using the RWR algorithm to explore the human
PPI network and the multilayer PPI platform enriched
with gene expression data sets. 259 sequences of CoVs,
infecting different animal hosts (Additional file 1:
Table S1), were downloaded by GSAID and NCBI data-
base in order to evaluate the variability in the S gene. SARS-CoV, HCoV-229E and MERS-CoV and other CoV
full genome sequence groups were aligned with MAFFT
[14], synonymous and non-synonymous mutations, and
amino acid similarity were calculated using the SSE pro-
gram with a sliding windows of 250 nucleotides and a
pass of 25 nu [15]. A homology model was built for the
amino acid sequences of the S-glycoprotein, derived from
the full genome sequence obtained at “SARS-CoV-2/
INMI1/human/2020/ITA” (MT066156.1). The Swiss pdb
server was used to construct three-dimensional mod-
els for the S-glycoprotein of SARS-CoV-2 [16]. Among
proteins with a 3D structure, the best match with the
“SARS-CoV-2/INMI1/human/2020/ITA” sequence was
the 6VSB.1, that was evaluated considering the iden-
tity of two amino acid sequences and the QMEN value
included in Swiss pdb server. The model of a single chain
was overlapped with the three-dimensional structure
of S-glycoprotein single chain belonging to SARS-CoV
(5WRG), HCoV-229E (6U7H.1) and MERS-CoV (5X59),
using Chimera 1.14 [17]. In order to better evaluate the
conservation of the sequence in each site, all sequences
were aligned with MAFFT and the topology of all struc-
tures were compared. The detailed description of the
reconstruction of S-glycoprotein structure is reported in
Additional file 2. The investigation of structural genomics and inter-
actomics of SARS-CoV-2 can be implemented through
systematical mapping of protein–protein interactions
(PPI) between SARS-CoV-2 and human host, and an
integrated bioinformatics approach [12, 13]. Structural
analysis of specific SARS-CoV-2 proteins, in particular
Spike glycoproteins (S-glycoproteins), and their interac-
tions with human proteins, can guide the identification of
the putative functional sites and help to better define the
pathologic phenotype of the infection. This functional
interaction analysis between the host and other HCoVs,
combined with an evolutionary sequence analysis of
SARS-CoV-2, can be used to guide new treatment and
prevention interventions. Methods Coronaviruses (CoVs) typically affect the respiratory
tract of mammals, including humans, and lead to mild
to severe respiratory tract infections [3]. Many emerg-
ing HCoV infections have spilled-over from animal res-
ervoirs, such as HCoV-OC43 and HCoV-229E which
cause mild diseases such as common colds [4, 5]. During
the past 2 decades, two highly pathogenic HCoVs, severe
acute respiratory syndrome coronavirus (SARS-CoV) and
Middle East respiratory syndrome coronavirus (MERS-
CoV), have led to global epidemics with high morbid-
ity and mortality [6]. In this period, a large amount of
experimental data associated with the two infections has
allowed to better understand molecular mechanism(s) of
coronavirus infection, and enhance pathways for devel-
oping new drugs, diagnostics and vaccines and identi-
fication of host factors stimulating (proviral factors) or
restricting (antiviral factors) infection remains poorly
understood [7]. Structures of many proteins of SARS-
CoV and MERS-CoV, and biological interactions with
other viral and host proteins have been widely explored;
through experimental testing of small molecule inhibi-
tors with anti-viral effects [8, 9]. ACE2, expressed in type
2 alveolar cells in the lung, has been identified as recep-
tor of SARS-CoV and SARS-CoV-2, while dipeptidyl
peptidase DPP4 was identified as the specific receptor for
MERS-CoV [10, 11]. PPI and gene co‑expression network Network analysis, based on protein–protein interactions
and gene expression data, was performed in order to view
all possible virus–host protein interactions during the
HCoV infections. Since the SARS-CoV-2 genome exhibits
substantial similarity to the SARS-CoV genome [18] and Messina et al. J Transl Med (2020) 18:233 Page 3 of 10 subsequently also the proteome [19], we hypothesized
that several molecular interactions that were observed
in the SARS-CoV interactome will be preserved in the
SARS-CoV-2 interactome. Virus–host interactomes
(SARS-CoV, MERS-CoV, HCoV-229E) were inferred
through published PPI data, using two publicly accessi-
ble databases (STRING Viruses and VirHostNet), as well
as published scientific reports with a focus on virus–host
interactions [20–22]. As a next step, the virus–host PPI
list, extracted in this first step, was merged with addi-
tional PPI databases, i.e. BioGrid, InnateDB-All, IMEx,
IntAct, MatrixDB, MBInfo, MINT, Reactome, Reactome-
FIs, UniProt, VirHostNet, BioData, CCSB Interactome
Database, using R packages PSICQUIC and biomaRt [23,
24]. In total, a large PPI interaction database was assem-
bled, including 13,020 nodes and 71,496 interactions.h sequence obtained at Laboratory of Virology, National
Institute for Infectious Diseases “L. Spallanzani” IRCCS,
using Swiss pdb viewer server (Additional file 2: Figure
S2a, b). The SARS-CoV-2 S-glycoprotein structure was
then compared to other HCoVs as shown in Additional
file 2: Figure S2. The S-glycoprotein structures of the
various HCoV were very similar overall. In particular, a
strong similarity was shown in the RBD (nCov: residues
319–591) [30], and this was most evident for the compar-
ison between SARS-CoV-2 and SARS-CoV, which share
the same cell receptor (ACE2). The amino acid differ-
ences among the S-glycoproteins of the selected HCoVs
(SARS-CoV-2, MERS-CoV, SARS-CoV, HCoV-229E)
are shown in Additional file 2: Figure S3, where a lower
topology similarity was observed with HCoV-229E S-gly-
coprotein, which binds a different host receptor. The gene expression data set was built from the Pro-
tein Atlas database, using tissue and cell line data [25]. To
identify the most likely interactions, and to obtain func-
tional information, Random walk with restart (RWR), a
state-of-the-art guilt-by-association approach by R pack-
age RandomWalkRestartMH [26] was used. It allows to
establish a proximity network from a given protein (seed),
to study its functions, based on the premise that nodes
related to similar functions tend to lie close to each other
in the network. For each node, a score was computed as
measure of proximity to the seed protein. Human CoV and host interactome An interactome map was built to highlight biological
connections among S-glycoprotein and the human pro-
teome. Using the analysis pipeline described in the meth-
ods, a large PPI interaction database was assembled,
including 13,020 nodes and 71,496 interactions between
human host and the three selected viruses (SARS-CoV,
MERS-CoV and HCoV-229E).h The interactome reconstruction was obtained with the
RWR analysis, finding 200 closest proteins to seed, or
S-glycoproteins of HCoV-229E, SARS-CoV and MERS-
CoV (Additional file 2: Figures S4–S6). In Additional
file 1: Tables S2–S4, lists of genes selected by RWR algo-
rithm for HCoV-229E, SARS-CoV and MERS-CoV, along
with proximity score were reported. In order to further
dissect the S-glycoprotein-host interactions, enrichment
analysis was carried out with Reactome and KEGG data-
bases. Reactome pathway enrichment analysis revealed
biological pathways of DNA repair, transcription and
gene regulation for the HCoV-229E S-glycoprotein, with
high significance (FDR < 0.01%). KEGG pathway enrich-
ment analysis revealed ubiquitin mediated proteolysis
as the most significant pathway (FDR < 0.01%), as well
as cellular proliferation pathways, associated with other
viral infections (Hepatitis B, measles, Epstein–Barr virus
infection and Human T-cell leukemia virus 1 infection)
as well as with carcinogenesis (Fig. 1). Next, the RWR
algorithm was applied to a multilayer network built on
the PPI interactome and on the Gene Coexpression
(COEX) network, again with S-glycoprotein of HCoV-
229E as seed. The results highlighted a set of genes that
are connected in both PPI and COEX analysis, including
ANPEP, RAD18, APEX, POLH, APEX1, TERF2, RAD51, Functional enrichment analysis To evaluate functional pathways of proteins involved in
host response, gene enrichment analysis was performed,
using Kyoto Encyclopedia of Genes and Genomes
(KEGG) human pathways and Gene Ontology databases. Network representation from the gene enrichment anal-
ysis was performed using ShinyGO v0.61 [27]. The sta-
tistical significance was obtained, calculating the False
Discovery Rate (FDR). PPI and gene co‑expression network S-glycoproteins
of SARS-CoV, MERS-CoV and HCoV-229E were used as
seed in the application of the RWR algorithm. f
Overall, the pattern arising from such comparison was
consistent with specific host receptors, as well as with
different host reservoirs and ancestry [31]. Structure of S‑glycoprotein CoVs To evaluate the diversity along the full genome, pairwise
distance was calculated on 259 HCoV genomes. Diversity
was distributed along the entire CoV genome, with the
most conserved region located in Orf1ab, as expected,
while the spike gene region exhibited a rather high diver-
sity (Additional file 2: Figure S1), due to key role of the
S-glycoprotein during viral entry in specific hosts [28]. i
Consequently, the analysis was focused on the S-gly-
coprotein, as a key virus component involved in host
interaction [29]. A 3D model of S-glycoprotein of the
SARS-CoV-2 sequence (MT066156.1) was built on the Messina et al. J Transl Med (2020) 18:233 Page 4 of 10 Fig. 1 KEGG human pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein of
HCoV-229E an pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein Fig. 1 KEGG human pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein of
HCoV-229E proliferation, TGF-β and other infection-related path-
ways (FDR < 0.0001%) (Fig. 3). The PPI-COEX multilayer
analysis highlighted a set of genes that are connected in
both PPI and COEX analysis, i.e.CLEC4G, CLEC4M,
CD209, ACE2, RPSA, all associated to the GO biologi-
cal process category of SARS-CoV entry into host cell
(FDR < 0.01%) (Fig. 4). In MERS-CoV, the Reactome
pathway enrichment analysis showed a strong associa-
tion with membrane signals activated by GPCR ligand
binding (FDR < 0.0001%), and chemokine/chemokine
receptor pathways. Consistent results were obtained with
KEGG pathway enrichment, that highlighted cytokine–
cytokine receptor and chemokine signalling pathways
(FDR < 0.0001%) (Fig. 5). Finally, PPI-COEX multilayer
analysis evidenced, for both PPI and COEX, CCR4,
CXCL2, CXCL10, CXCL9, PF4, PF4V1, CCL11, CXCL11,
XCL1, CXCR4 and CXCL14, all genes identified by the
GO biological processes involved in the chemokine cas-
cade (FDR < 0.0001%), in line with the results obtained
with enrichment analyses (Fig. 6). Fig. 2 PPI-COEX multilayer analysis, based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified by
RWR, using S-glycoprotein of HCoV-229E. Edges in blue represent
protein-protein interactions, while red edges are coexpressions Fig. 2 PPI-COEX multilayer analysis, based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified by
RWR, using S-glycoprotein of HCoV-229E. Edges in blue represent
protein-protein interactions, while red edges are coexpressions Discussion
In‑depth comparative analysis of S‑glycoprotein
l d
k
l
b
d CDC7, USP7, XRCC5, RAD18, FEN1, PCNA, all associ-
ated to the GO biological process category of DNA repair
(FDR < 0.0001%) (Fig. 2). The same analyses were con-
ducted for SARS-CoV and MERS-CoV. In‑depth comparative analysis of S‑glycoprotein
l d
k
l
b
d In‑depth comparative analysis of S‑glycoprotein
We applied network analysis, based on protein–pro-
tein interactions and gene expression data, in order to
describe the interactome of the coronavirus S-glycopro-
tein and host proteins, with the aim to better understand
SARS-CoV-2 pathogenesis. A preliminary structural
analysis was conducted on the S-glycoprotein of SARS-
CoV-2 as compared to the other 3 HCoV, using the
S-glycoprotein as a model to shed light on the host–path-
ogen interaction in the dynamic process of SARS-CoV-2 The Reactome pathway enrichment analysis for the
SARS-CoV revealed S-glycoprotein connection with
early activation of innate immune system, such as the
Toll Like Receptor Cascade and TGF-β, with a strong
significance (FDR < 0.0001%), while the KEGG pathway
enrichment analysis revealed an association with cellular Messina et al. J Transl Med (2020) 18:233 Page 5 of 10 Fig. 3 KEGG human pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm using S-glycoprotein of
SARS-CoV ig. 3 KEGG human pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm usin
ARS C V pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm using S-glycoprotein of Fig. 4 PPI-COEX multilayer analysis based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified
by RWR, using S-glycoprotein of SARS-CoV. Edges in blue represent
protein-protein interactions, while red edges are coexpressions and SARS-CoV-2, consistent with the shared ACE2 pre-
dicted receptor. Of note, the newly discovered SARS-CoV-2 genome
has revealed differences between SARS-CoV-2 and
SARS or SARS-like coronaviruses [31]. Although no
amino acid substitutions were present in the recep-
tor-binding motifs, that directly interact with human
receptor ACE2 protein in SARS-CoV, six mutations
occurred in the other region of the RBD [31, 32] were
identified. On the other hand, the genomic comparative
analysis highlighted the strong diversity in the S gene
among CoV in different hosts, confirming the biologi-
cally vital role of the S-glycoprotein as a key factor in
viral entry in cross-species transmission events [28]. y
In addition, the comparative 3D structural data may
facilitate the definition of already known antibody
epitopes in the S-glycoprotein of other coronaviruses,
it will also be useful in rational vaccine design and in
gauging anti-virus directed immune responses after
vaccination [30]. In‑depth comparative analysis of S‑glycoprotein
l d
k
l
b
d In fact, S-glycoprotein remains an
important target for vaccines and drugs previously
evaluated in SARS and MERS, while a neutralizing
antibody targeting the S-glycoprotein protein could
provide passive immunity. The host interactome,
linked to S-glycoprotein of SARS-CoV and MERS-CoV,
mainly highlighted innate immunity pathway com-
ponents, such as Toll Like receptors, cytokines and
chemokines. The 3D structural analysis confirmed that Fig. 4 PPI-COEX multilayer analysis based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified
by RWR, using S-glycoprotein of SARS-CoV. Edges in blue represent
protein-protein interactions, while red edges are coexpressions infection. Although the amino acid sequences of the
S-glycoprotein were different between the various
HCoVs, the structural analysis exhibited high similarity;
the best 3D structural overlap was found for SARS-CoV Messina et al. J Transl Med (2020) 18:233 Page 6 of 10 Fig. 5 KEGG human pathway and Reactome pathways enrichment for 200 proteins identified by RWR algorithm using S-glycoprotein of MERS-CoV GG human pathway and Reactome pathways enrichment for 200 proteins identified by RWR algorithm using S-glycoprotein Fig. 6 PPI-COEX multilayer analysis based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified
by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent
protein-protein interactions, while red edges indicate coexpressions infections indicated the presence of several hub proteins. In the HCoV-229E–host interactome hub position was
hold by RAD18 and APEX, which play an important role
in DNA repair due to UV damage in phase S [33]. For the SARS-CoV interactome, the gene hubs were
identified in ACE2, CLEC4G and CD209, which are
known interactors with S-glycoprotein of SARS-CoV [34,
35]. In fact, two independent mechanisms were described
as trigger of SARS-CoV infection: proteolytic cleavage of
ACE2 and cleavage of S-glycoprotein. The latter activates
the glycoprotein for cathepsin L-independent host cell
entry. Activated the S-glycoprotein by cathepsin L mech-
anism in host cell entry was reported in many infections
of CoV, such as HCoV-229E and SARS-CoV [36, 37]. A
recent study speculated that this interaction will be pre-
served in SARS-CoV-2 [19], but might be disrupted of a
substantial number of mutations in the receptor binding
site of S gene will occur. Likewise, the S-glycoprotein in
SARS-CoV-2 is expected to interact with type II trans-
membrane protease (TMPRSS2) and probably is involved
in inhibition of antibody-mediated neutralization [38,
39]. In‑depth comparative analysis of S‑glycoprotein
l d
k
l
b
d It is rather unexpected that, for this virus, no intra-
cellular pathways were highlighted by the multilayer
analysis, suggesting that this field is still open to further
investigation. Fig. 6 PPI-COEX multilayer analysis based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified
by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent
protein-protein interactions, while red edges indicate coexpressions Fig. 6 PPI-COEX multilayer analysis based on human PPI interactome
and COEX network, with top 50 closest proteins/genes identified
by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent
protein-protein interactions, while red edges indicate coexpressions we established that S-glycoprotein of SARS-CoV-2 has
strong similarity in the 3D structure with SARS-CoV
[18]. In MERS-CoV infection a gene hub role was described
for DPP4, which is known to regulate cytokine levels
through catalytic cleavage [40]. Immune cell—recruit-
ing chemokines and cytokines, such as IP-10/CXCL-
10, MCP-1/CCL-2, MIP-1α/CCL-3, RANTES/CCL-5,
can be strongly induced by MERS-CoV, showing higher
inducibility in human monocyte—derived macrophages Host interactome in all three HCoV infectionsh The reconstruction of virus–host interactome was car-
ried out using RWR algorithm to explore the human PPI
network and studying PPI and COEX multilayer. The
PPI network topology of host interactome in all three Messina et al. J Transl Med (2020) 18:233 Page 7 of 10 aid to design a ‘blue print’ for SARS-CoV-2 associated
pathogenicity. by MERS-CoV as compared to than SARS-CoV infec-
tion [41]. The cellular proliferation pathways, involved
immediately after virus entry, were described in all three
models, resulting consistent with inhibiting activity on
cell proliferation and cytotoxic effect due to HCoV infec-
tions [42, 43]. Finally, biological pathways, revealed by
enrichment analysis in over all models, supported early
activation of innate immune system, as Toll Like recep-
tor Cascade and TGF-β for SARS-CoV, or chemokine and
cytokine pathways and infection-related pathways for
MERS-CoV, with a strong significance for both. The severity and the clinical picture of SARS-CoV and
MERS-CoV infections could be related to the activation
of exaggerated immune mechanism, causing uncon-
trolled inflammation [47]; however, the role of strong
immune response in SARS-CoV-2 infection severity is
still uncertain. However, we may consider that host kinases link mul-
tiple signalling pathways in response to a broad array
of stimuli, including viral infections. TGF-β, produced
during the inflammatory phase by macrophages, is an
important mediator of fibroblast activation and tissue
repair. High levels of systemic inflammatory cytokines/
chemokines has been widely reported for MERS-CoV
infections [48–50], correlating with immunopathology
and massive pulmonary infiltration into the lungs [51]. Also the HCoV-229E infection can be described with
this distance model, although this infection was not asso-
ciated with a severe respiratory disease. In fact, HCoV-
229E is responsible for mild upper respiratory tract
infections, such as common colds, with only occasional
spreading to the lower respiratory tract, but it interacts
with dendritic cells in the upper respiratory tract, induc-
ing a cytopathic effect [52]. Conclusions
I
l
i In conclusion, we developed a network-based model,
which could be the framework for structure-guided
research process and for the pathogenetic evaluation of
specific clinical outcome. Accurate structural 3D protein
models and their interaction with host receptor proteins
can allow to build a more detailed theoretical disease
model for each HCoV infection, and support the drawing
of a disease model for COVID-19. Our analyses suggests
it is important to carry out in silico experiments and sim-
ulations through specific algorithms. Second, Mitogen activated protein kinase (MAPK) is
a major cell signalling pathway that is known to be acti-
vated by diverse groups of viruses, and plays an impor-
tant role in cellular response to viral infections. MAPK
interacting kinase 1 (MNK1) has been shown to regulate
both cap-dependent and internal ribosomal entry sites
(IRES)-mediated mRNA translation; Third, The identification of the MAPK pathway in
SARS-CoV model is highly consistent with in vivo model,
where P38 MAPK was found increased in the lungs of
mice infected with SARS-CoV [44];hi Pathogenic model for HCoV infections We constructed a host molecular interactome with SARS-
CoV, MERS-CoV and HCoV-229E in patients with can-
cer, assuming that most of these interactions, especially
for SARS-CoV, are shared with SARS-CoV-2. A network-
based methodology, along with guilt-by-association algo-
rithm (RWR), was applied to define the pathological model
of COVID-19 and provide a treatment of SARS-CoV-2,
using existing transcriptomic and proteomic information.i Based on the main pathways identified by the network-
based interactome analysis, the following issues require
focus further study: First, The predicted receptor for SARS-CoV-2 has been
inferred to be ACE-2, i.e. the same used by SARS-CoV,
based on the high similarity of the S-glycoprotein of the
two viruses, and this is the basis for hypothesizing to
use SARS-CoV as a model for virus–host interactome in
COVID-19; Funding INMI authors are supported by the Italian Ministry of Health (Ricerca Corrente
Linea 1). G. Ippolito and A. Zumla are co-principal investigator of the Pan-Afri-
can Network on Emerging and Re-emerging Infections (PANDORA-ID-NET),
funded by the European & Developing Countries Clinical Trials Partnership,
supported under Horizon 2020. Sir Zumla is in receipt of a National Institutes
of Health Research senior investigator award. M. Maeurer is a member of the
innate immunity advisory group of the Bill & Melinda Gates Foundation, and is
funded by the Champalimaud Foundation. Supplementary information accompanies this paper at https://doi.
org/10.1186/s12967-020-02405-w. Supplementary information acco
org/10.1186/s12967-020-02405-w. Supplementary information accompanies this paper at https://doi. org/10.1186/s12967-020-02405-w. pp
y
org/10.1186/s12967-020-02405-w. Additional file 1: Table S1. List of accession numbers of H-CoV. Table S2. List of genes selected by RWR algorithm for HCoV-229E, along with
proximity score. Table S3. List of genes selected by RWR algorithm for
SARS-CoV, along with proximity score. Table S4. List of genes selected by
RWR algorithm for MERS-CoV, along with proximity score. Limitations to our study A single protein, namely S-glycoprotein was used as seed,
therefore the highlighted interactions were limited to
those connected with this unique viral protein. However,
this is a proof of concept study, from which it appears
that a similar approach may be used to study other viral
proteins interacting with host cell pathways. Fourth, The identification of the TGF-β pathway in
S-glycoprotein-induced interactome for SARS-CoV of
particular interest, due to the previous evidence that this
virus, and in particular its protease, triggered the TGF-β
through the p38 MAPK/STAT3 pathway in alveolar basal
epithelial cells [45, 46];i Another limitation is that the pathway analysis did
not consider tissue and cell type diversity. Finally, the
low threshold established for the number of nodes
found by RWR (200) limited the reconstruction of the
entire pathways. However, this was a software-imposed
threshold. Fifth, Innate immune pathways were identified in S-gly-
coprotein-induced models of SARS-CoV and MERS-CoV,
as Toll Like receptor, cytokine and chemokine. Every described pathway can be matched with clinical
aspects, the data presented in this report may therefore Messina et al. J Transl Med (2020) 18:233 Messina et al. J Transl Med (2020) 18:233 Page 8 of 10 Page 8 of 10 In summary, the interactome analysis aided to guide
the design of novel models of SARS-CoV pathogenicity. Author details 1 National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome,
Italy. 2 Department of Biology, University of Rome “Tor Vergata”, Rome, Italy. 3 Department of Pediatric Hematology and Oncology, IRCCS Ospedale
Pediatrico Bambino Gesu, Rome, Italy. 4 Département de Microbiologie‑Infec-
tiologie et d’Immunologie, Université Laval, Quebec, QC, Canada. 5 Immu-
noSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal. 6 I. Medizinische Klinik Johannes Gutenberg-Universität, University of Mainz,
Mainz, Germany. 7 Department of Infection, Division of Infection and Immu-
nity, University College London, London, UK. 8 National Institute for Health
Research Biomedical Research Centre, University College London Hospitals
NHS Foundation Trust, London, UK. Acknowledgements We gratefully acknowledge: Collaborators Members of INMI COVID-19 Study
Group; COVID 19 INMI Network Medicine for IDs Study Group: We gratefully acknowledge: Collaborators Members of INMI COVID-19 Study
Group; COVID 19 INMI Network Medicine for IDs Study Group:
Isabella Abbate, Chiara Agrati, Samir Al Moghazi, Tommaso Ascoli Bartoli,
Barbara Bartolini, Maria R. Capobianchi , Alessandro Capone, Delia Goletti,
Gabriella Rozera, Carla Nisii, Roberta Gagliardini, Fabiola Ciccosanti, Gian Maria
Fimia, Emanuele Nicastri, Emanuela Giombini, Simone Lanini, Alessandra
D’Abramo, Gabriele Rinonapoli, Enrico Girardi, Chiara Montaldo, Raffaella Mar-
coni, Antonio Addis, Bradley Maron, Ginestra Bianconi, Bertrand De Meulder,
Jason Kennedy, Shabaana Abdul Khader, Francesca Luca, Markus Maeurer,
Mauro Piacentini, Stefano Merler, Giuseppe Pantaleo, Rafick-Pierre Sekaly,
Serena Sanna, Nicola Segata, Alimuddin Zumla, Francesco Messina, Francesco Abbreviations CoVs: Coronaviruses; HCoV: Human coronavirus; PPI: Protein–protein interac-
tions; COEX: Gene coexpression data; SARS-CoV: Severe acute respiratory syn-
drome coronavirus; MERS-CoV: Middle East respiratory syndrome coronavirus;
S-glycoprotein: Spike glycoprotein; RWR: Random walk with restart; FDR: False
Discovery Rate. Received: 25 April 2020 Accepted: 4 June 2020 Received: 25 April 2020 Accepted: 4 June 2020 References 1. Johns Hopkins University. Global-cases-covid-19. 2020. https://www.gisai
d.org/epiflu-applications/global-cases-covid-19/. 2. Jernigan DB. Update: public health response to the coronavirus disease
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Vairo, Francesco Nicola Lauria, Giuseppe Ippolito. 4. Walsh EE, Shin JH, Falsey AR. Clinical impact of human coronaviruses
229E and OC43 infection in diverse adult populations. J Infect Dis. 2013;208(10):1634–42. https://doi.org/10.1093/infdis/jit393. Consent for publication
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de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ,
et al. A kinome-wide small interfering rna screen identifies proviral and
antiviral host factors in severe acute respiratory syndrome coronavirus
replication, including double-stranded RNA-activated protein kinase and 1.
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Jernigan DB. Update: public health response to the coronavirus disease
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Wkly Rep. 2020;69(8):216–9. https://doi.org/10.15585/mmwr.mm6908e1.
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Paules CI, Marston HD, Fauci AS. Coronavirus infections-more than just
the common cold. JAMA. 2020. https://doi.org/10.1001/jama.2020.0757.
4.
Walsh EE, Shin JH, Falsey AR. Clinical impact of human coronaviruses
229E and OC43 infection in diverse adult populations. J Infect Dis.
2013;208(10):1634–42. https://doi.org/10.1093/infdis/jit393.
5.
Hendley JO, Fishburne HB, Gwaltney JM Jr. Coronavirus infections in
working adults. Eight-year study with 229 E and OC 43. Am Rev Respir
Dis. 1972;105(5):805–11. https://doi.org/10.1164/arrd.1972.105.5.805.
6.
de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS:
recent insights into emerging coronaviruses. Nat Rev Microbiol.
2016;14(8):523–34. https://doi.org/10.1038/nrmicro.2016.81.
7.
de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ,
et al. A kinome-wide small interfering rna screen identifies proviral and
antiviral host factors in severe acute respiratory syndrome coronavirus
replication, including double-stranded RNA-activated protein kinase and Received: 25 April 2020 Accepted: 4 June 2020 Ethics approval and consent to participate Ethics approval and consent to participate Availability of data and materials PPI data of SARS-CoV, MERS-CoV, HCoV-229E S-glycoprotein were inferred
through published PPI data, using STRING Viruses (http://viruses.string-db. org/) and VirHostNet (http://virhostnet.prabi.fr/), as well as published scientific
reports with a focus on virus-host interactions [20–22]. Human PPI databases
(BioGrid, InnateDB-All, IMEx, IntAct, MatrixDB, MBInfo, MINT, Reactome,
Reactome-FIs, UniProt, VirHostNet, BioData, CCSB Interactome Database),
using R packages PSICQUIC (https://bioconductor.org/packages/release/bioc/
html/PSICQUIC.html) and biomaRt (https://bioconductor.org/packages/relea
se/bioc/html/biomaRt.html) [23, 24]. The gene expression data set was built
from the Protein Atlas database (https://www.proteinatlas.org/) [25]. Additional file 2: Figure S1. Pairwise distances along 259 full length CoV
genomes. In the bottom of picture, indicative gene positioning along
CoVs genomes is reported. The list of all considered genomes is reported
in Additional file 1: Table S1. Figure S2. 3D structure of S-glycoprotein
of SARS-CoV-2 and comparison with the ortholog from HCoV-229E,
SARS-CoV, and MERS-CoV. Lateral (a) and superior (b) representation of
SARS-CoV-2 S-glycoprotein, deducted for the sequence of patient INMI1
(MT066156.1). Each subunit chain has a different color. Structure com-
parison of S-glycoprotein subunit between: HCoV-229E and SARS-CoV-2,
in purple and blue respectively (c); SARS-CoV and SARS-CoV-2, in red
and blue, respectively (d); MERS-CoV and SARS-CoV-2, in green and blue,
respectively (e). Figure S3. Amino acid alignment and secondary motifs
in the receptor binding domain (RBD) of S-glycoprotein of HCoV-229E,
SARS-CoV, MERS-CoV and SARS-CoV-2 are shown. Legend of secondary
motifs identifiers: H = α Helix, E = β Sheet, X = Random coil. Figure S4. HCoV-229E–host interactome resulting from RWR applied to the top 200
closest proteins identified by RWR, using S-glycoprotein of HCoV-229E. Figure S5. SARS-CoV–host interactome resulting from RWR applied to the
top 200 closest proteins identified by RWR, using S-glycoprotein of SARS-
CoV. Figure S6. MERS-CoV–host interactome resulting from RWR applied
to the top 200 closest proteins identified by RWR, using S-glycoprotein of
MERS-CoV. Ethics approval and consent to participate
Not applicable. Authors’ contributions 5. Hendley JO, Fishburne HB, Gwaltney JM Jr. Coronavirus infections in
working adults. Eight-year study with 229 E and OC 43. Am Rev Respir
Dis. 1972;105(5):805–11. https://doi.org/10.1164/arrd.1972.105.5.805. Conceptualization: FM, EG, FNL. Data curation: FM, EG. Formal analysis: FM,
EG.Funding acquisition: MRC, GI, FV, MM, AZ. Investigation: FM, EG, FNL. Meth-
odology: FM, EG, TA, SA. Resources: MRC, GI. Software: FM, EG. Supervision:
MRC, FNL. Validation: CA, FV, GK, MM, MP. Visualization: FM, EG. Writing ± origi-
nal draft: FM, EG, MRC, FNL, GK, AZ, MM. Writing ± review and editing: FM,
EG, MRC, FNL, AZ. All authors reviewed the manuscript. All authors read and
approved the final manuscript. 6. de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS:
recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016;14(8):523–34. https://doi.org/10.1038/nrmicro.2016.81. g
7. de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ,
et al. A kinome-wide small interfering rna screen identifies proviral and
antiviral host factors in severe acute respiratory syndrome coronavirus
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https://openalex.org/W3009055364 | https://eprints.ncl.ac.uk/fulltext.aspx?url=286498/A85E21C1-9E04-4C1B-BF63-8E783736A9CE.pdf&pub_id=286498 | English | null | Ankle Motion Is Associated With Soft Tissue Displacement in the Dorsal Thigh: An in vivo Investigation Suggesting Myofascial Force Transmission Across the Knee Joint | Frontiers in physiology | 2,020 | cc-by | 5,782 | ORIGINAL RESEARCH
published: 06 March 2020
doi: 10.3389/fphys.2020.00180 Keywords: myofascial force transmission, ultrasound, range of motion, fascia, myofascial chains Citation: Wilke J, Debelle H, Tenberg S,
Dilley A and Maganaris C (2020) Ankle
Motion Is Associated With Soft Tissue
Displacement in the Dorsal Thigh: An
in vivo Investigation Suggesting
Myofascial Force Transmission Across
the Knee Joint. *Correspondence:
Jan Wilke *Correspondence:
Jan Wilke
wilke@sport.uni-frankfurt.de Specialty section:
This article was submitted to
Striated Muscle Physiology,
a section of the journal
Frontiers in Physiology Received: 18 December 2019
Accepted: 17 February 2020
Published: 06 March 2020 Ankle Motion Is Associated With Soft
Tissue Displacement in the Dorsal
Thigh: An in vivo Investigation
Suggesting Myofascial Force
Transmission Across the Knee Joint Jan Wilke1*, Heloise Debelle2, Sarah Tenberg1, Andrew Dilley3 and
Constantinos Maganaris2 1 Department of Sports Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany, 2 School of Sport and Exercise
Sciences, Liverpool John Moores University, Liverpool, United Kingdom, 3 Department of Neuroscience, University
of Sussex, Brighton, United Kingdom Experiments in cadavers have demonstrated significant mechanical interactions
between constituents of myofascial chains. However, evidence for such force
transmission effects is scarce under in vivo conditions. The purpose of this trial was
to examine the impact of ankle motion on soft tissue displacement of the dorsal thigh. Eleven healthy active individuals (26.8 ± 4.3 years, six males), in prone position and with
the knee extended, underwent passive calf stretches (ankle dorsal extension) imposed
by an isokinetic dynamometer. High-resolution ultrasound was used to simultaneously
capture the displacement of the semimembranosus muscle, which was quantified by
means of cross-correlation analysis. Inactivity of the leg muscles was controlled using
surface electromyography (EMG). One participant had to be excluded due to major
EMG activity during the experiment. According to a one-sample t test testing the
difference to the neutral zero position, ankle dorsal extension induced substantial caudal
muscle displacements (5.76 ± 2.67 mm, p < 0.0001). Correlation analysis (Spearman),
furthermore, revealed a strong association between maximal dorsal extension and
semimembranosus motion (rho = 0.76, p = 0.02). In conclusion, the present trial
provides initial in vivo evidence for a mechanical force transmission between serially
connected skeletal muscles. This means that local alterations of the mechanical tissue
properties may modify flexibility in neighboring (superior or inferior) joints. Edited by:
Can A. Yucesoy,
Bo ˘gaziçi University, Turkey
Reviewed by:
Filiz Ates,
Mayo Clinic, United States
Dieter Blottner,
Charité - Medical University Berlin,
Germany
*Correspondence:
Jan Wilke
wilke@sport.uni-frankfurt.de Edited by:
Can A. Yucesoy,
Bo ˘gaziçi University, Turkey
Reviewed by:
Filiz Ates,
Mayo Clinic, United States
Dieter Blottner,
Charité - Medical University Berlin,
Germany g
ç
y,
y
Reviewed by:
Filiz Ates,
Mayo Clinic, United States
Dieter Blottner,
Charité - Medical University Berlin,
Germany *Correspondence:
Jan Wilke
wilke@sport.uni-frankfurt.de INTRODUCTION As a consequence of intermuscular continuity (Yucesoy,
2010; Wilke et al., 2016a; Wilke and Krause, 2019) it has been
hypothesized that the modification of local tissue properties
can affect adjacent structures (Wilke et al., 2019a): if the
linkages connecting two muscles are stiffenough, they may
transmit force. In fact, experimental trials made such observation,
showing that length changes of lower leg muscles induced
mechanical strains in neighboring synergists and antagonists
(Huijing and Baan, 2001; Huijing et al., 2011). Since removing
the fibrous linkages between the muscles reduced this effect
(Huijing and Baan, 2001), the previously produced strains
seem to stem from a mechanical force transmission (Yucesoy,
2010). In their systematic review of cadaveric studies, Krause
et al. (2016) aimed to answer the question as to whether
mutual interactions would also occur between serially connected
muscles. According to their findings, substantial forces can
be transmitted, particularly in the posterior myofascial chain
(plantar aponeurosis, gastrocnemius, hamstring muscles, lumbar
fascia/erector spinae muscle). For instance, traction applied to
the biceps femoris leads to a force transmission to the lumbar
fascia (Vleeming et al., 1995). However, as cadavers (a) frequently
exhibit alterations of mechanical tissue properties (e.g., due to
fixation in solutions like formalin) and (b) do not produce
neuromuscular activity, the findings of most studies investigating
in-series mechanical force transmission cannot be extrapolated to
in vivo conditions. INTRODUCTION Fascia, the collagenous connective tissue surrounding the skeletal muscles, has long been regarded
as a passive packing organ with limited significance for the locomotor system (van der Wal,
2009). However, recent research unveiled a far more complex role. Firstly, histological studies
have demonstrated the intrafascial existence of myofibroblasts (e.g., in the gastrocnemius fascia; Front. Physiol. 11:180. doi: 10.3389/fphys.2020.00180 Front. Physiol. 11:180. doi: 10.3389/fphys.2020.00180 March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org Dorsal Myofascial Force Transmission Wilke et al. Bhattacharya et al., 2010). Their contraction, most probably
mediated by the vegetative nervous system, can produce
substantial increases of tissue stiffness in the long-term (Schleip
et al., 2019). Secondly, already within minutes or hours,
alterations of the water content, e.g., induced by isometric
stretching, have been shown to significantly impact viscoelastic
tissue properties (Schleip et al., 2012). The capacity of fascia to
soften or harden in response to mechanical stimuli may be of
particular importance due to another newly discovered feature. In contrast to prior assumptions, the surrounding fasciae do not
separate, but connect the skeletal muscles. This architecture can
be found between synergists and antagonists located parallel to
each other (Yucesoy, 2010) as well as between muscles arranged
in-series (Wilke et al., 2016a; Wilke and Krause, 2019). through the linkage, a visible displacement of the non-stretched
tissue should occur. Using a simple experimental approach (Cruz-Montecinos
et al., 2015) showed that an anterior pelvic tilt leads to a
recognizable displacement of the gastrocnemius fascia. Their
sonographic examination provides first indications for a cranial-
caudal force transmission effect originating at the hip joint. However, in many movements of daily life and sports (e.g.,
walking, sprinting, jumping, squatting), forces are generated
in the legs and hypothetically transmitted in direction of the
trunk. In addition to this, all above described available in vivo
trials examining the functional relevance of myofascial chains
were (1) based on caudal-cranial force transmission and (2)
mainly focused treatments around the ankle joint (plantar fascia
massage, calf stretching). The present proof-of-principle study,
therefore, aimed to elucidate for the first time, if a dorsal
extension movement (also often referred to as dorsal flexion) of
the ankle leads to a myofascial force transmission to the posterior
thigh under in vivo conditions. Ethical Standard The experimental ultrasound study was approved by the local
ethics committee and conducted according to the Declaration of
Helsinki as well as the guidelines of Good Clinical Practice. All
enrolled participants provided written informed consent. Sample Eleven healthy active individuals (26.8 ± 4.3 years, 6♂,
5♀) volunteered to participate. Exclusion criteria included
severe orthopedic, cardiovascular, neurological, endocrine and
psychiatric diseases, acute inflammation or history of surgery
in the lower limb, intake of drugs that modify pain perception
and proprioception, muscle soreness and pregnancy or nursing
period. Recruitment was performed by word of mouth. Outcome To reveal the spatial relations in the area of interest of
the United States image, the thickness of the subcutaneous
tissue and the deep fascia of the semimembranosus muscle
were
determined
using
ImageJ
(NIH,
Bethesda,
MD,
United States). Five equidistant measurements were taken
at rest and averaged. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone
position and with the knee extended, the ankle joint was passively moved
between plantar flexion and dorsal extension (arrow shows way into dorsal
extension). Maximal dorsal extension was calculated as the distance from a
calibrated neutral zero position (dashed line). Ultrasound recordings were
made over the semimembranosus muscle in order to estimate tissue
displacement induced by the ankle motion. EMG (not depicted here) used as
biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation
with a strap was required to prevent body motion induced by the
dynamometer action. As the belt was not in contact with the Hamstrings, it
did not affect tissue displacement. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone
position and with the knee extended, the ankle joint was passively moved
between plantar flexion and dorsal extension (arrow shows way into dorsal
extension). Maximal dorsal extension was calculated as the distance from a
calibrated neutral zero position (dashed line). Ultrasound recordings were
made over the semimembranosus muscle in order to estimate tissue
displacement induced by the ankle motion. EMG (not depicted here) used as
biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation
with a strap was required to prevent body motion induced by the
dynamometer action. As the belt was not in contact with the Hamstrings, it
did not affect tissue displacement. The
maximal
horizontal
displacement
of
the
semimembranosus muscle [mm distance from resting position]
during maximal passive ankle dorsal extension represented
the primary outcome. It was quantified using a frame-by-
frame cross-correlation analysis of the obtained ultrasound
videos, which reveals the maximum displacement of the muscle
relative to the zero position without ankle movement (see
Figure 2). The employed algorithm, created in MATLAB (The
MathWorks, Inc., Natick, MA, United States), was developed
by Dilley et al. (2001) and has been shown to represent a
highly reliable method to quantify tissue displacement (ICC:
0.77 to 0.99). Experimental Approach EMG (not depicted here) used as
biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation
with a strap was required to prevent body motion induced by the
dynamometer action. As the belt was not in contact with the Hamstrings, it
did not affect tissue displacement. prevent artifacts induced by variations in pressure to the skin,
a custom made template consisting of thermoplastic polymer
was used for fixation (Cruz-Montecinos et al., 2015). To detect
potential probe movement over the skin, acoustically reflective
markers (thin stripes of micropore tape) which are clearly
visible in the ultrasound image, were placed on the skin
(Morse et al., 2008). Frontiers in Physiology | www.frontiersin.org Outcome Briefly, the software calculates the correlation
coefficient between the pixel gray levels of successive frames
within previously defined, rectangle-shaped regions of interest
(ROI) of the successive frames. The pixel shift revealing the
highest coefficient represents the relative movement between
two frames. In video recorded in this trial, six equidistant
ROIs (approximate size: 5 × 1 mm) were placed within the
semimembranosus. Mean maximal horizontal displacement
of the ROIs was calculated and analyzed as quantification of
muscle displacement. Excellent reliability of this approach (use
of the described software and six ROIs including interpretation
procedure) has been demonstrated in a previous trial of our
workgroup, which also examined fascial displacement in the
thigh (Krause et al., 2019). surface electromyography (Biopac MP 160, Biopac Systems
Inc., Goleta, CA, United States) was used to monitor muscle
activity, providing the participants with live biofeedback. After
preparation of the skin (shaving and alcohol cleansing), Ag-
AgCl electrodes (8 mm diameter) were positioned over the
muscle bellies of the m. semimembranosus, m. gastrocnemius,
m. quadriceps femoris and m. tibialis anterior as well as
over the lateral malleolus and the lateral femur condyle with
the latter two being reference electrodes. Sensor placement
was determined according to the SENIAM (surface EMG
for non-invasive assessment of muscles) recommendations
(Hermens et al., 2000). Electrodes were placed at 1/3 of
the distance between the ischial tuberosity and the knee’s
medial joint line (semimembranosus), on the most prominent
bulge of the gastrocnemius muscle, at 50% of the distance
between the anterior spina iliaca superior and the superior
part of the patella (quadriceps femoris) and at 1/3 of the
way between the tips of the fibula and the medial malleolus
(tibialis anterior). Data were sampled at a rate of 1.600 kHz
and filtered with a high- and low-pass filter of 10 and
500 Hz, respectively. Experimental Approach A schematic depiction of the experimental approach is shown
in Figure 1. All experiments were conducted in the same room
and at constant temperature and daytime. The participants were
positioned in a standardized prone position on an isokinetic
dynamometer (Cybex Norm, Cybex, Ronkonkoma, New York,
United States), having their ankle joint axis aligned with the
rotational axis of the device. A fixation belt was attached over
dorsal pelvis (thus not compressing the Hamstring muscles) to
prevent body movement. In the experiment, the ankle (tested
leg chosen randomly) was moved passively between plantar
flexion and maximal achievable dorsal extension by means
of the dynamometer’s continuous passive motion function. During the measurements, ankle joint angle [◦], relative to
the neutral zero position, was constantly recorded by the
device. Three repetitions, averaged for analysis, were performed
at an angular velocity of 5◦/s (Krause et al., 2019). The
participants were instructed to remain completely passive,
avoiding any voluntary muscle activity. To confirm this, As indicated, to date, only few trials have examined the
relevance of myofascial chains in the living organism. A couple
of studies demonstrated remote flexibility increases following
local exercise treatments (Grieve et al., 2015; Wilke et al.,
2016b,
2017,
2019b;
Joshi
et
al.,
2018). These
findings
are intriguing, seemingly verifying the observations made
in vitro. It seems plausible that a decrease in tissue stiffness,
induced by the local interventions, can be transmitted to
more
cranial
structures
(e.g.,
from
Hamstrings
and
to
the
neck
muscles). However,
as
the
measured
outcome
(range of motion) represents a functional parameter, the
registration of non-local exercise effects does not provide a
definite proof for myofascial force transmission under living
conditions. The use of high-resolution ultrasound imaging
can resolve this research deficit as it is able to visualize a
non-stretched tissue during elongation of a neighboring,
connected structure: If substantial forces would be transmitted March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 2 Dorsal Myofascial Force Transmission Wilke et al. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone
position and with the knee extended, the ankle joint was passively moved
between plantar flexion and dorsal extension (arrow shows way into dorsal
extension). Maximal dorsal extension was calculated as the distance from a
calibrated neutral zero position (dashed line). Ultrasound recordings were
made over the semimembranosus muscle in order to estimate tissue
displacement induced by the ankle motion. Hamstring Displacement Calculating tissue displacement was highly reliable, revealing
almost
perfect
agreement
between
the
five
repetitions
(ICC = 0.81, 95%CI: 0.66 to 0.97, p < 0.0001). Corrected
for probe movement over the skin, which was negligible
(0.09 ± 0.10 mm), passive ankle dorsal extension induced
a
significant
caudal
semimembranosus
displacement
of
5.76 ± 2.67 mm (95%CI: 3.86 to 7.68, p < 0.0001, d = 2.16). The highest value (10.87 ± 1.57 mm) was registered in a
22-year old female while the lowest displacement was found
in a 24-year old male (1.22 ± 0.64 mm). In sum, higher
values (6.74 ± 3.03 mm) occurred in women when compared
to men (5.12 ± 2.46 mm), however, despite a moderate
effect size (d = 0.60), this difference did not reach statistical
significance (p = 0.38). Regarding the kinematic data indicating maximal ankle
dorsal
extension
(◦)
and
horizontal
tissue
displacement
(mm), mean values were calculated for the three movement
cycles in each condition. To answer the question as to
whether
ankle
movement
leads
to
cranial
displacement
of the semimembranosus myofascial soft tissue, a twofold
approach was chosen. Firstly, the one-sample t test and
95% confidence intervals (95% CI) were used in order
to examine whether movement of the semimembranosus
occurred (systematic difference to zero). Potential discrepancies
between men and women were detected using the t test
for independent samples. Effect sizes of both tests were
calculated and interpreted according to Cohen (1992) as small
(d = 0.2), medium (0.5) or large (0.8). Secondly, to identify
significant associations between ankle dorsal extension and
semimembranosus displacement, Spearman’s rank correlation
was used. According to Evans (1996), resulting coefficients
were graded as poor (<0.2), weak (0.2 to 0.4), moderate
(0.4 to 0.6), strong (0.6 to 0.8) or optimal (>0.8). Finally,
to demonstrate the reliability of the software algorithm for
tissue displacement, the intraclass correlation coefficient was
used (Bland and Altman, 1996). Based on the suggestions
of Fleiss (1986), resulting reliability values were classified as
poor (<0.4), moderate (0.4 to 0.75), or excellent (>0.75). All calculations were made with BiAS for Windows 11.2
(Goethe-University,
Germany);
the
significance
level
was
set to α = 0.05. Correlation With Ankle Dorsal Extension
Maximal ankle dorsal extension, per average, was 19.8 ± 5.0
degrees. Spearman
analysis
revealed
a
strong
positive FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal
extension and dorsal thigh soft tissue displacement. Data Processing and Statistics g
The recorded ultrasound, dynamometer and EMG data were
synchronized using a common electrical impulse delivered
through an external trigger to the interface of the employed
software (Acqknowledge, Biopac Systems Inc., Goleta, CA,
United States). Besides providing biofeedback, EMG data
were used to detect involuntary muscle activity with two
approaches implemented in the software package: The first
was based on a normalization against maximum voluntary
contraction (MVC), which was determined by means of isometric
contractions of the included muscles. Here, muscle activity
was defined as any root mean square values (0.03 s) >5%
MVC. The second was based on the algorithm of Hodges
and Bui (1996). Briefly, it determines the mean and standard
deviation of the signal during a period of 0.25 s under
resting conditions and creates a filtered average rectified value In order to familiarize the participants with the device and
measurement conditions and to practice keeping the lower leg
muscles inactive, a warm-up of three flexion-extension cycles
was performed prior to the actual measurements. This approach
has already been used successfully in a previous, similar study
(Krause et al., 2019). A high-resolution ultrasonography device (My Lab 70, Esaote
Biomedica, Genoa, Italy) was used to assess tissue displacement
upon ankle joint movement. Video recordings, depicting the
soft tissue of the dorsal thigh, were made with a linear
array transducer (custom-made, 100 mm × 8 mm, 7.5 Hz)
positioned over the belly of the semimembranosus muscle. To March 2020 | Volume 11 | Article 180 3 Wilke et al. Dorsal Myofascial Force Transmission FIGURE 2 | Exemplary visualization of ultrasound-based cross-correlation analysis. Equidistant ROIs (red rectangles) are selected at rest (left image). In this example,
five ROIs have been positioned: three within the fascia and one in each, the subcutaneous tissue (SCT) and the muscle. Upon movement (right image), pixel
displacements relative to the center of the non-moving ROIs (small yellow square inside the red rectangles in left picture) are tracked (yellow line in right picture). The
end of the line indicates the maximal displacement, which is computed by the software algorithm. FIGURE 2 | Exemplary visualization of ultrasound-based cross-correlation analysis. Equidistant ROIs (red rectangles) are selected at rest (left image). In this example,
five ROIs have been positioned: three within the fascia and one in each, the subcutaneous tissue (SCT) and the muscle. Hamstring Displacement Black circles represent
males, open circles represent females. Data Processing and Statistics Upon movement (right image), pixel
displacements relative to the center of the non-moving ROIs (small yellow square inside the red rectangles in left picture) are tracked (yellow line in right picture). The
end of the line indicates the maximal displacement, which is computed by the software algorithm. the corresponding data were not included in the inferential
statistics. The subcutaneous tissue, per average, had a thickness
of 3.80 ± 2.17 mm. With 1.32 ± 0.49 mm, the deep fascia was
about two thirds smaller. (ARV). It then extracts the variance with regard to the
noise by means of dividing the difference between the ARV
and the mean by the standard deviation. For the resulting
signal, the median is calculated for the entire waveform. Any activity exceeding this median for at least 0.1 s is
considered as muscle activity. Once one of the two methods
described detected muscle activity, the corresponding trials were
discarded from analysis. DISCUSSION The mechanical role of the soft tissue has been a recent
focus of fascia research (Zügel et al., 2018). However, despite
compelling
evidence
from
cadaver
experiments,
pointing
toward the occurrence of in-series force transmission effects
across myofascial continuities (Krause et al., 2016), there
has been a lack of in vivo studies regarding this topic,
hitherto (Zügel et al., 2018). Our trial shows that maximal
ankle dorsal extension is associated with significant caudal
displacements
of
the
semimembranosus
muscle
and
its
encapsulating fascia. This finding may explain the remote
exercise effects detected in previous studies: It had been
shown that stretching or self-myofascial release treatments
induced flexibility increases in neighboring or even more
distant cranial joints (Grieve et al., 2015; Wilke et al., 2016b,
2017, 2019a; Joshi et al., 2018). Although representing an
intriguing observation, the occurrence of non-local changes
in such functional outcome could not only be related to a
force transmission across myofascial continuity but also be
due to other factors such as systemic neural adaptations,
i.e., altered stretch tolerance. Against this background, the
remote soft tissue displacements established here may, in
fact, demonstrate that mechanically relevant amounts of force
are transferred to serially connected skeletal muscles in the
living organism. When interpreting the novel findings, some noteworthy
methodological considerations need to be made. Firstly, the
measured soft tissue displacement represents a highly plausible
surrogate but not a direct measure of transferred force. While
this represents a rather theoretical concern, the effects observed
must not only stem from a serial force transmission. Ankle
movement has been demonstrated to modify the stiffness
of the sciatic nerve. As it crosses the knee joint, it may
have an impact on the mechanics of the thigh (Andrade
et al., 2016). In addition, the fascial bands spanning from
the gastrocnemius muscle to the dorsal thigh do not only
attach to the semimembranosus but also to the other parts
of the Hamstrings. Previous research revealed substantial
mutual interaction between muscles located in parallel (Huijing
and
Baan,
2001). If
force
was
hence
transmitted
from
the calf it is tenable to assume that it also reached the
biceps femoris and the semitendinosus. As a consequence,
particularly the forces acting on the latter (pulling it in the
caudal direction in the same way as occurring with the
semimembranosus), could have induced a (minor) part of
the muscle displacement. Another issue relates to the sample
size of our investigation. DISCUSSION Evidently, it was sufficient to reveal
the presence of semimembranosus motion and its correlation
to ankle movement. However, our study may have been
underpowered with regard to the influence of sex: female
participants had higher displacements but the significance
threshold was failed for this observation. Future studies, further
delineating the role of sex on serial force transmission are
therefore warranted. Finally, a couple of additional outcomes
may be of particular value for upcoming research. Besides
visualizing other muscles (e.g., those located in parallel and
the calf muscles), it would be intriguing to measure the
pennation angle in order to complement the displacement data. From a mechanical point of view, our experimental set-up
did not allow for a judgment of tissue stiffness which could
be another relevant effect modifier. It may be argued that
higher stiffness of the implicated transmitting structures (in
this case the gastrocnemius) would allow for a higher degree
of force transmission. One possibility to assess this outcome
would be using the isokinetic dynamometer to calculate the
passive resistive torque produced during ankle movement. As a
supplement, elastography, which has recently been used to study
the mechanical properties of the lower leg muscles (Ates et al.,
2017), could be added to gain further insight the mechanical
properties of the leg muscles. Particularly, it would allow the
measurement of stiffness changes in the entire Hamstring group As indicated, this is one of the first studies examining
serial myofascial force transmission under in vivo conditions. The only similar trial conducted by Cruz-Montecinos et al. (2015) demonstrated a coupling of pelvic movement and
displacement
of
the
gastrocnemius
fascia. The
absolute
magnitude
of
fascial
displacement
was
higher
in
our
data
(5.8
mm
vs. 1.5
mm). This
difference
may
be
explained by various factors, including differences in the
imaged
muscle
(semimembranosus
vs. gastrocnemius),
the moved joint (ankle vs. pelvis) and the direction of
force
transmission
(caudal-cranial
vs. cranial-caudal). Notwithstanding, a common finding of both studies was
the strong correlation of local ROM alterations and consecutive
remote tissue displacements. The practical implications of our research span from
sports performance to musculoskeletal disorders. Coaches
and exercise professionals should be aware that stretching
treatments
do
affect
both
the
targeted
tissue
but
also
morphologically linked skeletal muscles. The relevance of
the exercise position, for instance having the knee extended
or not when targeting the calf, thus extends beyond the
question of mono- or bi-articularity of muscles. RESULTS FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal
extension and dorsal thigh soft tissue displacement. Black circles represent
males, open circles represent females. FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal
extension and dorsal thigh soft tissue displacement. Black circles represent
males, open circles represent females. All participants completed the experiment. However, while the
analyses of the EMG confirmed absence of muscle activity in
10 individuals, one showed above-threshold values and hence, March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 4 Dorsal Myofascial Force Transmission Wilke et al. accordance with previous data (Wilke et al., 2018). Besides
its potential relevance under normal conditions, myofascial
force transmission could also play a role in the development of
overuse disorders. It had been speculated that the occurrence
of non-local abnormalities (e.g., increased hamstring stiffness
in patients with plantar fasciitis) stems from a pathologically
altered/excessive
degree
of
myofascial
force
transmission
(Wilke
et
al.,
2019a). In
order
to
further
substantiate
this assumption, it seems of interest to conduct similar
experiments in both healthy individuals and patients with
musculoskeletal disorders. correlation between the extent of caudal semimembranosus
displacement and dorsal extension (p = 0.02, rho = 0.76),
which suggests that higher ankle movement amplitudes were
associated with larger displacements of the semimembranosus
muscle (Figure 3). Frontiers in Physiology | www.frontiersin.org REFERENCES Huijing, P. A., and Baan, G. C. (2001). Myofascial force transmission causes
interaction between adjacent muscles and connective tissue: effects of blunt
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controlled trial. J. Bodyw. Mov. Ther. 22, 832–837. doi: 10.1016/j.jbmt.2018. 01.008 Bhattacharya, V., Barooah, P. S., Nag, T. C., Chaudhuri, G. R., and Bhattacharya, S. (2010). Detail microscopic analysis of deep fascia of lower limb and its surgical
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Sanzana-Cuhce, R., and Cuesta-Vargas, A. (2015). In vivo relationship between
pelvis motion and deep fascia displacement of the medial gastrocnemius:
anatomical and functional implications. J. Anat. 227, 665–672. doi: 10.1111/joa. 12370 Krause, F., Wilke, J., Vogt, L., and Banzer, W. (2016). Intermuscular force
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gastrocnemius muscle tendon unit. Exp. AUTHOR CONTRIBUTIONS JW contributed to the concept, design, data acquisition,
analysis and interpretation, drafting and critical revision
of the manuscript, and final approval of the manuscript. HD contributed to the data acquisition, critical revision of
the manuscript, and final approval of the manuscript. ST
contributed to the analysis and interpretation, critical revision
of the manuscript, and final approval of the manuscript. AD contributed to the analysis and interpretation, and final
approval of the manuscript. CM contributed to the concept,
design, critical revision of the manuscript, and final approval of
the manuscript. CONCLUSION Our
study
demonstrated
under
in
vivo
conditions
that
mechanical force is transmitted between the ankle and the dorsal
thigh upon passive stretching of the gastrocnemius. This finding
may represent the morphological substrate of remote exercise
effects occurring after treatments based on myofascial chains. The correlation of semimembranosus displacement and ankle
dorsal extension, furthermore, may suggest that fascial tissue
can restrict flexibility. Future research should elucidate the
functional implications of the observed transmission effects in
sports and disease. DATA AVAILABILITY STATEMENT The datasets generated for this study are available on request to
the corresponding author. DISCUSSION In essence,
it may be argued that fascial tissues represent a potential
contributor to restrictions in flexibility, which would be in March 2020 | Volume 11 | Article 180 5 Dorsal Myofascial Force Transmission Wilke et al. ETHICS STATEMENT in order to quantify the degree of myofascial force transmission
from muscle arranged in parallel. in order to quantify the degree of myofascial force transmission
from muscle arranged in parallel. The studies involving human participants were reviewed
and
approved
by
the
University
Research
Ethics
Committee
of
Liverpool
John
Moores
University. The
patients/participants provided their written informed consent
to participate in this study. REFERENCES Physiol. 586, 97–106. doi: 10.1113/
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454–461. doi: 10.1016/j.apmr.2015.07.023 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Wilke, J., Macchi, V., De Caro, R., and Stecco, C. (2018). Fascia thickness, aging and
flexibility: is there an association? J. Anat. 234, 43–49. doi: 10.1111/joa.12902 Wilke, J., Niederer, D., Vogt, L., and Banzer, W. (2016b). Remote effects of lower
limb stretching: preliminary evidence for myofascial continuity? J. Sport Sci. 34,
2145–2148. doi: 10.1080/02640414.2016.1179776 Copyright © 2020 Wilke, Debelle, Tenberg, Dilley and Maganaris. This is an open-
access article distributed under the terms of the Creative Commons Attribution
License (CC BY). The use, distribution or reproduction in other forums is permitted,
provided the original author(s) and the copyright owner(s) are credited and that the
original publication in this journal is cited, in accordance with accepted academic
practice. No use, distribution or reproduction is permitted which does not comply
with these terms. limb stretching: preliminary evidence for myofascial continuity? J. Sport Sci. 34,
2145–2148. doi: 10.1080/02640414.2016.1179776 Wilke, J., Vleeming, A., and Wearing, S. (2019a). Overuse injury: the result of
pathologically altered myofascial force transmission? Exerc. Sport Sci. Rev. 47,
230–236. doi: 10.1249/JES.0000000000000205 Wilke, J., Vogt, L., Niederer, D., and Banzer, W. (2017). Is remote stretching
based on myofascial chains as effective as local exercise? A randomised, March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 7 |
https://openalex.org/W4394950750 | https://www.researchsquare.com/article/rs-4232249/latest.pdf | English | null | Robot-assisted Treatment Contributes to Regaining Upper Limb Motility in Stroke Patients:a Randomized-controlled Trial Based on Functional Near Infrared Spectroscopy | Research Square (Research Square) | 2,024 | cc-by | 7,044 | Jiayue Xu Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China
University of Technology
Guiyuan Cai Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China
University of Technology Junbo Jiang Page 1/19 Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China
University of Technology Research Article Keywords: Stroke, Robot-assisted treatment, Upper extremity motor rehabilitation, Functional near
infrared spectroscopy Posted Date: April 19th, 2024 Posted Date: April 19th, 2024 DOI: https://doi.org/10.21203/rs.3.rs-4232249/v1 DOI: https://doi.org/10.21203/rs.3.rs-4232249/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Page 2/19 Objective This study concentrated on the treatment effect and brain functional responses to RAT obtained with
functional near infrared spectroscopy (fNIRS) in individuals having experienced a stroke with upper limb
mobility impairment to direct the application of clinical therapy. Methods Eighteen stroke patients were randomly distributed to the robotics group (RG) to receive RAT and the
control group (CG) to receive motor training without robot-assistance. Therapies were administered five
days per week, for one month, and the outcome indicators were assessed at baseline and 30 days after
treatment onset. The clinical evaluations included administration of the Fugl-Meyer assessment for
upper-extremity(FMA-UE), action research arm test(ARAT), together with fNIRS recordings.The relative
variations in oxyhemoglobin (OxyHb) concentrations measured by fNIRS were used to determine cortical
activity levels. Results After four weeks of rehabilitation training, the FMA-UE and ARAT points of both groups considerably
increased. The FMA-UE and ARAT points of the RG improved more than those of the CG. In comparison
to the CG, fNIRS recordings showed enhanced cortical activation of the primary motor cortex in the
ipsilateral hemisphere (i-M1) in the RG. Correlation analysis demonstrated a significant positive
correlation between FMA-UE points improvements and therapy-evoked increases in the OxyHb of i-M1 in
both the RG(r = 0.88, p < 0.001) and CG (r = 0.71, p = 0.03).It also showed a substantial positive
association of the ARAT score changes and therapy-evoked increases in the OxyHb of M1 in the RG (r =
0.92, p < 0.001) and CG(r = 0.87, p < 0.002). Background Robot-assisted treatment(RAT) has drawn a lot of interest in stroke motor rehabilitation. Theoretically,
the best protocol for a patient should be selected based on features of the brain's functional reactions
associated with RAT. However, due to a paucity of techniques for dynamic brain functional testing, the
cortical reaction response to RAT has yet to be thoroughly understood. Conclusion Page 3/19 Our findings suggest that RAT performed as well or better than classic therapy methods that could help
patients with stroke with upper extremity motor dysfunction and activate M1. This activation may
promote reorganization of brain function. Our findings suggest that RAT performed as well or better than classic therapy methods that could help
patients with stroke with upper extremity motor dysfunction and activate M1. This activation may
promote reorganization of brain function. ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/
ChiCTR1800019783 ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/
ChiCTR1800019783 ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/
ChiCTR1800019783 Introduction Prior research has shown that increases in neuroplasticity in the adult human brain are associated with
upper extremity motor recovery[1]. Many investigations have demonstrated the close relationship
between activation of particular cortical area activation and upper extremity motor recovery following
stroke[2]. It is vital for stroke patients to undergo rehabilitation to restore the movement capabilities of
their paralyzed limbs for the purpose of maintaining their social engagement and quality of life [3]. According to previous research, the prognosis of motor function can be accurately assessed between
four to five weeks following a stroke [3, 4]. Therefore, it is crucial for physical therapists to offer effective
treatment after stroke. Repetitive task-specific training for poststroke patients can promote neuroplasticity and improve motor
function[5] .Traditional rehabilitation techniques are mainly performed under the guidance of a physical
therapist, thus, these techniques are time-consuming and laborious.Rehabilitation robots have the
advantages of being fatigue-free, quantitative, and individualized, and can administer high-dose, high-
repetition exercise training, while also providing objective and immediate training data and assessment
data; these robots are expected to be useful tools for promoting patients' functional recovery[6, 7]. Robot-assisted therapy (RAT) for the upper extremities has recently become a well-regarded stroke
recovery method.Numerous investigations have confirmed the clinical efficacy of RAT based on clinical
evaluation[8] and biomechanical characteristics[9, 10]. Moreover, recent investigations have documented
the variable results of RAT among stroke patients[11, 12]. Some studies have shown that RAT does not
more substantially enhance motor performance in sufferers with poststroke upper extremity dyskinesia
or improve chronic poststroke upper limb impairment compared to other assistive therapies[13,
14].There are not enough clinically useful evaluation methods available to allow physical therapists
provide the most appropriate therapeutic therapies based on each patient's unique needs. Therefore, it is
important to specifically assess the unique functional responses to RAT of stroke patients with upper
extremity motor impairment. The adaptation of adequate training protocols to achieve a significant
improvement over current clinical practices depends heavily on the actual assessment of brain function
in response to particular kinds of interventions. However, the treatment efficacy of RAT in promoting
brain plasticity is unclear. Introduction Repetitive task-specific training for poststroke patients can promote neuroplasticity and improve motor
function[5] .Traditional rehabilitation techniques are mainly performed under the guidance of a physical
therapist, thus, these techniques are time-consuming and laborious.Rehabilitation robots have the
advantages of being fatigue-free, quantitative, and individualized, and can administer high-dose, high-
repetition exercise training, while also providing objective and immediate training data and assessment
data; these robots are expected to be useful tools for promoting patients' functional recovery[6, 7]. Robot-assisted therapy (RAT) for the upper extremities has recently become a well-regarded stroke
recovery method.Numerous investigations have confirmed the clinical efficacy of RAT based on clinical
evaluation[8] and biomechanical characteristics[9, 10]. Moreover, recent investigations have documented
the variable results of RAT among stroke patients[11, 12]. Some studies have shown that RAT does not
more substantially enhance motor performance in sufferers with poststroke upper extremity dyskinesia
or improve chronic poststroke upper limb impairment compared to other assistive therapies[13,
14].There are not enough clinically useful evaluation methods available to allow physical therapists
provide the most appropriate therapeutic therapies based on each patient's unique needs Therefore it is 14].There are not enough clinically useful evaluation methods available to allow physical therapists
provide the most appropriate therapeutic therapies based on each patient's unique needs. Therefore, it is
important to specifically assess the unique functional responses to RAT of stroke patients with upper
extremity motor impairment. The adaptation of adequate training protocols to achieve a significant
improvement over current clinical practices depends heavily on the actual assessment of brain function
in response to particular kinds of interventions. However, the treatment efficacy of RAT in promoting
brain plasticity is unclear. Page 4/19 Page 4/19 Due to the recent major advancements in functional near infrared spectroscopy (fNIRS) technology,
fNIRS has received significant attention in both research and clinical contexts[15]. Because several types
of imaging devices, for example, functional magnetic resonance imaging (fMRI) and
electroencephalography (EEG) have a low tolerance for motion artifacts, monitoring cortex responses
during exercise interventions in real time is still challenging[16]. As a noninvasive technique that
measures cortical hemodynamics, fNIRS has benefits like mobility, safety, and the capacity to tolerate
motion artifacts[17]. FNIRS can not only be used to deliver tailored neurological modulation with a
closed loop control approach ultimately accomplishing individualized brain disease treatment, but also
provide knowledge of the mechanisms underpinning neuroregulation in neurological rehabilitation[18]. Furthermore, a thorough review detailing fNIRS-related applications for stroke indicated that fNIRS is a
technology with a future monitoring cerebrum activity in the period of particular rehabilitative
interventions [19]. In particular, fNIRS technology has been extensively used for recovery studies of
persons who had suffered a stroke [20, 21]. By sensing variations in the consistency of oxyhemoglobin
(OxyHb) and deoxygenated hemoglobin (DeoxyHb) in the target cerebral cortices,fNIRS evaluates both
neuronal activity and neurovascularization[22]. Therefore, our study used an fNIRS system to assess the
mechanisms behind the helpful role of robot-assisted recuperation. Accordingly, the main objectives of this research were to verify the effectiveness of robot coaching for
upper extremity recovery and brain function remodeling by evaluating the functional improvement after
RAT of patients with upper extremity motor impairment after stroke and the particular corticostriatal
response pattern of these patients to RAT on the basis of the Fugl-Meyer assessment for upper-
extremity (FMA-UE), action research arm test (ARAT) and OxyHb fNIRS analysis.Assessment of
functional brain reactions in real time can offer a rationale for patient selection of proper protocols to
back up the decision making in the clinic. Participants During their first week of hospitalization, we screened every patient with a first- time stroke who checked
into our department of rehabilitation. Patients who had been enrolled in the study were randomized and
assessed immediately. At the time of hospital discharge, a second evaluation took place. The First
People's Hospital in Guangzhou's ethical committee accepted this study (approval No. K-2021-020-01),
and ChiCTR1800019783 is the register number in the China Clinical Trial Registry. Additionally, the trials
were conducted in the rehabilitation department's clinical laboratory at the First People's Hospital in
Guangzhou, Guangdong, China. All subjects signed an informed consent form. Figure 1 depicts the
flowchart for this study(see Fig. 1). llowing were the inclusion criteria for stroke patients:(1) subacute stage The following were the inclusion criteria for stroke patients:(1) subacute stage
hemiparesis/hemiplegia(see Table 1) with severe movement disorders due to the first stroke;(2) lesion
locations recognized by computed tomography or magnetic resonance imaging;(3) between 30 and 80 hemiparesis/hemiplegia(see Table 1) with severe movement disorders due to the first stroke;(2) lesion
locations recognized by computed tomography or magnetic resonance imaging;(3) between 30 and 80 Page 5/19 Page 5/19 years of age ; (4) being able to agree to be involved in research and follow protocol requirements. The
following were the exclusion criteria: (1) existence of sequelae of cerebrovascular accident or any other
chronically disabling condition with subarachnoid hemorrhage;(2)arthritic impairments,or arm skin
lesions that may affect movement; (3)a Mini-Mental State Examination (MMSE) score < 24[23];(5)
hemilateral neglect. Table 1
Clinical characteristics of patients in the study. Participants No
Age
Gender
Type
Lesion site
Duration(days)
MMSE
ARAT
FMA-UE
1
63
M
Infarction
R-NC
45
28
13
17
2
72
M
Infarction
L-FL,NC
37
25
9
8
3
62
F
Infarction
R-FL
71
27
17
11
4
63
M
Infarction
R-TL,NC
65
26
21
20
5
68
F
Infarction
R-TL,FL
58
29
14
16
6
75
M
Infarction
R-TL,PL
27
28
19
35
7
47
M
Hemorrhage
L-NC
86
29
22
27
8
67
F
Infarction
L-FL,PL
121
29
25
46
9
54
M
Infarction
R-NC
78
27
16
38
10
79
F
Infarction
R-PL,NC
76
26
23
13
11
60
M
Infarction
R-FL
92
27
21
25
12
43
F
Infarction
L-FL,NC
56
29
17
10
13
68
M
Hemorrhage
L-TL,PL
126
28
22
33
14
64
M
Infarction
R-NC
47
28
13
44
15
64
F
Infarction
L-FL
78
25
10
16
16
58
M
Infarction
L-FL
35
29
16
10
17
66
M
Infarction
L-TL,FL,PL
69
28
18
36
18
71
F
Infarction
R-FL,PL
25
26
15
28
S
i
d b
li
l
ti RAT work and fNIRS data acquisition Patients were required to sit in a resting state for 5 minutes during the fNIRS experiment.For this
investigation, patients' hemiparetic forearms were placed on a robot-aided upper body workout device (a
type of terminal effects device) during the task state, with armature fastening around their forearm and a
handle on the paralyzed hand. With an "aided as needed" control method, the robotization delivered
target oriented, flat shoulder and elbow extensions at an identical velocity (5.0 cm/s) and movement
extent about the center object (Y-axis = 20 cm, X-axis = 30 cm). The patients were instructed to restrict
their movements to those required for their motor tasks while in the task state. To assure the
participants' safety, a licensed therapist was involved in every step of the trial. A continuum wave fNIRS system (Nirscan, Danyang Huichuang Mechanical Instrument Co.Ltd., China)
configured with 24 sources and 24 detectors and a sample rate of 11 Hz was used to continually
measure cerebral hemodynamics during each session. In accordance with the universal 10–20
electrochemical positioning technique, 63 channels were distributed across both the left and right
prefrontal cortex (symmetrically with FpZ as standard reference), motor cortex (corresponding to zones
C3 and C4), and occipital lobe (symmetrical with OZ as standard reference). On the basis of the
amended Beer-Lambert law, the optical density variation was used to determine the comparative
variation in the levels of OxyHb. We used the OxyHb measurement, which is known to be more
susceptible to mission-relevant hematologic variations than other fNIRS measures, i.e.,deoxygenated
hemoglobin (DeoxyHb), and total hemoglobin (TotalHb), to produce corticostriatal activation maps; the
OxyHb in every region of interest (ROI) was then considered, to analyze the cortical activation pattern. OxyHb indirectly measures brain activity by identifying changes in the cerebral cortex's underlying
hemodynamics. Based on the physical placements of the brain's regions and Brodmann's area (BA),
three ROIs and their corresponding subsets of the total number of channels were chosen to study
corticostriatal activity: the somatosensory cortex(SC), primary motor cortex (M1), and the premotor
cortex(PMC)(see Fig. 2). The selected channels for every ROI were chosen based on their anatomical
placement in accordance with Brodmann's domain areas, and the OxyHb was estimated from each
channel. By reversing the fNIRS channels from right to left across the middle sagittal line for individuals
with a right-sided pathology during analysis, the pathological side was consistently considered to be the
left hemisphere. Screening and baseline evaluation The baseline assessment was conducted by our study center coordinator if patients met the criteria for
inclusion and exclusion. Baseline data such as age, sex, the length of time after the stroke, the site of the
lesion, and clinical evaluations such as the FMA-UE[24], MMSE and current upper limb rehabilitation
therapies were collected(see Table 1). Page 6/19 Table 1 Clinical characteristics of patients in the study. Table 1 M:Male; F:Female; L:Left; R:Right; FL:Frontal Lobe, PL:Parietal Lobe, TL:Temporal Lobe, OL:
Occipital Lobe, NC:Nucleocapsular). MMSE: Mini-mental State Examination; ARAT: Action Research Arm
Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Table 1 M:Male; F:Female; L:Left; R:Right; FL:Frontal Lobe, PL:Parietal Lobe, TL:Temporal Lobe, OL:
Occipital Lobe, NC:Nucleocapsular). MMSE: Mini-mental State Examination; ARAT: Action Research Arm
Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Preprocessing of fNIRS data Using the revised Beer-Lambert law and the assumption of constant scattering[25], variations in
measured light intensities were used to determine variations in the concentrations of ΔOxyHb and Page 7/19 ΔDeoxyHb. After obtaining the ΔOxyHb and ΔDeoxyHb signals, data preprocessing was carried out. Movement artifacts were subsequently eliminated using a shifting normal bias and cubic spline
interpolation processing technique[26]. Finally, we filtered the signal to improve its signal-to-noise(SNR)
ratio using a 0.021-2 Hz 6th order Butterworth Bandpass Filter. For the remaining analyses, we focused
on the ΔOxyHb signal since it has a superior SNR and a larger association with the oxygen level
dependent signaling detected by fMRI.[27, 28] Statistical Analysis Variables are provided as the mean and standard deviation (SD), All statistical analyses were done
utilizing SPSS 20.0 (IBM SPSS, Inc., Armonk, NY, USA). The Kolmogorov–Smirnov test was utilized to
identify whether the assessed values were normally distributed. Certain demographic variables, including
sex and category of stroke were compared between groups by applying a chi-square test. Age, stroke
duration, and performance evaluation (MMSE, FMA-UE and ARAT) were compared by employing two
independent sample t tests. On the basis of this grouping, notable intra and intergroup disparities in
increases in oxyhemoglobin, FMA-UE and ARAT were evaluated using paired sample t tests and
independent two sample t tests. We further evaluated the correlation between changes in OxyHb and the
FMA-UE and ARAT points for each group of stroke patients to determine the correlations of the cerebrum
responses to RAT and the virtual state of the upper limb. Statistical significance was considered for p <
0.05. Demographic information Along with routine rehabilitation procedures, 21 patients who were evaluated between May 2021 and
November 2022 were allocated to robotic or classical therapies. One patient allocated to classical
therapies and two patients allocated to robotic therapies both dropped out of the research.Finally the
robotics group(RG) included 9 individuals and the CG(control group) included 9 individuals. The Table 1
shows that baseline patient characteristics were not substantially different between groups. Age, sex,
poststroke length, stroke category, and MMSE, ARAT, and FMA-UE scores for baseline patient identity
were not much of a difference across groups (p > 0.05)(see Table 2). Page 8/19 Table 2
Comparison of the fundamental data between the two patient groups. Characteristics
Robotic group(n = 9)
Control group(n = 9)
Statistical result
Sex (M/F)
6/3
5/4
χ2 = 0.234
p = 0.629
Age (years)
63.44 ± 8.68
63.67 ± 9.91
t=-0.051
p = 0.960
Duration (days)
65.33 ± 28.41
67.11 ± 30.86
t=-0.127
p = 0.900
MMSE
27.56 ± 1.42
27.33 ± 1.41
t = 0.332
p = 0.744
FMA-UE
24.22 ± 13.06
23.89 ± 12.34
t = 0.560
p = 0.956
ARAT
17.33 ± 4.97
17.22 ± 4.29
t = 0.510
p = 0.960
Comparisons of basic information of two groups of patients. Data are presented as mean ±
Mi i
t l St t E
i
ti
ARAT A ti
R
h A
T
t FMA UE F
l M Table 2 omparison of the fundamental data between the two patient groups. Table 2 Comparisons of basic information of two groups of patients. Data are presented as mean ± SD. MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer
assessment for upper-extremity. Table 2 Comparisons of basic information of two groups of patients. Data are presented as mean ± SD. MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer
assessment for upper-extremity. Table 2 Comparison of the fundamental data between the two patient groups. Table 2 Comparison of the fundamental data between the two patient groups. Table 2 Comparison of the fundamental data between the two patient grou Effectiveness The changes in FMA-UE, ARAT points from baseline to completion of treatment for the two groups are
reported in Fig. 3(see Fig. 3). There was no remarkable difference in FMA-UE and ARAT scores among
the two groups at baseline (p = 0.956 and p = 0.960 respectively), no obvious difference in FMA-UE and
ARAT points in both groups after the intervention (p = 0.372 and p = 0.054, respectively), and a significant
difference between the two groups in the change in FMA-UE and ARAT points from baseline to
completion of treatment (p = 0.015 and p = 0.044). There was a noticeable improvement in FMA-UE (p =
0.002) and ARAT (p = 0.003) scores before and after RAT training in the robotic group, and a significant
increase in the FMA-UE points (p = 0.038) and nonsignificant improvement in ARAT scores (p = 0.149)
before and after conventional treatment in the control group. The hemodynamic findings demonstrated an enhancement in OxyHb concentration in the left and right
hemispheres after the RAT. Figure 4 displays the topographic map of the OxyHb averaged across all
subjects after training. Significant activation in the ipsilesional M1 was observed in the robotic group(p = Page 9/19 0.048) but not in the control group( p = 0.158). There was a nominal but insignificant increase in OxyHb
in the contralateral M1 in both the robotic and control groups( p > 0.05)(see Fig. 4). Correlation analysis revealed a distinct positive correlation between FMA-UE points and changes in
intraregional OxyHb in the robotic group ipsilesional M1(i-M1) (r = 0.88, p < 0.001) and control group i-M1
(r = 0.71, p = 0.03), It also revealed a distinct positive correlation between ARAT scores and changes in
intraregional OxyHb in the robotic group i-M1 (r = 0.92, p < 0.001) and control group i-M1 (r = 0.87, p =
0.002), as shown in Fig. 5(see Fig. 5).Figure 5 The relationships between the ΔHBO of i-M1 and ΔFMA-
UE score, and ΔARAT score.A represents the correlation of ΔHBO and ΔFMA-UE score in RG,B represents
the correlation of ΔHBO and ΔARAT score in RG,C represents the correlation of ΔHBO and ΔFMA-UE
score in CG,D represents the correlation of ΔHBO and ΔARAT score in CG. Discussion The objective of this experiment was to examine the viability of RAT as a treatment and investigate its
impact on upper extremity motor deficits and brain functional capacity following subacute stroke. Our
results showed that the 4-week RAT program for upper extremity rehab following stroke was acceptable
and practical. No subject reported any trouble complying with study therapeutic guidelines, and no
serious adverse events took place. Additionally, we showed that RAT enhanced kinematic performance
and improved ARAT points over the improvements achieved with conventional therapy; moreover, RAT
reduced upper extremity dyskinesia, as evidenced by the FMA-UE points. Finally, the fNIRS assessment
revealed substantial improvements in cerebral excitability. The effectiveness of RAT in the rehab of upper extremity locomotor activity after stroke remains
somewhat controversial, some studies have shown that RAT is effective, while others have shown that
there is no significant difference between RAT and conventional rehabilitation techniques. Our study
showed that RAT is beneficial for the rehab of upper extremity locomotor function after stroke. Numerous studies have demonstrated the effectiveness of usage-dependent neuroplasticity
rehabilitation programs e.g., constraint-induced movement therapy and robot treatment[29–32]. In this
situation, RAT may promote neuroplasticity of brain regions related to upper extremity motor skill
learning in patients who are still recovering from a stroke. In terms of the processes leveraged by RAT,
the robot aids the user's voluntary movements by producing a potent proprioceptive sensation that is
then transmitted to the brain to increase the strength of the upper extremity motor output signals[33]. All
of the above studies support the application of RAT in upper extremity motor rehabilitation after stroke. The effectiveness of RAT in the rehab of upper extremity locomotor activity after stroke remains
somewhat controversial, some studies have shown that RAT is effective, while others have shown that
there is no significant difference between RAT and conventional rehabilitation techniques. Our study
showed that RAT is beneficial for the rehab of upper extremity locomotor function after stroke. y
Numerous studies have demonstrated the effectiveness of usage-dependent neuroplasticity
rehabilitation programs e.g., constraint-induced movement therapy and robot treatment[29–32]. In this
situation, RAT may promote neuroplasticity of brain regions related to upper extremity motor skill
learning in patients who are still recovering from a stroke. Discussion In terms of the processes leveraged by RAT,
the robot aids the user's voluntary movements by producing a potent proprioceptive sensation that is
then transmitted to the brain to increase the strength of the upper extremity motor output signals[33]. All
of the above studies support the application of RAT in upper extremity motor rehabilitation after stroke. Additionally, correlation analysis demonstrated a substantial link between the OxyHb alterations in the
functional network of the i-M1 zone and the status of patients' upper-limb motion capability. This finding
suggests that the ipsilesional M1 region in the brain functional network is more active during RAT of the
afflicted upper limb in motility-disabled patients. It was proposed that cortical function and structural
remodeling related to the lesion and its peripheral tissue[34] are linked to motor improvement in stroke
patients. An enlarged i-M1 area has been found to be related with functional recovery of restricted Page 10/19 evoked locomotion of the afflicted upper limb following stroke, according to a prior study[35]. All of the
evidence points to the fact that during aided mode RAT, patients with motor dysfunction show
dramatically increased involvement of the M1 regions on the ipsilesional side. This result was consistent
with earlier studies that indicated that high-intensity upper limb training can increase the activity of the
locomotive regions in the ipsilesional hemisphere and strengthen neuroplasticity[36] during the early
stages of recovery. Through task-directed training, the upper limb rehab robot can direct the recruitment
of the ipsilateral (ipsilateral to the hemiplegic limb) cortex and the expansion of the contralateral (the
opposite side of the hemiplegic limb) cortical locomotive area, thereby promoting the functional
reorganization of the functional cortex and the functional recovery of the upper limb[37]. Our findings suggest that neuroplasticity is induced by RAT therapy for upper limb locomotor function in
stroke patients. Additionally, the current fNIRS results demonstrated greater locomotor cortex activation
in the pathological hemisphere, suggesting that RAT treatment may have increased cortical activity in the
i-M1 with a considerable advancement in behavioral states in subacute stroke patients. RAT may speed
up upper extremity functional recovery compared to traditional rehabilitation, according to some prior
research on acute stroke cases[38]; moreover ,the current study may support this explanation. Limitations The study has several limitations. A small sample size was used, and the follow-up period was
insufficient. The lack of tracking patients over time means that this study may not accurately represent
the effectiveness of RAT for stroke survivors. The timing of the evaluations, which spanned from 25 to
126 days after the stroke, should be noted as this may have influenced the findings because prior
research revealed that the quantity of ipsilesional cortico-cortical activity is reportedly distinct between
acutely and chronically phases[40]. The study could be enhanced in numerous ways. To determine any
differences in rehabilitation results, the sample size might be enlarged and patients could be further
separated into subacute and chronic phases, with mid-term assessment and longer term follow-up. Discussion In a
randomized controlled trial that did not show a robotic advantage after treatment based on the
Functional Independence Measure (FIM)[10], it was argued that it was not possible to tell whether
locomotor manifestations improved or independence was due solely to the fact that the sufferers
learned to compensate for the handicap because of numerous shortcomings of the FIM[39], including
the sequential nature of the measurements, the absence of a particular trials for the limb involved, and
the paucity of discrimination. The difference with our experiment is that we found significan t gains in
upper extremity motor functionality in poststroke individuals upper extremity motor deficits after RAT
compared to controls by considering FMA and ARAT scores. Fundings This work is supported by the Guangzhou Municipal Science and Technology Program [Grant Number
202206010197 (YL)]; National Science Foundation of China [Grant Number 81772438 (YL),
81974357(YL), 82072548 (GX)]; Author Contribution Jiayue Xu: designed the work and let to the submission, acquired data, analyzed data, drafted and
revised the manuscript. Cailing Zhang: performed the experiments, analyzed data, edited and reviewed
paper. Wanqi Li: curated data, conducted the research and investigation process. Tuo Lin: Managed and
coordinated responsibility for the research activity planning and execution. Guiyuan Cai: conducted the
research and investigation process or.performing research, methodology. Junbo Jiang: performed the
experiments,curated data. Gengbin Chen: performed the data collection. Jialin Chen: recruited
participants. Quan Liu: annotated and maintained research data. Guangqing Xu: acquired financial
support. Yue Lan:designed research, edited and reviewed paper, acquired financial support. We sincerely thank all the subjects for their support and cooperation in this study We sincerely thank all the subjects for their support and cooperation in this study Conclusion In summary, this preliminary study showed that RAT is helpful for the restoration of upper extremity
locomotor function in stroke patients, as evidenced by significantly improved activation of the motor
cortex brain network and FMA-UE, and ARAT points of patients with stroke. In this study, fNIRS was used Page 11/19 Page 11/19 to assess variations in OxyHb linked with motor rehabilitation tasks in stroke survivors. Stroke survivors
demonstrated greater activation in ipsilateral motor areas than in contralateral motor areas throughout
the motor rehabilitation test, demonstrating that stroke survivors have asymmetrical cortical activation
patterns. After RAT, OxyHb in the ipsilateral M1 dramatically rose, indicating that stroke patients use
plastic restructuring of motor resources to compensate for reduced function during a rehabilitation
activities. To obtain an ideal therapeutic effect and exact rehabilitation treatment, RAT plans should be
customized in accordance with the brain functional network activation state of the patient. Conflict of Interest Statement: None of the authors have potential conflicts of interest to be disclosed Conflict of Interest Statement: None of the authors have potential conflicts of interest to be disclosed References 1. Wander, J. D., et al. (2013). Distributed cortical adaptation during learning of a brain-computer
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revised the manuscript. Guiyuan Cai: performed the experiments, analyzed data, edited and reviewed
paper. Wanqi Li: curated data, conducted the research and investigation process. Tuo Lin: Managed and
coordinated responsibility for the research activity planning and execution. Cailing Zhang: conducted the
research and investigation process or.performing research, methodology. Junbo Jiang: performed the
experiments,curated data. Gengbin Chen: performed the data collection. Jialin Chen: recruited
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using moving standard deviation and spline interpolation. Physiological Measurement, 31(5), 649–
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signals during motor tasks. Annu Int Conf IEEE Eng Med Biol Soc, 2013: pp. 2628-31. 27. Anwar, A. R. (2013). Comparison of causality analysis on simultaneously measured fMRI and NIRS
signals during motor tasks. Annu Int Conf IEEE Eng Med Biol Soc, 2013: pp. 2628-31. 28. Visani, E., et al. (2015). Hemodynamic and EEG Time-Courses During Unilateral Hand Movement in
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915–925. Page 14/19 29. Takebayashi, T., et al. (2015). A one-year follow-up after modified constraint-induced movement
therapy for chronic stroke patients with paretic arm: a prospective case series study. Topics In
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research. Nature Reviews Neuroscience, 3(3), 228–236. 31. Wahl, A. S., & Schwab, M. E. (2014). Finding an optimal rehabilitation paradigm after stroke:
enhancing fiber growth and training of the brain at the right moment. Frontiers In Human
Neuroscience, 8, 381. 32. Wolf, S. L., et al. (2008). References Retention of upper limb function in stroke survivors who have received
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Motor Recovery after Stroke: Current Practice and Future Perspectives. Neurol Med Chir (Tokyo),
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diffusion tensor imaging. Neurology, 86(20), 1924–1925. 34. Buch, E. R., et al. (2016). Predicting motor improvement after stroke with clinical assessment and
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in subjects 3 to 9 months after stroke. Neurorehabil Neural Repair, 22(5), 505–513. 35. Sawaki, L., et al. (2008). Constraint-induced movement therapy results in increased motor map area
in subjects 3 to 9 months after stroke. Neurorehabil Neural Repair, 22(5), 505–513. 36. Zhang, C., Li-Tsang, C. W., & Au, R. K. (2017). Robotic approaches for the rehabilitation of upper limb
recovery after stroke: a systematic review and meta-analysis. International Journal Of Rehabilitation
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rehabilitation: a randomized controlled trial. Journal Of Neuroengineering And Rehabilitation, 18(1),
76. 38. Fukuda, H., et al. (2016). Tailor-made rehabilitation approach using multiple types of hybrid assistive
limb robots for acute stroke patients: A pilot study. Assistive Technology : The Official Journal Of
Resna, 28(1), 53–56. 39. Daly, J. J., et al. (2005). Response to upper-limb robotics and functional neuromuscular stimulation
following stroke. Journal Of Rehabilitation Research And Development, 42(6), 723–736. 39. Daly, J. J., et al. (2005). Response to upper-limb robotics and functional neuromuscular stimulation
following stroke. Journal Of Rehabilitation Research And Development, 42(6), 723–736. 40. Ward, N. S., et al. (2003). Neural correlates of motor recovery after stroke: a longitudinal fMRI study. Brain, 126(Pt 11), 2476–2496. 40. Ward, N. S., et al. (2003). Neural correlates of motor recovery after stroke: a longitudinal fMRI study. Brain, 126(Pt 11), 2476–2496. Figures Page 15/19 Figure 1 Figure 2
Fnirs multichannael configurations in 10–20 systems and associated brain areas of interest.A
represents the serial number and distribution of channels and B represents the distribution of brain Figure 2 Figure 2 Fnirs multichannael configurations in 10–20 systems and associated brain areas of interest.A
represents the serial number and distribution of channels and B represents the distribution of brain Page 16/19 Page 16/19 regions.cluster{1} = [1 2 48]cluster{2} = [3 18 20 34 35];cluster{3} = [4 19];cluster{4} = [5 6 7 22];cluster{5}
= [44 45];cluster{6} = [1617];cluster{7} = [31 33 46 47 50];cluster{8} = [30 32];cluster{9} = [51];cluster{10} =
[42 43 58 59];cluster{11} = [13 52];cluster{12} = [11 24 25 29 39];cluster{13} = [12 26];cluster{14} = [8 9 10
23];cluster{15} = [14 15];cluster{16} = [53 56];cluster{17} = [27 36 38 40];cluster{18} = [28 54 55
57];cluster{19} = [37 41];cluster{20} = [60 61 62 63]. regions.cluster{1} = [1 2 48]cluster{2} = [3 18 20 34 35];cluster{3} = [4 19];cluster{4} = [5 6 7 22];cluster{5}
= [44 45];cluster{6} = [1617];cluster{7} = [31 33 46 47 50];cluster{8} = [30 32];cluster{9} = [51];cluster{10} =
[42 43 58 59];cluster{11} = [13 52];cluster{12} = [11 24 25 29 39];cluster{13} = [12 26];cluster{14} = [8 9 10
23];cluster{15} = [14 15];cluster{16} = [53 56];cluster{17} = [27 36 38 40];cluster{18} = [28 54 55
57];cluster{19} = [37 41];cluster{20} = [60 61 62 63]. Figure 3 Page 17/19
Figure 3 Figure 3 Figure 3 Page 17/19 FMA-UE:Fugl-Meyer assessment for upper-extremity; ARAT: Action Research Arm Test; RAT: Robot-
assisted treatment; RG:Robotic group; CG:Control group; *p<0.05. A indicates the change in FMA-UE of
RG and CG before and after treatment. B indicates the change in ARAT of RG and CG before and after
treatment. treatment. Figure 4
The blood oxygen concentration in the brain changes before and after training, the redder the color
means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration
in the primary motor cortex of the affected hemisphere increased significantly after robot training, but
there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the
change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and
after treatment. Figure 4 The blood oxygen concentration in the brain changes before and after training, the redder the color
means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration
in the primary motor cortex of the affected hemisphere increased significantly after robot training, but
there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the
change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and
after treatment. The blood oxygen concentration in the brain changes before and after training, the redder the color
means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration
in the primary motor cortex of the affected hemisphere increased significantly after robot training, but
there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the
change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and
after treatment. Page 18/19 igure 5
The relationships between the ΔHBO of i-M1 and ΔFMA-UE score, and ΔARAT score.A represents the
orrelation of ΔHBO and ΔFMA-UE score in RG,B represents the correlation of ΔHBO and ΔARAT score
RG,C represents the correlation of ΔHBO and ΔFMA-UE score in CG,D represents the correlation of ΔHB
nd ΔARAT score in CG. Figure 5 The relationships between the ΔHBO of i-M1 and ΔFMA-UE score, and ΔARAT score.A represents the
correlation of ΔHBO and ΔFMA-UE score in RG,B represents the correlation of ΔHBO and ΔARAT score in
RG,C represents the correlation of ΔHBO and ΔFMA-UE score in CG,D represents the correlation of ΔHBO
and ΔARAT score in CG. Page 19/19 |
https://openalex.org/W4361962616 | https://figshare.com/articles/journal_contribution/Supplementary_Figure_S3_from_sup_89_sup_Zr_Zr-DFO-girentuximab_and_sup_18_sup_F_FDG_PET_CT_to_Predict_Watchful_Waiting_Duration_in_Patients_with_Metastatic_Clear-cell_Renal_Cell_Carcinoma/22489026/1/files/39940647.pdf | unk | null | Supplementary Figure S3 from [<sup>89</sup>Zr]Zr-DFO-girentuximab and [<sup>18</sup>F]FDG PET/CT to Predict Watchful Waiting Duration in Patients with Metastatic Clear-cell Renal Cell Carcinoma | null | 2,023 | cc-by | 9 | Supplemental fgure 3 Supplemental fgure 3 Supplemental fgure 3 |
https://openalex.org/W2121121791 | https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/1756-0500-7-320 | English | null | Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction | BMC research notes | 2,014 | cc-by | 11,664 | RESEARCH ARTICLE Open Access © 2014 Tran and Chen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication
waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise
stated. Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 *Correspondence: nhtran@ntu.edu.sg
School of Physical and Mathematical Sciences, Nanyang Technological
University, Singapore, Singapore Abstract Background: Enormous volumes of short read data from next-generation sequencing (NGS) technologies have
posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is
hardly applicable to NGS data due to the challenging problem of short read assembly. Thus alignment-free methods
are needed for the comparison of NGS samples of short reads. Results: Recently several k-mer based distance measures such as CVTree, dS
2, and co-phylog have been proposed or
enhanced to address this problem. However, how to choose an optimal k value for those distance measures is not
trivial since it may depend on different aspects of the sequence data. In this paper, we considered an alternative
parameter-free approach: compression-based distance measures. These measures have shown good performance for
the comparison of long genomic sequences, but they have not yet been tested on NGS short reads. Hence, we
performed extensive validation in this study and showed that the compression-based distances are highly consistent
with those distances obtained from the k-mer based methods, from the multiple sequence alignment approach, and
from existing benchmarks in the literature. Moreover, as the compression-based distance measures are
parameter-free, no parameter optimization is required and these measures still perform consistently well on multiple
types of sequence data, for different kinds of species and taxonomy levels. g
,
p
parameter-free, no parameter optimization is required and these measures still perform consistently well on multiple
types of sequence data, for different kinds of species and taxonomy levels. Conclusions: The compression-based distance measures are assembly-free, alignment-free, parameter-free, and thus
represent useful tools for the comparison of long genomic sequences as well as the comparison of NGS samples of
short reads. Keywords: Alignment-free sequence comparison, Sequence distance, Sequence compression,
Next-generation sequencing Ngoc Hieu Tran* and Xin Chen Ngoc Hieu Tran* and Xin Chen Background Sequence distance measures are often applied to compare
long genomic sequences such as 16S rRNA sequences,
mtDNA sequences, gene encoding sequences, or even
whole genome sequences [2-4]. The obtained distances
are then used for sequence clustering and classification,
for phylogenetic tree reconstruction, for inference of the
evolution and relationship of species, etc. Recent advances in next-generation sequencing (NGS)
technologies have produced massive amounts of short
read data, bringing up promising opportunities in many
biomedical research areas such as RNA-seq, ChIP-
seq, de novo whole genome sequencing, metagenome
sequencing, etc [1]. The short read data also poses
new challenges to the field of genomic sequence anal-
ysis, including the problem of sequence comparison. However, with the development of NGS technologies,
a new type of sequence data emerges: NGS short reads
are orders of magnitudes shorter than long genomic
sequences while being generated at unprecedented high
throughput. Hence, it is highly desirable to go beyond the Page 2 of 13 Page 2 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 have been successfully applied to many clustering and
classification problems with data of various types, includ-
ing DNA sequences, texts and languages, time series,
images, sound, video [16-19,21,22]. However, they have
not been tested on NGS short reads yet. comparison of long genomic sequences to develop new
methods for the comparison of NGS samples of millions
of short reads [5]. The multiple sequence alignment (MSA) approach is
hardly applicable to large data sets of NGS short reads
due to its prohibitive computational cost and the chal-
lenging problem of short read assembly, especially for
species without any reference genomes (de novo assem-
bly). Alignment-free methods [4] could overcome these
limitations of the alignment-based approach. They are
assembly-free and scalable to large data sets. Most exist-
ing alignment-free methods use k-mers (k-tuples or
k-words) as sequence signatures to measure sequence
distances [6-10]. Markov models were also proposed for
DNA sequence comparison [11], and could be incorpo-
rated with k-mer distributions to achieve more accurate
distances [12,13]. y
In this study we demonstrate that the compression-
based distance measures can be successfully applied not
only to long genomic sequences (including 16S rRNA,
mtDNA, and whole genome sequences) but also to
NGS samples of short reads. Background Extensive validation was
conducted to assess the accuracy of the compression-
based and k-mer based distances on four data sets: 29
mammalian mtDNA sequences, 29 Escherichia/Shigella
genomes, 70 Gammaproteobacteria genomes, and 39
mammalian gut metagenomic samples. The data sets
include various types of genomic sequences, in silico and
real NGS short reads, different species and taxonomy
levels. The validation results show that the compression-
based distances are highly consistent with those distances
obtained from the k-mer based methods, from the MSA
approach, and from existing benchmarks in the litera-
ture. Our results also show that the k-mer based distance
measures depend critically on the choice of k, and the
optimal k varies across different data sets. In contrast, the
compression-based distance measures are parameter-free
and thus perform consistently well on all data sets without
any optimization of parameters. The details are presented
in the following sections. Recently several studies have further refined existing
techniques or developed new ones for better applications
to NGS short read data. In particular, the following three
measures have shown impressive performance on both
NGS short reads and long genomic sequences: CVTree
[6,7], dS
2 [14,15] and co-phylog [10]. For a given k, CVTree
and dS
2 measure the distance between two NGS samples
(or two DNA sequences) based on the normalized k-mer
frequencies. co-phylog, on the other hand, computes the
distance from the average nucleotide substitution rate in
the observed k-mers. The k-mer based measures, however, depend consider-
ably on the parameter k. A non-optimal choice of k could
lead to a dramatically worse result in some cases. In gen-
eral, a larger value of k allows the measures to use more
parameters to better capture the full characteristics of the
input sequences (or NGS samples). However, there might
not be sufficient data available for an accurate estimation
of a large number of parameters. Moreover, the optimal
k value may depend on the types of sequence data, the
species of interest, and even the taxonomy level. When the
measures are applied to NGS data, we need to consider
even more factors such as the NGS platform, the sequenc-
ing depth, the read length, etc. Thus, how to choose an
optimal k is a very challenging task. Data sets We examined the above six alignment-free distance mea-
sures dNCD, d, dCDM, CVTree, dS
2, and co-phylog on both
NGS short reads and long genomic sequences (including
16S rRNA, mtDNA, and whole genome sequences). The
sequences and short reads were retrieved or simulated
from four data sets: 29 mammalian mtDNA sequences
[13,17,19,24], 29 Escherichia/Shigella genomes [10], 70
Gammaproteobacteria genomes [10], and 39 metage-
nomic mammalian gut samples [14,25]. The authors further refined the distance d and proposed
the following in [17] which they referred to as normalized
compression-based distance (NCD): dNCD(x, y) = max{C(x|y), C(y|x)}
max{C(x), C(y)}
. (3) (3) Moreover, they have shown that the dNCD distance is
a proper metric, satisfying the non-negativity, identity,
symmetry, and triangle inequality axioms. Readers are
referred to [16,17,19,20] for more formal theory about
sequence complexity, compression and distance metrics. The tool MetaSim [26] was used to simulate short reads
from genomic sequences. It offers four error models: 454,
Sanger, Empirical (Illumina), and Exact, corresponding to
three different NGS platforms and the non-error case,
respectively. We set the read length to be 100 and used
default settings for other parameters. Short reads were
simulated at four sampling depths: 1×, 5×, 10×, and 30×. For applications to real NGS data sets, we recommend
that the sequencing coverage should be 5× or higher. In
order to ensure a fair comparison, it is also desirable that
the samples are produced from the same NGS platforms,
with similar experimental conditions, sequencing cover-
age, read lengths, etc. Strictly identical numbers of reads
or identical read lengths, however, are not necessary. For
example, the real NGS data set of 39 metagenomic sam-
ples analyzed in our study was produced from the 454
FLX platform, with a total of 2,163,286 reads (an aver-
age of 55,469 ± 28,724 (standard deviation, SD) reads per
sample, 261 ± 83 nucleotides per read) [25]. The tool MetaSim [26] was used to simulate short reads
from genomic sequences. It offers four error models: 454,
Sanger, Empirical (Illumina), and Exact, corresponding to
three different NGS platforms and the non-error case,
respectively. We set the read length to be 100 and used
default settings for other parameters. Short reads were
simulated at four sampling depths: 1×, 5×, 10×, and 30×. q
p
y
p
In principle, any sequence compression tool can be used
to compute the above distances. Compression-based distance measures Let x and y denote the two sequences (or NGS samples) to
be compared and xy denote their concatenation. Let C(x)
denote the size (that is, the number of bytes) of x after
being compressed by a sequence compression tool. Data
compression is aimed at reducing as much redundant
information in the given data as possible. Hence, if x and y
share similar patterns, compressing them together should
use less storage space than compressing them separately,
that is, C(xy) ≤C(x) + C(y). Specifically, if x and y are
identical, one could expect that C(xy) ≃C(x) = C(y). On
the other hand, if x and y share no information, one could
expect that C(xy) ≃C(x)+C(y). These observations sug-
gest that one could measure the similarity/dissimilarity
between x and y based on their compressed sizes. In this paper, we consider an alternative parameter-free
approach: compression-based distance measures [16-18]. Roughly speaking, data compression is aimed at reducing
as much redundant information in the given data as pos-
sible. Hence, if two NGS samples share similar patterns,
compressing them together should be more efficient, that
is, should use less storage space, than compressing them
separately. The distance between the two NGS samples
can then be calculated based on the sizes of the reduced
storage space. Readers are referred to [16,17,19,20] for
more formal theory about sequence complexity, compres-
sion and distance metrics. Compression-based distances In particular, the following distance measure called
compression-based dissimilarity measure (CDM) was
proposed in [18]: dCDM(x, y) =
C(xy)
C(x) + C(y). (1) (1) This dCDM distance ranges from 1
2 (when x and y are
identical) to 1 (when x and y share no information). This dCDM distance ranges from 1
2 (when x and y are
identical) to 1 (when x and y share no information). Page 3 of 13 Page 3 of 13 Page 3 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 A more mathematically precise distance was proposed
in [16] using the notation of conditional compression: We used the implementations provided by the authors. The tools CVTree and dS
2 have options to input the param-
eter k. For CVTree, we tried k from 3 to 32 as allowed by
the tool. Compression-based distance measures For dS
2, we were not able to run it for k > 9 due
to some “segmentation fault” error, which seems to be a
problem of handling dynamic memory in the tool. There
is no input option for co-phylog, thus we simply used its
default settings. d(x, y) = C(x|y) + C(y|x)
C(xy)
. (2) (2) Here C(x|y) denotes the compressed size of sequence
x conditioning on sequence y. C(x|y) ≃0 indicates that x
and y are identical, while C(x|y) ≃C(x) indicates that x
and y share no information and thus they are expected to
be independent sequences. This distance ranges from 0 to
1 and satisfies the triangle inequality [16]. Data sets More efficient compres-
sion should lead to more accurate distance estimates,
but may require longer compression time. In this study,
we used the tool GenCompress [23] since it can per-
form conditional compression on x|y. We used the same
compression tool for both long genomic sequences and
NGS short reads to ensure a consistent and fair compari-
son. When applying GenCompress to an NGS sample, we
first concatenated all short reads together to form a sin-
gle sequence and then compressed it. Our experiment
results show that the compression-based distances are
quite robust against different orders of concatenating the
short reads. For applications to real NGS data sets, we recommend
that the sequencing coverage should be 5× or higher. In
order to ensure a fair comparison, it is also desirable that
the samples are produced from the same NGS platforms,
with similar experimental conditions, sequencing cover-
age, read lengths, etc. Strictly identical numbers of reads
or identical read lengths, however, are not necessary. For
example, the real NGS data set of 39 metagenomic sam-
ples analyzed in our study was produced from the 454
FLX platform, with a total of 2,163,286 reads (an aver-
age of 55,469 ± 28,724 (standard deviation, SD) reads per
sample, 261 ± 83 nucleotides per read) [25]. Accuracy assessment One possible
explanation is that co-phylog may be only suitable for
closely related species, as the authors mentioned in [10]. We also noted that the CVTree and dS
2 distances varied
remarkably with respect to k (Additional file 1: Table S2). For instance, the smallest symmetric difference between
the CVTree tree and the MSA tree is 6 (k = 10), but the
largest is up to 48 (k = 16, 17). Similarly, the highest cor-
relation between the dS
2 distance and the MSA distance is
0.88 (k = 8), but the lowest is down to 0.41 (k = 3). We also assessed the alignment-free distances by exam-
ining their corresponding phylogenetic trees. For each
distance matrix, the tool neighbor in the package PHYLIP
was used to construct a phylogenetic tree using the
neighbor joining method [29]. Subsequently, the tool
treedist in the package PHYLIP was used to calculate
the symmetric difference [30] between the resulting tree
from each alignment-free distance and the corresponding
MSA/benchmark tree. Each internal node in a phyloge-
netic tree corresponds to a subset of clustered leaf nodes. Given two phylogenetic trees with the same set of leaf
nodes, the symmetric difference between them is the
number of internal nodes that are present in one tree but
not in the other. Finally, to assess the clustering and classification abil-
ity of the alignment-free distances, we used the parsi-
mony score to measure how different a clustering tree
is from the true classification (using tools TreeClimber
[31], mothur [32]). The parsimony score of a clustering
tree is calculated by the tool TreeClimber as follows. First,
the parsimony score is set to 0 and the leaf nodes are
labeled according to their groups in the true classifica-
tion. The algorithm traverses from the leaf nodes to the
root and determine the labels of the internal nodes. The
labels of each internal node depend on the labels of its
two immediate child nodes. If they share common labels
then these common labels are assigned to the internal
node. If the two child nodes share no label, a penalty of
1 is added to the parsimony score and the internal node
is assigned with the union of the label sets of its two
child nodes. If a clustering tree is perfect, its parsimony
score is equal to the number of groups in the true clas-
sification minus one. Accuracy assessment In this study, we considered three k-mer based distance
measures: CVTree [6,7], dS
2 [14,15] and co-phylog [10]. Given two DNA sequences (or two NGS samples), CVTree
measures the correlation distance between their com-
position vectors, where each composition vector is the
collection of the normalized frequencies of k-mers. The
dS
2 distance is an NGS-extension of the D2, D∗
2, and DS
2
statistics which were proposed in [8,9] for the comparison
of long genomic sequences. The main difference between
dS
2 and CVTree lies in the normalization of the frequencies
of k-mers. The co-phylog distance is also based on k-mers
but not in the frequency context. It measures the distance
as the average nucleotide substitution rate in the observed
k-mers of the two sequences (or samples). To assess the accuracy of the alignment-free distances,
we compared them with those obtained from the MSA
approach if applicable and with existing benchmarks in
the literature. The tool Clustal Omega [27] was used to
perform MSA and then the tool dnadist in the package
PHYLIP [28] was used to calculate the distance matrix
from the MSA. Following [10,14], we used distance correlation, tree
symmetric difference, and parsimony score to measure
the accuracy of the alignment-free distances. In particular,
we computed the correlation between each alignment-free
distance and the MSA/benchmark distance to evaluate
their consistency. The correlation between two distance
matrices was calculated as follows. We first converted Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Page 4 of 13 Page 4 of 13 each matrix into a single vector by concatenating all of
its rows side by side and then calculated the Pearson
correlation between the two vectors. Performance on mtDNA sequences Performance on mtDNA sequences
First, we applied the six alignment-free distance measures
dNCD, d, dCDM, CVTree, dS
2, co-phylog to the mtDNA
sequences and compared the results with those obtained
from the MSA method and from existing benchmarks. Additional file 1: Table S1 shows that both compression-
based distances dNCD, d, dCDM and k-mer based distances
CVTree, dS
2 (for optimal choices of k) are in good agree-
ment with the MSA distance. The dS
2 distance has the
highest correlation with the MSA distance, whereas the
CVTree tree has the smallest symmetric difference from
the MSA tree. The compression-based distances, lead-
ing by dCDM, performed slightly worse. The co-phylog
measure, however, failed for this data set. Accuracy assessment The higher the parsimony score is,
the more different the clustering tree is from the true
classification. (
)
(
)
The MSA tree (Additional file 2: Figure S1a) is highly
consistent with existing benchmarks in the literature
[13,17,19,24]. In particular, the MSA tree is nearly iden-
tical to those reported in [13,19], except for two minor
differences in the branches of dog, cat and the branches
of non-murid rodents (fat dormouse, squirrel, guinea pig). Additional file 2: Figures S1a and S1b show that the main
difference between the MSA tree and the dCDM tree also
lies in the group Rodents. In addition, the dCDM tree indi-
cates that pig is closer to cow and sheep than to other
species in the group Ferungulates. The branches of dog,
cat in the dCDM tree are slightly different from those in the
MSA tree, but consistent with previously reported trees in
[13,19]. The trees reported by CVTree and dS
2 (Additional
file 2: Figures S1c and S1d, respectively) also show differ-
ent results for the group Rodents. The phylogeny of the
group Rodents is actually still a controversial question, as
mentioned in previous studies [13,19]. The position of the
cluster of dog, cat, and seals in the group Ferungulates
reported by CVTree is not consistent with the other trees
and the benchmarks. Overall, all four trees support the
hypothesis of (Rodents, (Ferungulates, Primates)), as sug-
gested in [13,17,19,24], and have identical phylogeny of
the group Primates. The main differences among them
include the phylogeny of the group Rodents, the positions
of pig and hippo, and the subtree of dog, cat and seals in
the group Ferungulates. The tool TreeGraph 2 [33] was used to plot phylogenetic
trees. Results and discussion Alignment-free comparison of mammalian mtDNA
sequences or their NGS short reads reconfirms the
hypothesis (Rodents, (Ferungulates, Primates)) Alignment-free comparison of mammalian mtDNA
sequences or their NGS short reads reconfirms the
hypothesis (Rodents, (Ferungulates, Primates)) One of the key advantages of the alignment-free distance
measures over the alignment-based approach is their scal-
ability to large data sets of whole genome sequences
or NGS short reads. However, in this section we first
want to assess their accuracy on a small, but very well-
studied data set of 29 mammalian mtDNA sequences. This data set has been widely used for validation in exist-
ing literatures and hence reliable benchmarks are available
[13,17,19,24]. Performance on NGS short reads Next, we ask if similar results could be obtained from
the comparison of NGS samples of short reads. We used Page 5 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 the tool MetaSim [26] to simulate short reads from the
mtDNA sequences with four error models 454, Exact,
Empirical (Illumina), Sanger, and four different sampling
depths 1×, 5×, 10×, and 30×. The read length was set at
100 bp. We used k = 10 for the CVTree distance and k = 8
for the dS
2 distance as suggested by their optimal perfor-
mance on the mtDNA sequences in the previous section. Since the MSA method is difficult to apply to NGS short
reads, we still kept the MSA distance and tree obtained
from the mtDNA sequences as benchmark. At the 1×
sampling depth, we found that the alignment-free results
were considerably different from the MSA benchmark
due to the low coverage. However, at the 5× sampling
depth, all five measures dNCD, d, dCDM, CVTree, and
dS
2 produced comparably accurate results as when they
were applied to the mtDNA sequences. Further increasing
the sampling depth to 10× and 30× did not significantly
improve the accuracy of the distances. identical to the MSA tree (Additional file 2: Figure S1a)
and existing benchmarks in the literature [13,17,19,24],
supporting
the
hypothesis
(Rodents,
(Ferungulates,
Primates)). The dS
2 tree, however, has more inconsistent branches
in the group Ferungulates, although it has the highest cor-
relation with the MSA distance. Last but not least, we
also noted that the alignment-free results obtained from
the simulated NGS short reads were consistent with their
corresponding counterparts obtained from the mtDNA
sequences in the previous section, especially for the non-
error (Exact) model (Table 2). When applying GenCompress to an NGS sample, we
concatenated all short reads of the sample to form a sin-
gle sequence and then compressed it. Hence, it is also
important to examine if the compression-based distances
are robust against different ways of concatenation. We
repeated the experiment with the Empirical (Illumina)
samples for 10 different runs in each of which the reads
from each sample were concatenated in a random order. Additional file 1: Table S8a shows that the compression-
based distances obtained from those runs are highly
consistent with each other. Performance on NGS short reads We also compared those dis-
tances with the MSA distance and the performance results
(Additional file 1: Table S8b) are similar to those reported
earlier in Table 1. Table 1 summarizes the results for the 5× sampling
depth, similar results for 1×, 10×, and 30× can be found
in Additional file 1: Table S2. We highlighted in boldface
both the best and the second best of the tree symmet-
ric difference and the distance correlation for each error
model because they are usually not very different. As
shown in Table 1, the dS
2 distance achieved the highest cor-
relation with the MSA distance, followed by the CVTree
distance. In summary, we have shown that all five alignment-
free distance measures dNCD, d, dCDM, CVTree, and dS
2
can be successfully applied to both mtDNA sequences
and their NGS short reads. The distances obtained from
the NGS short reads were consistent with those obtained
from the mtDNA sequences, and they were all in good
agreement with the MSA distance as well as with exist-
ing benchmarks in the literature. The compression-based
measures dNCD, d and dCDM produced comparably accu-
rate distances as those optimal results obtained from the
k-mer based measures CVTree and dS
2. The compression-
based distances were also shown to be quite robust against
different concatenations of short reads. In terms of the symmetric difference from the MSA
tree, the dCDM distance performed consistently well
for all four error models, followed by the dS
2 and dNCD
distances. Figure 1 shows the phylogenetic trees recon-
structed from the dCDM, CVTree, and dS
2 distances for the
NGS short reads simulated using the Empirical (Illumina)
error model. The dCDM and CVTree trees are almost Table 1 Comparison of the alignment-free distances and
the MSA distance for NGS short reads of the mtDNA
sequences
dNCD
d
dCDM
CVTree (k = 10)
dS
2(k = 8)
454
14
16
10
10
6
Exact
8
8
8
8
8
Empirical
6
8
4
8
12
Sanger
10
14
8
14
8
454
0.68
0.66
0.68
0.75
0.88
Exact
0.69
0.68
0.68
0.71
0.88
Empirical
0.69
0.69
0.66
0.69
0.81
Sanger
0.67
0.67
0.65
0.74
0.87
The short reads were simulated from the mtDNA sequences using four error
models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling
depth. Performance on NGS short reads The two smallest tree symmetric differences and the two highest
distance correlation coefficients for each error model are highlighted in
boldface. Similar results for 1×, 10×, and 30× sampling depths can be found in
Additional file 1: Table S2. Table 1 Comparison of the alignment-free distances and
the MSA distance for NGS short reads of the mtDNA
sequences The CVTree and dS
2 distances varied remarkably with
respect to k, and the optimal k was selected according
to the MSA benchmark. This may pose a challenging
problem when there is no benchmark available for vali-
dation. In contrast, the compression-based measures are
parameter-free and hence no optimization of any param-
eter is required. Phylogeny of closely related Escherichia/Shigella genomes
In this section we assess the accuracy of the alignment-
free distances on a data set of 29 Escherichia/Shigella
genomes. Two main differences between this data set
and the previous one are: (i) it consists of whole genome
sequences and (ii) the species are closely related bacte-
ria in the genus Escherichia and the genus Shigella. This Page 6 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Figure 1 Phylogenetic trees reconstructed from NGS short reads of 29 mtDNA sequences using: (A) dCDM, (B) CVTree (k = 10), (C)
dS
2(k = 8). The short reads were simulated from the tool MetaSim using the Empirical model and 5× sampling depth. The group of three species
platypus, opossum, and wallaroo was used as the outgroup to root the tree. Figure 1 Phylogenetic trees reconstructed from NGS short reads of 29 mtDNA sequences using: (A) dCDM, (B) CVTree (k = 10), (C)
dS
2(k = 8). The short reads were simulated from the tool MetaSim using the Empirical model and 5× sampling depth. The group of three species
platypus, opossum, and wallaroo was used as the outgroup to root the tree. the co-phylog measure. Table 3 shows that the dCDM dis-
tance performed the best in terms of both tree symmetric
difference and distance correlation. The results of dNCD
and d are also better than the best results of CVTree and
dS
2, especially with the remarkably high correlation with
the benchmark co-phylog distance. The dS
2 distance failed
for this data set and its correlation with the benchmark
co-phylog distance is much lower than that of the other
measures. Table 2 Comparison of the phylogenetic trees
reconstructed from the mtDNA sequences and from their
NGS short reads Table 2 Comparison of the phylogenetic trees
reconstructed from the mtDNA sequences and from their
NGS short reads p
p y
g
reconstructed from the mtDNA sequences and from their
NGS short reads
dNCD
d
dCDM
CVTree (k = 10)
dS
2(k = 8)
454
10
14
8
8
4
Exact
2
0
4
2
2
Empirical
8
6
6
6
10
Sanger
12
10
8
10
8
The short reads were simulated from the mtDNA sequences using four error
models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling
depth. The two smallest tree symmetric differences for each error model are
highlighted in boldface. Similar results for 1×, 10×, and 30× sampling depths
can be found in Additional file 1: Table S2. dNCD
d
dCDM
CVTree (k = 10)
dS
2(k = 8)
454
10
14
8
8
4
Exact
2
0
4
2
2
Empirical
8
6
6
6
10
Sanger
12
10
8
10
8 Performance on whole genome sequences g
q
We first applied the five measures dNCD, d, dCDM,
CVTree, and dS
2 to the whole genome sequences and
compared the results with the benchmark obtained from Performance on NGS short reads The phylogenetic trees produced by the CVTree
distance are inconsistent for different values of k: it is
not clear whether the genus Shigella violates the mono-
phyleticity of the genus Escherichia (k = 15) or the mono-
phyleticity of the E.coli strains (k = 9, 21) (Additional
file 2: Figure S2). This was also mentioned previously
in [10]. data set has been studied previously in [10,34] and the
authors have shown that the co-phylog distance was highly
consistent with the MSA distance in terms of both tree
symmetric difference and distance correlation. Hence, to
avoid the time-consuming MSA, we used the co-phylog
distance as benchmark. Performance on NGS short reads Next, we tested the measures on the data sets of NGS
short reads which were simulated from the whole genome
sequences. We used MetaSim with four error models and
different sampling depths as described earlier. Interest-
ingly, even at the lowest 1× sampling depth, we already
obtained accurate results from the three compression-
based distances dNCD, d, and dCDM. Figure 2 shows the
case of the dCDM distance in which the phylogenetic tree The short reads were simulated from the mtDNA sequences using four error
models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling
depth. The two smallest tree symmetric differences for each error model are
highlighted in boldface. Similar results for 1×, 10×, and 30× sampling depths
can be found in Additional file 1: Table S2. Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Page 7 of 13 Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella
genomes
dNCD
d
dCDM
CVTree (k = 9)
CVTree (k = 15)
CVTree (k = 21)
dS
2(k = 8)
Symmetric difference
16
14
12
20
20
16
24
Distance correlation
0.97
0.95
0.99
0.80
0.79
0.80
0.20
The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella
genomes
dNCD
d
dCDM
CVTree (k = 9)
CVTree (k = 15)
CVTree (k = 21)
dS
2(k = 8)
Symmetric difference
16
14
12
20
20
16
24
Distance correlation
0.97
0.95
0.99
0.80
0.79
0.80
0.20
The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella
genomes
dNCD
d
dCDM
CVTree (k = 9)
CVTree (k = 15)
CVTree (k = 21)
dS
2(k = 8)
Symmetric difference
16
14
12
20
20
16
24
Distance correlation
0.97
0.95
0.99
0.80
0.79
0.80
0.20
The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. In summary, the compression-based distances dNCD, d,
and dCDM were consistent with the benchmark co-phylog
distance on both types of data, whole genome sequences
and NGS short reads of 29 Escherichia/Shigella bacte-
ria. Performance on NGS short reads They outperformed the two k-mer based distances
CVTree and dS
2, which either failed or produced incon-
sistent results for different values of k. The results in
this section further emphasize the wide applicability and
the consistency of the compression-based distances. They
represent useful measures for accurate comparison of dif-
ferent types of long genomic sequences and NGS short
read data, for both mammalian and bacteria species. reconstructed from the NGS short reads (Exact model) is
almost identical to the tree reconstructed from the whole
genome sequences. Moreover, both trees are very similar
to the benchmark co-phylog tree. The main difference is
that in the benchmark co-phylog tree the group of S.boydii
and S.sonnei is clustered with E.coli first, whereas in the
dCDM trees this group is clustered with S.flexneri first. Table 4 clearly shows that the compression-based dis-
tances dNCD, d, and dCDM outperformed the CVTree and
dS
2 distances for all NGS data sets, in terms of both tree
symmetric difference and distance correlation. We also noted that while the results of the compression-
based distances for the whole genome sequences (Table 3)
and for the NGS short reads (Table 4) were comparable,
the performance of the CVTree and dS
2 distances became
worse when they were applied to the NGS short reads. Similar results for the NGS data sets obtained from the
5× sampling depth can be found in Additional file 1:
Table S3. Classification of 70 genomes in the class
Gammaproteobacteria into their correct orders Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29
Escherichia/Shigella genomes son of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 2
ella genomes Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for N
Escherichia/Shigella genomes n of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29 e Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling
differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5×
nal file 1: Table S3. The short reads were simulated from the Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling
depth. The two smallest tree symmetric differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5×
sampling depth can be found in Additional file 1: Table S3. 16S rRNA sequences. Table 5 shows that the alignment-
free distances are highly correlated with the MSA dis-
tance and they all have similar parsimony scores (17-18),
except for the co-phylog distance. Overall, the dNCD dis-
tance performed slightly better than the others in terms
of parsimony score, tree symmetric difference, and dis-
tance correlation. Its clustering tree in Figure 3 shows
that the genomes of six orders Aeromonadales, Enter-
obacteriales, Legionellales, Pasteurellales, Vibrionales, and
Xanthomonadales are all correctly classified into their
groups. Most of the genomes in the remaining orders are
also well clustered. of 70 genomes that were randomly chosen from 15 orders
of the class Gammaproteobacteria (Additional file 1: Table
S4). As the number of genomes is large and they come
from different groups, it is interesting to ask if the dis-
tance measures can cluster and classify those genomes
into their correct orders. We used the parsimony score to
measure the difference between a clustering tree and the
true classification [31,32]. As the number of groups is 15, the optimal parsimony
score is 14. The higher the parsimony score is, the more
different the clustering tree is from the true classification. This data set has been studied previously in [10] and the
authors found that the co-phylog distance did not perform
well because the bacteria of interest are not closely related. Performance on 16S rRNA sequences Then, we applied the alignment-free distance measures to
the 70 whole genome sequences and their simulated NGS
short reads. As it is challenging to perform MSA of 70 whole genome
sequences, we applied the MSA method to 16S rRNA
sequences of those 70 genomes to obtain the benchmark
distance and clustering tree (Additional file 2: Figure S3,
parsimony score = 18). The clustering results obtained from the NGS short
reads are comparable to those obtained from the whole
genome sequences, and both are worse than those
obtained from the 16S rRNA sequences (Table 5). Since
this experiment was conducted at a high taxonomy level We then applied all six alignment-free distance mea-
sures dNCD, d, dCDM, CVTree, dS
2, and co-phylog to the Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria
genomes
dNCD
d
dCDM
CVTree
dS
2
co-phylog
parsimony score
17
18
18
17
18
25
16s rRNA sequences
tree symmetric difference
50
52
52
50
62
108
distance correlation
0.93
0.90
0.93
0.92
0.92
0.65
parsimony score
22
22
21
21
31
26
Genome sequences
tree symmetric difference
80
78
76
84
110
110
distance correlation
0.47
0.46
0.47
0.67
0.50
0.45
parsimony score
21
19
23
24
32
28
NGS short reads
tree symmetric difference
90
70
84
88
114
116
distance correlation
0.60
0.58
0.53
0.63
0.48
0.42
The NGS short reads were simulated from the whole genome sequences using the Exact model of MetaSim at 1× sampling depth . The two smallest parsimony scores,
the two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. For CVTree, we used k = 7 for the 16S rRNA data
set and k = 12 for the whole genome and NGS data sets. For dS
2, we used k = 6 for the 16S rRNA data set and k = 8 for the whole genome and NGS data sets. Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria
genomes Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gamm n of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria The NGS short reads were simulated from the whole genome sequences using the Exact model of MetaSim at 1× sampling depth . Classification of 70 genomes in the class
Gammaproteobacteria into their correct orders The previous section has focused on closely related bac-
teria at the genus level. We next applied the MSA and the
alignment-free distance measures to a larger data set at a
higher taxonomy level. In particular, the data set consists Figure 2 Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using (A) co-phylog, (B) dCDM, and from NGS short reads
using (C) dCDM. The short reads were simulated from the tool MetaSim using the Exact model and 1× sampling depth. Escherichia Fergusonii was
used as the outgroup to root the tree. f
29 E
h
i hi /Shi
ll
i
(A)
h l Figure 2 Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using (A) co-phylog, (B) dCDM, and from NGS short reads
using (C) dCDM. The short reads were simulated from the tool MetaSim using the Exact model and 1× sampling depth. Escherichia Fergusonii was
used as the outgroup to root the tree. Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Page 8 of 13 Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29
Escherichia/Shigella genomes
dNCD
d
dCDM
CVTree (k = 9)
CVTree (k = 15)
CVTree (k = 21)
dS
2(k = 8)
454
16
14
12
22
22
54
50
Exact
12
10
10
22
24
36
50
Empirical
16
12
14
24
18
42
54
Sanger
12
10
10
28
24
40
50
454
0.96
0.96
0.97
0.74
0.87
0.31
0.04
Exact
0.97
0.97
0.98
0.82
0.82
0.61
0.05
Empirical
0.96
0.96
0.96
0.77
0.85
0.38
0.01
Sanger
0.97
0.97
0.97
0.78
0.86
0.36
0.04
The short reads were simulated from the Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling
depth. The two smallest tree symmetric differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5×
sampling depth can be found in Additional file 1: Table S3. Performance on 16S rRNA sequences The two smallest parsimony scores,
the two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. For CVTree, we used k = 7 for the 16S rRNA data
set and k = 12 for the whole genome and NGS data sets. For dS
2, we used k = 6 for the 16S rRNA data set and k = 8 for the whole genome and NGS data sets. Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Page 9 of 13 Acidithiobacillales
Aeromonadales
Alteromonadales
Cardiobacteriales
Chromaales
Enterobacteriales
Legionellales
Methylococcales
Oceanospirillales
Pasteurellales
Pseudomonadales
Thiotrichales
Vibrionales
Xanthomonadales
Outgroup
Figure 3 Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the dNCD distance. Those 70
genomes belong to 15 orders which are indicated by different colors in the figure. and the species were selected from different orders of
the class Gammaproteobacteria, one could expect that
the 16S rRNA sequences should be more reliable for the
especially for the whole genome sequences and NGS short
reads. Last but not least, we noted that the optimal k of
CVTree and dS
2 for the whole genome sequences were dif- Figure 3 Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the dNCD distance. Those 70
genomes belong to 15 orders which are indicated by different colors in the figure. and the species were selected from different orders of
the class Gammaproteobacteria, one could expect that
the 16S rRNA sequences should be more reliable for the
classification than the whole genome sequences and their
short reads. It can also be seen from Table 5 that the four
distances dNCD, d, dCDM, and CVTree performed slightly
better than the other two distances, dS
2 and co-phylog, especially for the whole genome sequences and NGS short
reads. Last but not least, we noted that the optimal k of
CVTree and dS
2 for the whole genome sequences were dif-
ferent from those for the 16S rRNA sequences (Additional
file 1: Table S5). The optimal k was selected to opti-
mize the parsimony score of the clustering trees. This
will not be possible if we have no prior knowledge about Page 10 of 13 Page 10 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 classified to the group of hindgut-fermenting herbivores. Performance on 16S rRNA sequences Although the optimal tree obtained from the CVTree
distance (k = 4) also has the same parsimony score of
3, it seems to have a serious mistake when classifying the
two carnivores Polar Bear and Lion to the groups of her-
bivores (Additional file 2: Figure S7). The clustering tree
obtained from the dCDM distance (parsimony score = 5)
is shown in Additional file 2: Figure S8. It correctly distin-
guished carnivores from herbivores. However, it wrongly
classified Rock Hyraxes, Colobus and Visayam Warty Pig
to the group of hindgut-fermenting herbivores. the true classification, which is usually the case in real
applications. Performance on the full data set Then, we added back the 11 omnivore samples and
repeated the experiment with the full data set. As there
are now four groups in the true classification, the optimal
parsimony score is 3. We found that the best parsimony score was obtained
from the dNCD distance, followed by CVTree (k = 6) and
dS
2 (k = 7) (Table 6). It should be noted that the optimal
k of the CVTree and dS
2 distances for the sub-data set and
for the full data set are different (Table 6, Additional file 1:
Table S7). Performance on the sub-data set with 11 omnivore samples
excluded The clustering tree of the dNCD distance is shown in
Figure 4. The samples from foregut-fermenting herbivores
were well clustered together, except for Rock Hyraxes,
Colobus, and Visayam Warty Pig, which were classified
to the group of hindgut-fermenting herbivores. This is
similar to the earlier observation when the 11 omni-
vore samples were excluded. Figure 4 also shows that the
carnivore samples were grouped together. The omnivore
samples, however, were scattered throughout the groups
of herbivores and carnivores. This indicates the diversity
of the gut microbial communities of omnivores, as men-
tioned previously in [14,25]. Another important observa-
tion from Figure 4 is that the primates samples, including
Baboon 1 and 2, Chimpanzee 1 and 2, Orangutan, Gorilla,
Callimicos, Saki, Black Lemur, were clustered together
into one group. This may suggest that those primates
share common features in their gut microbial environ-
ments. Finally, it can be seen that two samples of the same
host species were often clustered close to each other such
as Chimpanzee 1 and 2, Lion 1 and 2, Okapi 1 and 2,
Bighorn Sheep 1 and 2, supporting the accuracy of the
classification and the dNCD distance. Following [14,25], we first excluded 11 omnivore sam-
ples due to their complicated microbial compositions. The
remaining 28 samples belong to three groups: foregut-
fermenting herbivores, hindgut-fermenting herbivores,
and carnivores. Since there is no benchmark tree for this
clustering problem, we only used the parsimony score to
evaluate the clustering trees. The optimal parsimony score
is 2 as there are only three groups in the true classification. Table 6 shows that the parsimony scores of the CVTree
and dS
2 distances for the optimal k are better than
those of the compression-based distances dNCD, d, and
dCDM. We also noted that the parsimony score of the
CVTree distance varied considerably (up to 11), while that
of the dS
2 distance was more stable (Additional file 1:
Table S7). The optimal tree obtained from the dS
2 distance (k = 5,
parsimony score = 3) is shown in Additional file 2: Figure
S6. Classification of metagenomic samples from
mammalian gut reveals the diet and gut physiology of
the host species In this section we consider a real metagenomic data set
that includes NGS short reads of 39 fecal samples from
33 mammalian host species. The host species can be clas-
sified into four groups according to their diet and gut
physiology: foregut-fermenting herbivores (13 samples),
hindgut-fermenting herbivores (8 samples), carnivores
(7 samples), and omnivores (11 samples) (Additional file 1:
Table S6). This data set has been studied previously in
[14,25]. In [14] the authors applied the CVTree and dS
2
distances to these 39 metagenomic samples and found
that the sequence signatures (that is, the k-mers) of the
samples were strongly associated with the diet and gut
physiology of the host species. Hence we want to test if
the compression-based distance measures dNCD, d and
dCDM can also reveal any interesting results from this
metagenomic data set. Performance on the sub-data set with 11 omnivore samples
excluded Only two samples Rock Hyrax 1 and 2 were wrongly Table 6 Parsimony score for the classificationof 39
metagenomic samples using the alignment-free distances
dNCD
d
dCDM
CVTree
dS
2
Sub-data set
6
7
5
3
3
(omnivore samples excluded)
Full data set
9
12
12
10
10
For CVTree, we used k = 6 for the full data set and k = 4 for the sub-data set in
which the omnivore samples were excluded. For dS
2, we used k = 7 for the full
data set and k = 5 for the sub-data set. The two smallest parsimony scores for
each data set are highlighted in boldface. The results obtained in this section have demon-
strated another application of the alignment-free mea-
sures of sequence distance: comparison and classification
of metagenomic samples of NGS short reads. This task
is of critical importance for the understanding of micro-
bial communities. Both k-mer based and compression-
based distance measures have revealed interesting results
about the microbial communities of mammalian gut from
their metagenomic samples. In particular, the information For CVTree, we used k = 6 for the full data set and k = 4 for the sub-data set in
which the omnivore samples were excluded. For dS
2, we used k = 7 for the full
data set and k = 5 for the sub-data set. The two smallest parsimony scores for
each data set are highlighted in boldface. Page 11 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 Herbivore Foregut
Herbivore Hindgut
Carnivore
Omnivore
Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ colors indicate their diet
and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and omnivores (blue). Herbivore Hindgut Herbivore Foregut Carnivore Omnivore Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ colors indicate their diet
and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and omnivores (blue). Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ c
and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and o Conclusions contained in the samples was found to be strongly asso-
ciated with the diet and gut physiology of herbivores,
carnivores, and omnivores. This agrees well with previous
studies in [14,25]. Moreover, our results obtained from
the compression-based distance measures also discovered
a strong similarity between the gut microbial communi-
ties of the primates. This interesting finding has not been
observed in previous studies. In this paper we studied the application of compression-
based distance measures for the problem of sequence
comparison, with a special focus on NGS short read data. Their key advantages are assembly-free, alignment-free,
and parameter-free. We conducted extensive validation
on various types of sequence data: NGS short reads, 16S
rRNA sequences, mtDNA sequences, and whole genome Page 12 of 13 Page 12 of 13 Tran and Chen BMC Research Notes 2014, 7:320
http://www.biomedcentral.com/1756-0500/7/320 sequences. The sequence data was obtained from several
mammalian and bacteria genomes at different taxonomy
levels, as well as from microbial metagenomic samples. The results show that the compression-based distance
measures produced comparably accurate results as the k-
mer based methods, and both were in good agreement
with the alignment-based approach and with existing
benchmarks in the literature. compression tools should be more efficient and hence
provide more accurate distances. Our future research will
focus on reducing the running time and studying the
effects of different compression tools. In this study we have demonstrated the accuracy
and the consistency of the compression-based distance
measures on both NGS short reads and long genomic
sequences. Those findings underscore the advantages
of the compression-based distance measures, suggest-
ing that these measures represent useful tools for the
alignment-free sequence comparison. An implementation
of the compression-based distance measures is provided
in the attached Perl scripts (Additional file 3). The k-mer based distance measures, however, may pro-
duce inconsistent results depending on the parameter k,
the type of sequence data, or the species under con-
sideration. For example, the co-phylog measure was not
applicable to species with far evolutionary distances from
each other (data set of 29 mammalian, data set of 70
Gammaproteobacteria, data set of 39 metagenomic sam-
ples). The dS
2 measure failed for the data set of 29 closely
related Escherichia/Shigella bacteria. The CVTree mea-
sure produced inconsistent results for the data set of
29 Escherichia/Shigella bacteria. Additional files Clustering tree reconstructed from 16S
rRNA sequences of 70 Gammaproteobacteria genomes using the distance
dS
2 (k = 6). Figure S6. Clustering tree reconstructed from the metagenomic
samples (omnivore samples excluded) using the distance dS
2(k = 5). Figure S7. Clustering tree reconstructed from the metagenomic samples
(omnivore samples excluded) using the distance CVTree (k = 4). Figure
S8. Clustering tree reconstructed from the metagenomic samples
(omnivore samples excluded) using the distance dCDM. Additional file 2: Figure S1. Phylogenetic trees reconstructed from 29
mtDNA sequences using: (a) MSA, (b) dCDM, (c) CVTree (k = 10), (d)
dS
2(k = 8). Figure S2. Phylogenetic trees reconstructed from 29
Escherichia/Shigella genomes using: (a) co-phylog, (b) CVTree (k = 9), (c)
CVTree (k = 15), (d) CVTree (k = 21). Figure S3. Clustering tree
reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria
genomes using the MSA distance. Figure S4. Clustering tree reconstructed
from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the
distance CVTree (k = 7). Figure S5. Clustering tree reconstructed from 16S
rRNA sequences of 70 Gammaproteobacteria genomes using the distance
dS
2 (k = 6). Figure S6. Clustering tree reconstructed from the metagenomic
samples (omnivore samples excluded) using the distance dS
2(k = 5). Figure S7. Clustering tree reconstructed from the metagenomic samples
(omnivore samples excluded) using the distance CVTree (k = 4). Figure
S8. Clustering tree reconstructed from the metagenomic samples
(omnivore samples excluded) using the distance dCDM. One possible drawback when using the compression-
based distance measures is the running time. Obviously,
compressing a DNA sequence (or an NGS sample) takes
longer time than counting its k-mers. Moreover, the
compression-based methods need to perform pairwise
compression of the input sequences, whereas the k-mer
methods only need to calculate one frequency vector for
each input sequence. However, in general one may also
need to test a wide range of k to find the optimal results
when using the k-mer methods. As an example, for the data set of 39 metagenomic sam-
ples in our study, the running time of the CVTree measure
was ∼1-7 minutes for each k = 2, 3, . . ., 10, and ∼10-60
minutes for each k = 11, 12, . . ., 20. Thus, a test cov-
ering all values of k = 2, 3, . . Additional files Additional file 1: Table S1. Comparison of alignment-free distances and
the benchmark MSA distance for 29 mtDNA sequences. Table S2. Comparison of alignment-free distances and the benchmark MSA distance
for 29 mtDNA sequences and their short reads. Table S3. Comparison of
alignment-free distances and the benchmark co-phylog distance for 29
Escherichia/Shigella genomes and their short reads. Table S4. The list of 70
genomes in the class Gammaproteobacteria, their orders, and their
accession numbers. Table S5. Comparison of alignment-free distances and
the benchmark MSA distance for 70 Gammaproteobacteria genomes and
their short reads. Table S6. The list of 39 metagenomic samples and their
host species’ diet and gut physiology. Table S7. The parsimony score of
the clustering trees for 39 metagenomic samples. Table S8. Performance
of the compression-based distances on 10 different random
concatenations of the NGS short reads simulated from the mtDNA
sequences using the Empirical (Illumina) model. Additional file 1: Table S1. Comparison of alignment-free distances and
the benchmark MSA distance for 29 mtDNA sequences. Table S2. Comparison of alignment-free distances and the benchmark MSA distance
for 29 mtDNA sequences and their short reads. Table S3. Comparison of
alignment-free distances and the benchmark co-phylog distance for 29
Escherichia/Shigella genomes and their short reads. Table S4. The list of 70
genomes in the class Gammaproteobacteria, their orders, and their
accession numbers. Table S5. Comparison of alignment-free distances and
the benchmark MSA distance for 70 Gammaproteobacteria genomes and
their short reads. Table S6. The list of 39 metagenomic samples and their
host species’ diet and gut physiology. Table S7. The parsimony score of
the clustering trees for 39 metagenomic samples. Table S8. Performance
of the compression-based distances on 10 different random
concatenations of the NGS short reads simulated from the mtDNA
sequences using the Empirical (Illumina) model. Additional file 2: Figure S1. Phylogenetic trees reconstructed from 29
mtDNA sequences using: (a) MSA, (b) dCDM, (c) CVTree (k = 10), (d)
dS
2(k = 8). Figure S2. Phylogenetic trees reconstructed from 29
Escherichia/Shigella genomes using: (a) co-phylog, (b) CVTree (k = 9), (c)
CVTree (k = 15), (d) CVTree (k = 21). Figure S3. Clustering tree
reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria
genomes using the MSA distance. Figure S4. Clustering tree reconstructed
from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the
distance CVTree (k = 7). Figure S5. Authors’ contributions The running time when using GenCompress to cal-
culate the compression-based measures for this data set
was ∼25 hours, about 3 times longer than that of CVTree. Compression tools developed specifically for NGS short
reads such as BEETL [35] and SCALCE [36] can be applied
to reduce the running time. We also expect that such NGS Conclusions The compression-based
measures, although not always producing the best dis-
tances, performed consistently well across all data sets
in the study without any optimization required. We
believe such a consistent performance is due to their
parameter-free feature. On the other hand, choosing
an optimal parameter k for each data set is of criti-
cal importance for using the k-mer based methods. This
task would become daunting when there is no bench-
mark (e.g., true phylogenetic trees or true classifica-
tions) available to guide the analysis and the selection
of k. Additional files ., 10 only took less than
20 minutes, but if all the values of k = 11, 12, . . ., 20
were included, the running time increased up to ∼8
hours. Additional file 3: Perl scripts and the example data set of 29 mtDNA
sequences. Additional file 3: Perl scripts and the example data set of 29 mtDNA
sequences. Competing interests
Th
h
d
l
h p
g
The authors declare that they have no competing interests. Authors’ contributions
XC designed the project. NHT performed the analysis and wrote the paper. Both authors have read and approved the manuscript. Authors’ contributions
XC designed the project. NHT performed the analysis and wrote the paper. Both authors have read and approved the manuscript. 1.
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Published: 29 May 2014 Received: 11 February 2014 Accepted: 16 May 2014
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Cite this article as: Tran and Chen: Comparison of next-generation
sequencing samples using compression-based distances and its
application to phylogenetic reconstruction. BMC Research Notes 2014 7:320. 15. Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F: Alignment-free sequence
comparison based on next-generation sequencing reads. J Comput
Biol 2013, 20:64–79. 16. Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H: An
information-based sequence distance and its application to whole
mitochondrial genome phylogeny. Bioinformatics 2001, 17:149–154. y
information-based sequence distance and its application to whole
mitochondrial genome phylogeny. Bioinformatics 2001, 17:149–154. 17. Li M, Chen X, Li X, Ma B, Vitanyi PMB: The similarity metric. IEEE Trans
Inform Theory 2004, 50:3250–3264. 18. Keogh E, Lonardi S, Ratanamahatana CA: Towards parameter-free data
mining. In Proceedings of the Tenth ACM SIGKDD International Conference
on Knowledge Discovery and Data Mining, 22-25 August 2004. Seattle, WA,
USA; 2004:206–215. 19. Otu HH, Sayood K: A new sequence distance measure for
phylogenetic tree construction. Bioinformatics 2003, 19:2122–2130. 20. Li M, Vitanyi PMB: An introduction to Kolmogorov complexity and its
applications: Springer; 2008. [http://www.springer.com/computer/
theoretical+computer+science/book/978-0-387-33998-6] 21. Benedetto D, Caglioti E, Loreto V: Language tree and zipping. Phys Rev
Lett 2002, 88:048702. 1.
Metzker ML: Sequence technologies - the next generation. Nat Rev
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and take full advantage of: 22. Ito K, Zuegmann T, Zhu Y: Recent experiences parameter-free data
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https://openalex.org/W3112721604 | https://europepmc.org/articles/pmc7794138?pdf=render | English | null | Characteristics of healthcare workers who died during the fight against COVID-19 in China | Pakistan journal of medical sciences | 2,020 | cc-by | 2,163 | ABSTRACT Coronavirus disease 2019 (COVID-19), first reported in December 2019 in Wuhan, China, has progressed
to a pandemic associated with substantial morbidity and mortality. Little is known about the healthcare
workers who died fighting the disease in China. This paper analyzed the data of 78 Chinese healthcare
workers who died in the fight against COVID-19 between 23 January and 2 June, 2020, and revealed the
following characteristics. First, compared to the number of deaths directly attributable to COVID-19,
more healthcare workers died from pre-existing disease attack induced by excessive fatigue or died from
accidents. Second, the median age of the healthcare workers who died directly from COVID-19 was younger
than that of the Wuhan non- healthcare workers who died of COVID 19. Third, although more women than
men were involved in fighting the pandemic, more men died. Fourth, more healthcare workers died in
Hubei than in other provinces. Fifth, most of the healthcare workers who died directly from COVID-19 were
non-professionals. KEYWORDS: Characteristics, healthcare workers, Fatality, COVID-19, China. doi: https://doi.org/10.12669/pjms.37.1.3384
How to cite this:
Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci. 2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. doi: https://doi.org/10.12669/pjms.37.1.3384
How to cite this:
Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci. 2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Short Communication Short Communication Characteristics of healthcare workers who died
during the fight against COVID-19 in China Yujun Wang1, Yun Ji2, Yuedong Wang3 Yujun Wang1, Yun Ji2, Yuedong Wang3 ABSTRACT Coronavirus disease 2019 (COVID-19), first
reported in December 2019 in Wuhan, Hubei
province, China, has progressed to a pandemic
associated
with
substantial
morbidity
and
mortality.1 By June 13, 2020, 83132 confirmed cases
had been reported in China, causing 4634 deaths.2
Responding to the pandemic, China focused on traditional public health outbreak response
tactics-isolation, quarantine, social distancing,
and community containment,3 which have never
before been implemented on such a large scale.4,5
Further, a total of 42,600 healthcare workers
(28,000 women) from other provinces were sent to
Hubei to fight the disease.6 i g
Although the disease has been controlled, the
whole country has paid a high price. Asides from
more than 116.9 billion RMB (approximately 16.5
billion USD) allocated for pandemic prevention
and control,7 there were public health interventions
and sacrifices that cannot be estimated in monetary
terms. On March 5, the Chinese government
announced a commendation list of advanced
collectives and individuals of the national health
system who had contributed to the prevention
and control of COVID-19 pandemic. A total of 506
healthcare workers were honored, but 34 of them
had died.8 Little is known about the healthcare
workers who died fighting the disease. This paper
analyzed the characteristics of 78 Chinese healthcare
workers who died in the fight against COVID-19. Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292
1. Yujun Wang, PhD. School of Humanities and International Education,
Zhejiang University of Science and Technology, Hangzhou, China;
Zhejiang Institute of New Media for Government Affairs,
Hangzhou, China. 2. Yun Ji, MD. Department of Surgical Intensive Care Unit,
3. Yuedong Wang, MD. Department of General Surgery,
2,3: Second Affiliated Hospital Zhejiang University School of Medicine,
Hangzhou, China. Correspondence:
Yuedong Wang, MD. Department of General Surgery,
Second Affiliated Hospital Zhejiang University School of Medicine,
Hangzhou 310009, China. E-mail: wydong2003@hotmail.com
* Received for Publication:
July 28, 2020
* Accepted for Publication:
October 5, 2020
Although the disease has been controlled, the
whole country has paid a high price. Asides from
more than 116.9 billion RMB (approximately 16.5
billion USD) allocated for pandemic prevention
and control,7 there were public health interventions
and sacrifices that cannot be estimated in monetary
terms. On March 5, the Chinese government
announced a commendation list of advanced
collectives and individuals of the national health
system who had contributed to the prevention
and control of COVID-19 pandemic. ABSTRACT A total of 506
healthcare workers were honored, but 34 of them
had died.8 Little is known about the healthcare
workers who died fighting the disease. This paper
analyzed the characteristics of 78 Chinese healthcare
workers who died in the fight against COVID-19. doi: https://doi.org/10.12669/pjms.37.1.3384
How to cite this:
Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci.
2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Correspondence: * Accepted for Publication: 292 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292 Yujun Wang et al. Based on official reports from government
agencies9 and reports from news websites, we
searched for information on the deaths of 78
Chinese medical workers during the pandemic
between 23 January and 2 June, 2020. The following
public access data were collected: age, gender, cause
of death, professional or not, and their location. Continuous variables are described as medians
and interquartile ranges (IQRs) and categorical
variables were described as numbers (proportions). The Mann-Whitney U test was applied to compare
continuous variables and the χ2 test or Fisher’s exact
test was used for categorical variables. respiratory medicine and intensive care, respiratory
medicine, gastroenterology, and traditional Chi-
nese medicine. Nine were from tertiary hospitals
(32.1%), including an otolaryngologist, three oph-
thalmologists and five surgeons (Fig.1). gi
g
(
g )
An analysis of the 78 healthcare workers revealed
the following characteristics. First, compared
to the number of deaths directly attributable to
COVID-19, more healthcare workers died from
pre-existing disease attack induced by excessive
fatigue or died from accidents. This means that
people with underlying morbidities such as heart
disease and encephalopathy are more at risk when
they are overtired or stressed. Second, the median
age of the 28 healthcare workers who died directly
from COVID-19 in the study was younger than that
of the Wuhan 44 non- healthcare workers who died
of COVID 19 as reported by Wu et al (55 versus 69
years).10 Not only were healthcare workers mostly
in employment who were younger than 60 years11,
but they were also under enormous physical and
psychological pressure during the pandemic. Third, although more women than men were
involved in fighting the pandemic, more men died. This may be because the female healthcare workers,
mostly nurses, were generally younger; the older
male healthcare workers may have had more
chronic diseases. In addition, the more difficult and
dangerous jobs are usually held by men. Fourth,
more healthcare workers died in Hubei than in
other provinces. This is likely because the outbreak g
Of the 78 deaths, 14 were female (17.9%) and 64
were male (82.1%), with a median age of 50 (IQR,
41-56) years. Forty-four came from Hubei province
(56.4%) and 34 from other provinces (43.6%). Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 293 a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments,
respiratory departments, or critical care departments. Correspondence: Twen-
ty-eight (35.9% ) died directly from COVID-19, and
the rest (64.1%) died from heart attacks, cerebrovas-
cular accidents, traffic or hotel collapse accidents,
fatigue and sudden unexplained death (Table-I). g
p
(
)
Of the 28 healthcare workers who died directly
from COVID-19, six were women (21.4%) and 22
were men (78.6%), with a median age of 55 (IQR,
43-62) years. Twenty-seven were from Hubei prov-
ince (96.4%) and one from Hainan province (3.6%). Fifteen of the healthcare workers (53.6%) were from
community or primary hospitals, all but a 59-year-
old female nurse were general practitioners (includ-
ing the one from Hainan province). Four (14.3%)
were from secondary hospitals, with specialties in stics of healthcare workers who died during the fight against COVID-19 in China. Table-I: Characteristics of healthcare workers who died during the fight against COVID-19 in China. Characteristic
Patients, No. (%)
Total
(n = 78)
Died of COVID-19
infection (n = 28)
Died of other diseases
(n = 50)
P value
Age, median (interquartile
range), y
50 (41-56)
55 (43-62)
49 (36-52)
0.005
Sex
0.549
Female
14 (17.9)
6 (21.4)
8 (16.0)
Male
64 (82.1)
22 (78.6)
42 (84.0)
Professionalsa
Yes
7 (9.0)
2 (7.1)
5 (10.0)
0.992
No
71 (91.0)
26 (92.9)
45 (90.0)
Died in Hubei province
Yes
44 (56.4)
27 (96.4)
17 (34.0)
< 0.001
No
34 (43.6)
1 (3.6)
33 (66.0)
a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments,
respiratory departments, or critical care departments. a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments,
respiratory departments, or critical care departments. Yujun Wang et al. Fi
1 Fig.1 was first and most severe in Hubei province, and the
whole society was unprepared and with a critical
shortage of personal protective equipment and
healthcare workers. Finally, most of the healthcare
workers who died directly from COVID-19 were
non-professionals. Non-professionals may not have
understood the severity of COVID-19 and likely
had not received relevant professional training or
received appropriate protection measures. 3. Wilder-Smith A, Freedman DO. Isolation, quarantine, social
distancing and community containment: pivotal role for old-style
public health measures in the novel coronavirus (2019-nCoV)
outbreak. J Travel Med. 2020:1-4 doi: 10.1093/jtm/taaa020 /j
/
4. Xiao Y, Torok ME. Taking the right measures to control COVID-19. Lancet Infect Dis 2020 Published Online March 5, 2020. doi: 10.1016/
S1473-3099(20)30152-3 5. Wu Z, McGoogan JM. Conflict of interests: Authors state no conflict of
interest. Conflict of interests: Authors state no conflict of
interest. Conflict of interests: Authors state no conflict of
interest. Correspondence: Characteristics of and Important Lessons
from the Coronavirus Disease 2019 (COVID-19) Outbreak in
China: Summary of a Report of 72 314 Cases from the Chinese Center
for Disease Control and Prevention. JAMA. 2020;323:1239–1242. doi:10.1001/jama.2020.2648 j
6. Feng H. Medical, Political, and Medical Bureau: National support to
the Hubei medical team exceeds 42,000 female medical staff accounts
for 2/3, Gmw.cn http://www.gmw.cn/, 2020-03-08, retrieved from
economy.gmw.cn http://economy.gmw.cn/, 2020-03-29. Therefore, rapid and transparent communication
is paramount when infectious diseases emerge12,
which can relieve people’s tension and anxiety. There must be enough healthcare workers who
know how to prevent and treat infectious diseases,
and they must be provided with adequate personal
protective equipment. y g
p
y g
7. The central people’s government of the People’s Republic of China,
The government at all levels allocated 116.9 billion yuan for epidemic
prevention and control, http://www.gov.cn/xinwen/2020-03/15/
content_5491446.htm. 2020-03-15 8. National Health Commission, Ministry of Human Resources
and Social Security, State Administration of Traditional Chinese
Medicine. Decision to commend advanced collectives and
individuals of the national health system for the prevention and
control of COVID-19 epidemic. 2020-03-05; http://fg.nujiang.cn/
html/2020/yaowen_0305_33323.htmli Funding: This work was supported by Zhejiang
University of Science and Technology basic science
research and special fund project (grant number
2019QN41). Funding: This work was supported by Zhejiang
University of Science and Technology basic science
research and special fund project (grant number
2019QN41). Funding: This work was supported by Zhejiang
University of Science and Technology basic science
research and special fund project (grant number
2019QN41). y
9. The State Council Information Office of the People’s Republic of
China. Fighting COVID-19: China in Action. http://www.scio.gov. cn/zfbps/ndhf/42312/Document/1682142/1682142.htm 10. Wu C, Chen X, Cai Y, Xia J, Zhou X, Xu S, et al. Risk Factors
Associated With Acute Respiratory Distress Syndrome and Death
in Patients With Coronavirus Disease 2019 Pneumonia in Wuhan,
China. JAMA Intern Med. Published online March 13, 2020; doi:
10.1001/jamainternmed.2020.0994 Conflict of interests: Authors state no conflict of
interest. REFERENCES /j
11. Wei Li , Jie Zhang , Shifu Xiao , Lin Sun , Characteristics of health
worker fatality in China during the outbreak of COVID-19 infection,
J Infect. 2020. doi: 10.1016/j.jinf.2020.03.030 1. Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. SARS-
CoV-2 Viral Load in Upper Respiratory Specimens of Infected
Patients. N Engl J Med. 2020;382:1177-1179 12. Petersen E, Hui D, Hamer DH, Blumberg L, Madoff LC, Pollack M,
et al. Li Wenliang, a face to the frontline healthcare worker. The first
doctor to notify the emergence of the SARS-CoV-2, (COVID-19),
outbreak. Int J Infect Dis. 2020;93:205-207. g
2. National Health Commission of the People’s Republic of China. Updates on the epidemic. June 14, 2020. http://www.nhc.gov.cn/
xcs/yqtb/list_gzbd. shtml (accessed June 14, 2020 [in Chinese]). 294 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 294 |
https://openalex.org/W4392168962 | https://www.mdpi.com/1996-1073/17/5/1113/pdf?version=1708951983 | English | null | Sintered Wick Heat Pipes with Excellent Heat Transfer Capabilities—Case Study | Energies | 2,024 | cc-by | 11,636 | energies energies Article Im-Nam Jang and Yong-Sik Ahn * Department of Materials Science and Engineering, Pukyong National University, Busan 48547, Republic of Korea;
imnam12@naver.com * Correspondence: ysahn@pknu.ac.kr; Tel.: +82-51-629-6361 Abstract: A sintered wick was formed in a heat pipe through the process of sintering a mixture
of copper powder with particle sizes of 100 µm and 200 µm, mixed with a pore-forming agent. The heat pipe’s thermal resistance, which affects its heat transfer efficiency, is determined during
manufacturing according to the powder type, thickness of the sintered wick, and filling rate of the
working fluid. Heat transfer efficiency was then tested at various inclination angles (0◦, 45◦, and 90◦)
to evaluate the performance of heat pipes. Regardless of the filling amount and test angle, the 200 µm
copper powder type exhibited superior heat transfer efficiency compared to the 100 µm type. After
analyzing heat transfer performance at various filling rates between 20% and 50%, it was determined
that the heat pipe’s optimal heat transfer capability occurred at a working fluid filling rate of 30%. The width of the wick was directly related to the heat transfer performance. Keywords: heat pipe; heat transfer performance; effective pore radius; capillary force; sintered wick;
working fluid filling ratio 1. Introduction https://doi.org/
10.3390/en17051113
Academic Editor: Marco Marengo
Received: 22 December 2023
Revised: 20 February 2024
Accepted: 23 February 2024
Published: 26 February 2024 1. Introduction The rapid development of the IT and electronics industries has recently complicated
the functional requirements for the performance of electronic equipment, and the high-
power consumption of this equipment has resulted in a shorter lifetime [1]. Due to the
limited space available, the heat dissipation system of aviation components experiences
high acceleration. Hence, the designer must take into account safety and operational
performance in dynamic conditions and various external environments, covering a wide
range of frigid temperatures (−30 ◦C to 45 ◦C). Therefore, it is important to ensure the
preservation of a specific standard of performance. Cylindrical copper heat pipes are
ideal for heat dissipation in aircraft electrical components due to their exceptional thermal
conductivity and efficient use of space. The heat pipes effectively maintain a consistent
temperature for the heating element. Originally designed to control satellite temperatures,
they are now widely used in different industries and applications in the electronics sector. These applications provide phase-change heat transfer with high thermal conductivity,
and a number of automatic temperature characteristics for lifetime and cost-effectiveness,
among other benefits [2]. The heat pipe utilizes copper wicks mounted on the inner wall
of the copper pipes to circulate the working fluid from the condensing portion to the
evaporation section and back again [3]. Heat is transferred to the working fluid in the
evaporator through conduction, causing vaporization at the wick surface. This increases the
local pressure inside the evaporator and enables the vapor to move towards the condenser. Heat is extracted at the condenser, causing the vapor to condense on the wick surface and
release latent heat. Heat pipes have a significant advantage over traditional devices due to
their high thermal conductance in a steady state [4]. Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with
Excellent Heat Transfer
Capabilities—Case Study. Energies
2024, 17, 1113. https://doi.org/
10.3390/en17051113
Academic Editor: Marco Marengo
Received: 22 December 2023
Revised: 20 February 2024
Accepted: 23 February 2024
Published: 26 February 2024 Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with
Excellent Heat Transfer
Capabilities—Case Study. Energies
2024, 17, 1113. https://doi.org/
10.3390/en17051113
Academic Editor: Marco Marengo
Received: 22 December 2023
Revised: 20 February 2024
Accepted: 23 February 2024
Published: 26 February 2024 Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with
Excellent Heat Transfer
Capabilities—Case Study. Energies
2024, 17, 1113. Of these requirements, achieving high porosity and permeabil-
ity through sintering technology is especially important for the production of heat pipe
wicks. Hence, this study applies the wick production parameters—porosity, permeability,
and capillary force—which have a notable influence on the heat pipes’ performance, using
the data obtained from previous research [5]. The heat transfer efficiency of heat pipes was
evaluated under various conditions, including different tilting angles, copper powder
sizes, wick thicknesses, and working fluid filling ratios. gli
g
Figure 1 shows the operational boundaries of a sintered wick heat pipe [6]. It defines
the limits of heat pipe performance. Each of these limitations is distinct, independent, and
not interconnected. By applying individual analysis techniques for each limitation, it is
possible to calculate the heat transport capacity based on the mean operating temperature
(adiabatic vapor temperature). The distinct performance limits define an operational range,
which is represented by the region enclosed by the combination of these individual limits. The operational range of the heat pipe is essentially the specific region or combination
of temperatures and maximum transfer capacity within which it is designed to operate. Therefore, it is possible to either improve the design or ensure that the heat pipe can
effectively transfer the necessary thermal load. Also, it is important to keep in mind that
the determination of the average operating temperature is essential for the calculation of
the heat transport capacity. The operating temperature of a standard heat pipe is generally
determined by the heat input. Therefore, the heat transfer and operating temperature are
interrelated. The transfer capacity of a heat pipe is influenced by several factors, including
the working fluid, the wick structure, the dimensions of the heat pipe, and the operating
temperature [7]. Figure 1 shows the operational boundaries of a sintered wick heat pipe [6]. It defines
the limits of heat pipe performance. Each of these limitations is distinct, independent, and
not interconnected. By applying individual analysis techniques for each limitation, it is
possible to calculate the heat transport capacity based on the mean operating temperature
(adiabatic vapor temperature). The distinct performance limits define an operational
range, which is represented by the region enclosed by the combination of these individual
limits. The operational range of the heat pipe is essentially the specific region or combina-
tion of temperatures and maximum transfer capacity within which it is designed to oper-
ate. Copyright: © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). The main factors affecting heat pipe performance include the maximum heat transfer
capacity, heat conduction coefficient, heat transfer limit, and thermal resistance. Specifically, https://www.mdpi.com/journal/energies Energies 2024, 17, 1113. https://doi.org/10.3390/en17051113 Energies 2024, 17, 1113
Energies 2024, 17, x FOR 2 of 12
2 of 12 the capillary limit of copper wick is the most important variable that determines the
temperature range and heat transfer limits of ground-based heat pipes, out of all the
different factors that affect heat transfer. Specifically, the capillary limit of copper wick is the most important variable that deter-
mines the temperature range and heat transfer limits of ground-based heat pipes, out of
all the different factors that affect heat transfer. Th
ill
li
i i
l i
d
i k h
i
i i fl
d b
l f the capillary limit of copper wick is the most important variable that determines the
temperature range and heat transfer limits of ground-based heat pipes, out of all the
different factors that affect heat transfer. Specifically, the capillary limit of copper wick is the most important variable that deter-
mines the temperature range and heat transfer limits of ground-based heat pipes, out of
all the different factors that affect heat transfer. Th
ill
li
i i
l i
d
i k h
i
i i fl
d b
l f The capillary limit in metal sintered wick heat pipes is influenced by several factors,
including the diameter and shape of pores, as well as the porosity, permeability, and thick-
ness of the sintered body. Of these requirements, achieving high porosity and permeability
through sintering technology is especially important for the production of heat pipe wicks. Hence, this study applies the wick production parameters—porosity, permeability, and
capillary force—which have a notable influence on the heat pipes’ performance, using the
data obtained from previous research [5]. The heat transfer efficiency of heat pipes was
evaluated under various conditions, including different tilting angles, copper powder sizes,
wick thicknesses, and working fluid filling ratios. The capillary limit in metal sintered wick heat pipes is influenced by several factors,
including the diameter and shape of pores, as well as the porosity, permeability, and thick-
ness of the sintered body. Therefore, it is possible to either improve the design or ensure that the heat pipe can
effectively transfer the necessary thermal load. Also, it is important to keep in mind that
the determination of the average operating temperature is essential for the calculation of
the heat transport capacity. The operating temperature of a standard heat pipe is generally
determined by the heat input. Therefore, the heat transfer and operating temperature are
interrelated. The transfer capacity of a heat pipe is influenced by several factors, including
the working fluid, the wick structure, the dimensions of the heat pipe, and the operating
temperature [7]. Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation
Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△𝑃,௫) to exceed the
overall pressure drop within the pipe for it to operate effectively. This pressure drop con-
sists of three components, namely the pressure drop (△𝑃) necessary for the liquid to be
transferred from the condenser back to the evaporator, the pressure differential (△𝑃௩) re-
quired for the vapor to move from the evaporator to the condenser, and the gravitational
head, which varies based on the heat pipe’s inclination, determines the pressure (△𝑃),
and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is
Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation
Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△Pc,max) to exceed the
overall pressure drop within the pipe for it to operate effectively. This pressure drop
consists of three components, namely the pressure drop (△Pl) necessary for the liquid to
be transferred from the condenser back to the evaporator, the pressure differential (△Pv)
required for the vapor to move from the evaporator to the condenser, and the gravitational
head, which varies based on the heat pipe’s inclination, determines the pressure (△Pg),
and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it
is essential that this condition is fulfilled; otherwise, the wick in the evaporator section Figure 1. Limitations to heat transport in a heat pipe. C
ill
Li it ti
Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation Figure 1. Limitations to heat transport in a heat pipe. Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation
Capillary Limitation p
y
Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△𝑃,௫) to exceed the
overall pressure drop within the pipe for it to operate effectively. This pressure drop con-
sists of three components, namely the pressure drop (△𝑃) necessary for the liquid to be
transferred from the condenser back to the evaporator, the pressure differential (△𝑃௩) re-
quired for the vapor to move from the evaporator to the condenser, and the gravitational
head, which varies based on the heat pipe’s inclination, determines the pressure (△𝑃),
and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is
Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△Pc,max) to exceed the
overall pressure drop within the pipe for it to operate effectively. This pressure drop
consists of three components, namely the pressure drop (△Pl) necessary for the liquid to
be transferred from the condenser back to the evaporator, the pressure differential (△Pv)
required for the vapor to move from the evaporator to the condenser, and the gravitational
head, which varies based on the heat pipe’s inclination, determines the pressure (△Pg),
and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it
is essential that this condition is fulfilled; otherwise, the wick in the evaporator section Energies 2024, 17, 1113 3 of 12 will become depleted of moisture (dried out). The capillary limit refers to the maximum
allowable heat flux at which Equation (1) [8] maintains valid. The Laplace–Young equation,
represented by Equation (2), determines the highest capillary pressure (△Pc) generated
within the wick structure of a heat pipe [8]. △Pc,max ≥△Pl + △Pv + △Pg
(1)
△Pc = 2σl
re f f
·cos(θ)
(2) (1) (2) where σl is the free surface energy of the working fluid and re f f corresponds the effective
pores radius of the wick, which can be determined for different wick structures, while θ
is the contact angle between the fluid and the wick. The contact angle refers to the extent
to which a liquid can spread or wet the surface of a wick structure. When a liquid wets a
surface, the contact angle θ will be between 0 and π/2 radians. Capillary Limitation
Capillary Limitation However, for liquids that
do not wet the surface, the contact angle θ will be greater than π/2. The capillary limitation
in heat pipes occurs when the combined capillary forces produced by the vapor–liquid
interfaces in the evaporator and condenser are insufficient to compensate for the pressure
losses caused by fluid movement. Consequently, the heat pipe evaporator becomes dried
out, causing a stoppage of thermal energy transfer from the evaporator to the condenser. 2.1. Experimental Set Up The opposite end was linked to a
vacuum pump in order to eliminate air and non-condensable gas from the tube. p
g p
p p
p
y
g
weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was
manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2
g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a
basic test was conducted to prevent any leakage or improper sealing, which could result
in a decline in the heat pipe’s efficiency. y
g
g
p
p
four hours. Subsequently, the temperature was increased to 950 °C and then held for two
and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol,
one of the pipe ends was completely sealed using specialized equipment. The opposite
end was linked to a vacuum pump in order to eliminate air and non-condensable gas from
the tube. reducing atmosphere, with the temperature raised to 850 ◦C and maintained for four hours. Subsequently, the temperature was increased to 950 ◦C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe
ends was completely sealed using specialized equipment. The opposite end was linked to a
vacuum pump in order to eliminate air and non-condensable gas from the tube. p
g p
p p
p
y
g
weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was
manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2
g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a
basic test was conducted to prevent any leakage or improper sealing, which could result
in a decline in the heat pipe’s efficiency. y
g
g
p
p
four hours. Subsequently, the temperature was increased to 950 °C and then held for two
and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol,
one of the pipe ends was completely sealed using specialized equipment. The opposite
end was linked to a vacuum pump in order to eliminate air and non-condensable gas from
the tube. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. Figure 2. 2.1. Experimental Set Up Schematic illustration of the internal layout of a pipe before the sintering. The working fluid, made up of distilled water, was filled after the vacuu
set up. The manufacturing process of a sintered heat pipe was completed by
weld pinch-off device to seal the opposite end in a similar manner. Each h
manufactured with the same dimensions for each filling ratio of the working
g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were
basic test was conducted to prevent any leakage or improper sealing, which
in a decline in the heat pipe’s efficiency. o preve
e’s effic Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. 2.2. Experimental Apparatus and Procedure
In order to measure the thermal efficiency of a heat pipe, a standardized testing ap-
paratus was set up. This apparatus included an experimental sector, a heating section, a
cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA,
DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating
system is usually used to evaluate the efficiency of heat pipes. This method is similar to
natural convection evaluation techniques except for the use of water cooling The temper
The working fluid, made up of distilled water, was filled after the vacuum pump was
set up. The manufacturing process of a sintered heat pipe was completed by using a cold
weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was
manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2 g),
30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a basic test
was conducted to prevent any leakage or improper sealing, which could result in a decline in
the heat pipe’s efficiency. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. 2.1. Experimental Set Up The experimental parameter is shown in Table 1. A copper tube sized 160 mm in
length was used in the manufacturing of sintered heat pipes. All heat pipes had an outer
diameter of 4 mm and an inner diameter of 3.6 mm. For the manufacturing of sintered heat
pipes, two distinct copper powders were used. The first type had an average particle size of
100 µm and showed a relatively consistent size distribution. On the other hand, the second
type of powder had an average particle size of 200 µm and showed a varied particle size
distribution. The experiment used potassium carbonate (K2CO3) as the pore-forming agent,
which exhibited a spherical morphology with an average diameter of 35 µm. A mixture
was prepared by combining copper powder with a pore-forming agent, which was present
at a concentration of 40%. Table 1. Experimental parameters of heat pipes with wick. Parameters
Value
Pipe material
Copper
Outer diameter of pipe, Dwall/mm
4
Inner diameter of pipe, Di/mm
3.6
Total length, L/mm
160
Evaporator length, Le/mm
23
Adiabatic length, La/mm
87
Condenser length, Lc/mm
50
Wick material
Copper powder
Spherical copper power size, d/µm
100 (uniformity), 200 (diversity)
Wick thickness [µm]
902, 534, 179
Working fluid
Distilled water
Filling ratio [% vol.]
20 (0.2 g), 30 (0.3 g), 40 (0.4 g), 50 (0.5 g) Table 1. Experimental parameters of heat pipes with wick. The heat pipe’s sintered wick was manufactured using a solid-state sintering method. Figure 2 represents a schematic of the heat pipe with wick before the process of sintering. A ceramic bar, with diameters of 1.5 mm, 2 mm, and 2.5 mm, was inserted into the pipe
as the inner mandrel after the swaging process, which had caused one end of the pipe to
shrink [9]. According to the study conducted by Jang et al. [5], the vertically positioned pipes
containing powdered substances were subjected to the predetermined temperature schedule
for sintering within the furnace. The sintering process was carried out under a hydrogen Energies 2024, 17, 1113 4 of 12
erature
d reducing atmosphere, with the temperature raised to 850 ◦C and maintained for four hours. Subsequently, the temperature was increased to 950 ◦C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe
ends was completely sealed using specialized equipment. q
ature of each component was measured us
l
d d h
h
h l
2.2. Experimental Apparatus and Procedure
2.2. Experimental Apparatus and Procedure
I
d
t
th th
l ffi The thermocouples were placed at distances
of Le = 23 mm, La = 87 mm, and Lc = 50 mm from the starting point of the evaporator
section. Each thermocouple was affixed to its respective center within each division using
heat-resistant polyimide tape (Kapton). Thermal grease was sprayed to the heat block and
cooling plate in order to enhance thermal conductivity where they were in contact with
the heat pipe. Each test sector was covered with an insulation block to reduce the heat loss
from the evaporator, adiabatic, and condenser sections, all of which were fastened with
jointers. The heat pipe inclination angle was adjusted from 0◦to 90◦for the tilting angle
test, using a variable angle holding table. The DC power supply is employed for setting the
heat power input for the evaporator section. Furthermore, the temperature data in a stable
state were recorded using a data logger, with an interval of approximately 60 min between
each input heating load. The computer also stored steady-state temperature data for the
purpose of data reduction and analysis [10]. been divided into two groups for the evaporator, with one group for the adiabatic section
and the other group for the condenser section. The thermocouples were placed at dis-
tances of Le = 23 mm, La = 87 mm, and Lc = 50 mm from the starting point of the evaporator
section. Each thermocouple was affixed to its respective center within each division using
heat-resistant polyimide tape (Kapton). Thermal grease was sprayed to the heat block and
cooling plate in order to enhance thermal conductivity where they were in contact with
the heat pipe. Each test sector was covered with an insulation block to reduce the heat loss
from the evaporator, adiabatic, and condenser sections, all of which were fastened with
jointers. The heat pipe inclination angle was adjusted from 0° to 90° for the tilting angle
test, using a variable angle holding table. The DC power supply is employed for setting
the heat power input for the evaporator section. Furthermore, the temperature data in a
stable state were recorded using a data logger, with an interval of approximately 60 min
between each input heating load. The computer also stored steady-state temperature data
for the purpose of data reduction and analysis [10]. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo-
couples. Figure 4. q
ature of each component was measured us
l
d d h
h
h l
2.2. Experimental Apparatus and Procedure
2.2. Experimental Apparatus and Procedure
I
d
t
th th
l ffi ply provided heat to the evaporator, while the chiller was used to cool the condenser with
water. In order to measure the thermal efficiency of a heat pipe, a standardized testing
apparatus was set up. This apparatus included an experimental sector, a heating section, a
cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA,
DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating
system is usually used to evaluate the efficiency of heat pipes. This method is similar
to natural convection evaluation techniques, except for the use of water cooling. The
temperature of each component was measured using K-type thermocouples. The DC
power supply provided heat to the evaporator, while the chiller was used to cool the
condenser with water. In order to measure the thermal efficiency of a heat pipe, a standardized testing ap-
paratus was set up. This apparatus included an experimental sector, a heating section, a
cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA,
DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating
system is usually used to evaluate the efficiency of heat pipes. This method is similar to
natural convection evaluation techniques, except for the use of water cooling. The temper-
ature of each component was measured using K-type thermocouples. The DC power sup-
ply provided heat to the evaporator, while the chiller was used to cool the condenser with
water. Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. ematic il Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. The experimental procedure for conducting the temperature rise test at each tilting
angle was as follows: At first, the samples were fastened onto the test bench. Secondly,
as shown in Figure 4, six thermocouples were positioned on the wall surfaces of the heat
tubes, cartridge heater, cooling plate, and ambient temperature. The thermocouples have Energies 2024, 17, 1113 5 of 12
ndly, as
he heat 5 of 12
ndly, as
he heat been divided into two groups for the evaporator, with one group for the adiabatic section
and the other group for the condenser section. q
ature of each component was measured us
l
d d h
h
h l
2.2. Experimental Apparatus and Procedure
2.2. Experimental Apparatus and Procedure
I
d
t
th th
l ffi Schematic illustration of the configuration of the test device and the locations of thermocouples. Th
ll th
l
i t
f
h
t
i
d fi
d b th f ll
i
E
ti
(3) [11] Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo-
Figure 4. Schematic illustration of the configuration of the test device and the locations of thermocouples. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo-
couples. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermocouples. Th
ll th
l
i t
f
h
t
i
d fi
d b th f ll
i
E
ti
(3) [11] uples. The overall thermal resistance of a heat pipe defined by the following Equation (3) [11]: e of a heat pipe defined by the following Equation (3)
𝑇
𝑇
R = Teva. −Tcon. . Q
(3) n (3)
(3) . Q 𝑅=
௩. . 𝑄ሶ
(3)
where 𝑇௩. and 𝑇. are the temperature of the evaporator and condenser sections, re-
spectively. The heat input power, denoted as Q ̇, is controlled by the voltage (V) and am-
perage (I). The occurrence of heat pipe dry-out has been attributed to a rapid increase in
thermal resistance If an abrupt change occurs the test is stopped and the sample is ex
where Teva. and Tcon. are the temperature of the evaporator and condenser sections, respec-
tively. The heat input power, denoted as
. Q, is controlled by the voltage (V) and amperage
(I). The occurrence of heat pipe dry-out has been attributed to a rapid increase in thermal
resistance. If an abrupt change occurs, the test is stopped, and the sample is extracted from
the device. Conversely, the input power gradually increases once more. 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type Figure 5c,d shows that the heat pipe encountered operational challenges and
showed a notable initial thermal resistance when the filling ratios were set at 40% and
50%. Therefore, even after subjecting the heat block to a rise in temperature of 120 °C, it
was not possible to determine the dry out point
Figure 5a shows the thermal resistance values of the 100 U and 200 D samples when
the working fluid filling level is at 20%. When the test is conducted at angles of 45◦and
90◦, the 100 U sample exhibits dry-out at a heat input of 3.5 W. However, the 200 D sample
has a higher Qmax value of 10 W or more. At a 30% filling ratio of the working fluid,
the thermal resistance of 100 U is higher than that of 200 D, as shown in Figure 5b. The
specimens showed comparable drying out points at both 45◦and 90◦, with few differences. Nevertheless, the thermal resistance of the 200 D specimen was determined to be lower
than 100 U. Figure 5c,d shows that the heat pipe encountered operational challenges and
showed a notable initial thermal resistance when the filling ratios were set at 40% and 50%. Therefore, even after subjecting the heat block to a rise in temperature of 120 ◦C, it was not
possible to determine the dry-out point. was not possible to determine the dry-out point. Based on the previous capillary force test results, it is evident that the capillary force
(△𝑃) is influenced by a complex correlation with both the porosity and the effective ra-
dius of the wick’s pores (𝑟). The 100 U sample had the largest 𝑟 value of 241.31 µm,
and the 200 D sample had the lowest one of 155.73 µm. Furthermore, the porosity value
of 100 U was found to be 59.07%, which was higher than the porosity value of 200 D, which
was estimated to be 56.47% [5]. Nevertheless, the 200 D sample exhibited stronger capil-
lary forces. This could be attributed to the smaller effective radius (𝑟) value, which in-
dicates that the capillary force is mainly affected by the 𝑟 value. Moreover, empirical
p
y
p
Based on the previous capillary force test results, it is evident that the capillary force
(△Pc) is influenced by a complex correlation with both the porosity and the effective radius
of the wick’s pores (re f f ). 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type Figure 5 shows the thermal resistance results for samples 100 U and 200 D. The test
angles of 0◦, 45◦, and 90◦are included, as well as the working fluid filling ratio, which ranges
from 20% to 50%. The sintering process used a mandrel of 2 mm in diameter, resulting in the
formation of a wick with a thickness of 534.7 µm. For heat inputs of 12 W or less, the overall
thermal resistance of the 200 D sample was lower than that of the 100 U sample. Energies 2024, 17, 1113 6 of 12
100 U Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and
filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and
filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and
filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and
filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5a shows the thermal resistance values of the 100 U and 200 D samples when
the working fluid filling level is at 20%. When the test is conducted at angles of 45° and
90°, the 100 U sample exhibits dry-out at a heat input of 3.5 W. However, the 200 D sample
has a higher Qmax value of 10 W or more. At a 30% filling ratio of the working fluid, the
thermal resistance of 100 U is higher than that of 200 D, as shown in Figure 5b. The speci-
mens showed comparable drying out points at both 45°and 90°, with few differences. Nev-
ertheless, the thermal resistance of the 200 D specimen was determined to be lower than
100 U. 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type The 100 U sample had the largest re f f value of 241.31 µm, and
the 200 D sample had the lowest one of 155.73 µm. Furthermore, the porosity value of
100 U was found to be 59.07%, which was higher than the porosity value of 200 D, which
was estimated to be 56.47% [5]. Nevertheless, the 200 D sample exhibited stronger capillary
forces. This could be attributed to the smaller effective radius (re f f ) value, which indicates
that the capillary force is mainly affected by the re f f value. Moreover, empirical evidence
suggests that the powder filling density of 200 D is higher than that of 100 U, primarily
because it covers a wider range of particle sizes. Therefore, applying a 200 D powder-based
wick has significant advantages in creating small, efficient pore sizes. This corresponds to
the observation that 200 D has superior thermal conductivity compared to 100 U. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The average thickness of the wick structure was measured to
534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectiv
4, 17, x FOR PEER REVIEW ing the wick to become wet in m
amount of working fluid that h
wick is excessively thick. Moreo
e in the cross-sectional area avail
uently, the friction coefficient of v
onstraint on the maximum heat
ough, the passage becomes too s section is contr
directions. As a
transported to
cessive thickne
the passage of
the vapor flow
capacity. Conv olled by the capillary force, cau
result, there is a decrease in the
he evaporation section when the
s of the wick leads to a decreas
vapor through the pipe. Consequ
passage rises, thus serving as a c
rsely, if the wick is not thick en lled b ng th Figure 6. SEM images of the cross-section of a sintered heat pipe according to the th
wick. (a) 902 µm (mandrel: 1.5 mm𝜙), (b) 534.7 µm (mandrel: 2 mm𝜙), and (c) 179.1
2.5 mm𝜙). Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thickness of the
wick. (a) 902 µm (mandrel: 1.5 mmϕ), (b) 534.7 µm (mandrel: 2 mmϕ), and (c) 179.1 µm (mandrel:
2.5 mmϕ). the condensed working fluid in the condensation sector to be transported to th
sector by capillary force. The experimental results in this study coincide with the theory mentioned
indicating that the optimal thermal transfer performance was attained by empl Figure 7 shows the thermal resistance measured in the 100 U sample wh
the mandrel diameters and tilt angles. The thermal resistance primarily dep
surface area of the interface between the liquid and vapor phases, as indicated
ical analysis [12]. The sample with the smallest wick thickness (tw) of 179.1 µ
diameter: 1.5 mm) showed the highest thermal resistance, indicating the low
transfer capability in comparison to all other tested samples. Furthermore, the
mal resistance of this sample exhibited a notable difference compared to the
sistance of the other samples. In addition, the temperature at the evaporator
creased quickly in response to the heat input, ultimately reaching a maximum
a heat input of 5 W. The substantial rise in temperature caused difficulties fo
determining the final Qmax value. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The present problems come from the inade
ness of the sintered wick, hindering the effective transfer of the condensed w
from the condenser section to the evaporator section via capillary force. Th
pipe with the thinnest wick exhibited a comparatively lower heat transfer effi
the pipe with a thicker wick. The heat resistance remained consistently low for both the 902 µm and 534
Figure 7 shows the thermal resistance measured in the 100 U sample while varying
the mandrel diameters and tilt angles. The thermal resistance primarily depends on
the surface area of the interface between the liquid and vapor phases, as indicated by
theoretical analysis [12]. The sample with the smallest wick thickness (tw) of 179.1 µm
(mandrel diameter: 1.5 mm) showed the highest thermal resistance, indicating the lowest
thermal transfer capability in comparison to all other tested samples. Furthermore, the
initial thermal resistance of this sample exhibited a notable difference compared to the
thermal resistance of the other samples. In addition, the temperature at the evaporator
section increased quickly in response to the heat input, ultimately reaching a maximum
of 70 ◦C at a heat input of 5 W. The substantial rise in temperature caused difficulties
for accurately determining the final Qmax value. The present problems come from the
inadequate thickness of the sintered wick, hindering the effective transfer of the condensed
working fluid from the condenser section to the evaporator section via capillary force. Therefore, the pipe with the thinnest wick exhibited a comparatively lower heat transfer
efficiency than the pipe with a thicker wick. medium-sized wick thickness of 534.7 µm, which was produced using a mandrel
diameter of 2 mm. When the angle is 0°, it is observed that the thermal resistance of the wick
thickness of 902 µm is relatively lower than that of the wick with a thickness of 53
This difference can be attributed to the preferential movement of the working fluid
the heat pipe towards one side, caused by the force of gravity. This bias results fr
basic assumption that the wick on one side initiates its operation at relatively low
peratures. Reducing the thickness of the wick causes the absorbed working fluid t
mulate mostly on the lower side of the heat pipe. The formation of a bubble barrier
as a result of the large amount of working fluid, even at lower temperatures, whi
ders the vapor’s movement. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle ickness of the wick increases, the surface area of liquid that ca
so increases. This leads to a reduction in the pressure drop be
e easily through the wick. However, Li, Y et al. [13] observed
eased in direct proportion to the increase in the thickness of thicknesses, re
with a wick th
pipe with a th
the heat pipe w
fer capability. por passage as
surface area th
As the thi
by the wick als
can flow more hrough the w
direct propor p
p
wick. They explained that the movement of the working fluid towards the
Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel d
and tilt angles: (a) 0°, (b) 45°, and (c) 90°. The wick was made with 100 U powder and fill
was 30%. Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel diameters
and tilt angles: (a) 0◦, (b) 45◦, and (c) 90◦. The wick was made with 100 U powder and filling ratio
was 30%. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ra
Figure 8 shows the heat transfer performance of the heat pipe in relation to the
ratio (Rf) of the working fluid at various tilting angles. The heat pipes in the experi
setup used a wick with the same wick thickness of 534.7 µm (mandrel diameter:
which was made by employing 200 D copper powder. Samples were prepared by in
0.2 g (Rf = 20%), 0.3 g (Rf = 30%), 0.4 g (Rf = 40%), and 0.5 g (Rf = 50%) of the workin
into the heat pipe, giving a total filling amount of 1 g. At a filling ratio (Rf) of 50%, the thermal resistance exhibited the highest valu
test angles. In addition, the thermal resistance showed a tendency to decrease as th
The heat resistance remained consistently low for both the 902 µm and 534.7 µm wick
thicknesses, regardless of the test angle. Furthermore, it can be observed that the heat
pipe with a wick thickness of 534.7 µm has a higher dry-out temperature compared to the
heat pipe with a thickness of 902 µm at all tilting angles. Therefore, it can be concluded
that the heat pipe with a medium-sized wick thickness of 534.7 µm has the superior heat
transfer capability. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The heat pipe wicks were fabricated by sintering copper powders, with the inclusion
of ceramic inner mandrels sized 1.5, 2, and 2.5 mm in diameter. Figure 6 exhibits cross-
sectional SEM images of a heat pipe with a wick that has been installed subsequent to the Energies 2024, 17, 1113 7 of 12
, with th sintering process. The average thickness of the wick structure was measured to be 902 µm,
534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectively. sectional SEM images of a heat pipe with a wick that has been installed subseq
sintering process. The average thickness of the wick structure was measured to
534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectiv
Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thi
wick. (a) 902 µm (mandrel: 1.5 mm𝜙), (b) 534.7 µm (mandrel: 2 mm𝜙), and (c) 179.1 µ
2.5 mm𝜙). Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thickness of the
wick. (a) 902 µm (mandrel: 1.5 mmϕ), (b) 534.7 µm (mandrel: 2 mmϕ), and (c) 179.1 µm (mandrel:
2.5 mmϕ). 4, 17, x FOR PEER REVIEW
section is controlled by the capillary force, causing the wick to become wet in m
directions. As a result, there is a decrease in the amount of working fluid that ha
transported to the evaporation section when the wick is excessively thick. Moreov
cessive thickness of the wick leads to a decrease in the cross-sectional area availa
the passage of vapor through the pipe. Consequently, the friction coefficient of v
the vapor flow passage rises, thus serving as a constraint on the maximum heat t
capacity. Conversely, if the wick is not thick enough, the passage becomes too sm
the condensed working fluid in the condensation sector to be transported to the
sector by capillary force. The experimental results in this study coincide with the theory mentioned
indicating that the optimal thermal transfer performance was attained by emplo sintering process. The average thickness of the wick structure was measured to be 902 µm,
534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectively. g
p p
q
sintering process. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle Consequently, it has been determined that the initial t
resistance exhibited a significant value [14]. Therefore, it is important to take into account two factors when determin
thickness of the wick. Firstly, the wick should be thick enough to enable the transfe
condensed internal working fluid from the condenser section to the vapor section
capillary force. Furthermore, it is also necessary that the internal space of the pipe
ficiently large to ensure a proper pathway for the flow of vapor. thicknesses, regardless of the test angle. Furthermore, it can be observed that th
with a wick thickness of 534.7 µm has a higher dry-out temperature compared
pipe with a thickness of 902 µm at all tilting angles. Therefore, it can be con
the heat pipe with a medium-sized wick thickness of 534.7 µm has the superior
fer capability. This phenomenon can be explained by the decrease in the widt
por passage as the wick thickness increases, along with the corresponding inc
surface area that comes into contact with the working fluid. As the thickness of the wick increases, the surface area of liquid that can b
by the wick also increases. This leads to a reduction in the pressure drop becau
can flow more easily through the wick. However, Li, Y et al. [13] observed th
sure loss increased in direct proportion to the increase in the thickness of th
wick. They explained that the movement of the working fluid towards the e
Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel di
and tilt angles: (a) 0°, (b) 45°, and (c) 90°. The wick was made with 100 U powder and filli
was 30%. Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel diameters
and tilt angles: (a) 0◦, (b) 45◦, and (c) 90◦. The wick was made with 100 U powder and filling ratio
was 30%. egardless of the test angle. Furthermore, it can be observed tha
hickness of 534.7 µm has a higher dry-out temperature compa
hickness of 902 µm at all tilting angles. Therefore, it can be c
with a medium-sized wick thickness of 534.7 µm has the supe
This phenomenon can be explained by the decrease in the w
s the wick thickness increases, along with the corresponding
hat comes into contact with the working fluid. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle This phenomenon can be explained by the decrease in the width of the
vapor passage as the wick thickness increases, along with the corresponding increase in the
surface area that comes into contact with the working fluid. test angles. In addition, the thermal resistance showed a tendency to decrease as th
input increased. The initial thermal resistance is very high due to the excessive am
As the thickness of the wick increases, the surface area of liquid that can be absorbed
by the wick also increases. This leads to a reduction in the pressure drop because the fluid Energies 2024, 17, 1113 8 of 12 can flow more easily through the wick. However, Li, Y et al. [13] observed that the pressure
loss increased in direct proportion to the increase in the thickness of the heat pipe wick. They explained that the movement of the working fluid towards the evaporation section is
controlled by the capillary force, causing the wick to become wet in multiple directions. As
a result, there is a decrease in the amount of working fluid that has to be transported to the
evaporation section when the wick is excessively thick. Moreover, excessive thickness of
the wick leads to a decrease in the cross-sectional area available for the passage of vapor
through the pipe. Consequently, the friction coefficient of vapor in the vapor flow passage
rises, thus serving as a constraint on the maximum heat transfer capacity. Conversely, if the
wick is not thick enough, the passage becomes too small for the condensed working fluid
in the condensation sector to be transported to the vapor sector by capillary force. 9
orking fluid, which requires more heat input to produce the latent heat of evapora p
p
y
p
y
The experimental results in this study coincide with the theory mentioned above,
indicating that the optimal thermal transfer performance was attained by employing a
medium-sized wick thickness of 534.7 µm, which was produced using a mandrel with a
diameter of 2 mm. g
q
p
p
p
he maximum permissible temperature for general electronic products employing s
onductors is 125 °C [15]. The dry-out temperature could not be determined, even w
he heat block temperature was raised to 130 °C or higher. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle Thus, when the heat pi
wick has a thickness of 534 7 µm it is evident that the heat transfer capacity significa When the angle is 0◦, it is observed that the thermal resistance of the wick with a thick-
ness of 902 µm is relatively lower than that of the wick with a thickness of
534.7 µm. This difference can be attributed to the preferential movement of the work-
ing fluid within the heat pipe towards one side, caused by the force of gravity. This bias
results from the basic assumption that the wick on one side initiates its operation at rela-
tively lower temperatures. Reducing the thickness of the wick causes the absorbed working
fluid to accumulate mostly on the lower side of the heat pipe. The formation of a bubble
barrier occurs as a result of the large amount of working fluid, even at lower temperatures,
which hinders the vapor’s movement. Consequently, it has been determined that the initial
thermal resistance exhibited a significant value [14]. ick has a thickness of 534.7 µm, it is evident that the heat transfer capacity significa
ecreases when it is filled to a rate of 50% due to excessive filling. On the other hand,
lling ratio (Rf) of 20%, the thermal resistance values consistently show the lowest lev
ndicating superior thermal transfer capability regardless of the tested angles. Howe
he dry-out point is relatively low, meaning that the pipe cannot effectively perform
ansfer at high temperatures. The samples with Rf = 30% and 40% exhibit the same
esistance values at angles of 45° and 90°, as shown in Figure 8b,c. Nevertheless, w
ubjected to a power exceeding 13 W, the sample with the Rf of 40% exhibits a slig
igher thermal resistance compared to the sample with the Rf of 30%. Two key requ
ments for an efficient heat pipe are low thermal resistance and a moderately high dry Therefore, it is important to take into account two factors when determining the
thickness of the wick. Firstly, the wick should be thick enough to enable the transfer of
the condensed internal working fluid from the condenser section to the vapor section
using capillary force. Furthermore, it is also necessary that the internal space of the pipe is
sufficiently large to ensure a proper pathway for the flow of vapor. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle ments for an efficient heat pipe are low thermal resistance and a moderately high dry
oint. According to these criteria, it can be concluded that this heat pipe exhibits optim
eat transfer properties when the filling ratio (Rf) of the working fluid is 30%. As the filling ratio (Rf) of the working fluid rises, there is a proportional increa
he amount of fluid that undergoes a phase transition into vapor, as well as an increa 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio
e quantity of fluid that returns back to a liquid state in the condenser section. Th
itial thermal resistance observed in the condenser section may be attributed to Figure 8 shows the heat transfer performance of the heat pipe in relation to the filling
ratio (Rf) of the working fluid at various tilting angles. The heat pipes in the experimental
setup used a wick with the same wick thickness of 534.7 µm (mandrel diameter: 2 mm),
which was made by employing 200 D copper powder. Samples were prepared by injecting
0.2 g (Rf = 20%), 0.3 g (Rf = 30%), 0.4 g (Rf = 40%), and 0.5 g (Rf = 50%) of the working fluid
into the heat pipe, giving a total filling amount of 1 g. nitial thermal resistance observed in the condenser section may be attributed to the p
nce of residual working fluid, which acts as a liquid barrier. Furthermore, when the
n extensive amount of fluid, the heat input required to convert the working fluid
apor also increases. In this case, the thermal resistance remains high at lower temp
ures. As the temperature rises, the liquid block reduces gradually, resulting in an incr
n heat transfer capacity. As it improves, the corresponding value of Qmax increases. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at di
ent test angles of (a) 0°, (b) 45°, and (c) 90°. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at different
test angles of (a) 0◦, (b) 45◦, and (c) 90◦. gure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at d
nt test angles of (a) 0°, (b) 45°, and (c) 90°. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at different
test angles of (a) 0◦, (b) 45◦, and (c) 90◦. Energies 2024, 17, 1113 9 of 12 At a filling ratio (Rf) of 50%, the thermal resistance exhibited the highest value at all
test angles. In addition, the thermal resistance showed a tendency to decrease as the heat
input increased. The initial thermal resistance is very high due to the excessive amount of
working fluid, which requires more heat input to produce the latent heat of evaporation. The maximum permissible temperature for general electronic products employing semicon-
ductors is 125 ◦C [15]. The dry-out temperature could not be determined, even when the
heat block temperature was raised to 130 ◦C or higher. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio
e quantity of fluid that returns back to a liquid state in the condenser section. Th
itial thermal resistance observed in the condenser section may be attributed to Thus, when the heat pipe’s wick has
a thickness of 534.7 µm, it is evident that the heat transfer capacity significantly decreases
when it is filled to a rate of 50% due to excessive filling. On the other hand, at a filling ratio
(Rf) of 20%, the thermal resistance values consistently show the lowest levels, indicating
superior thermal transfer capability regardless of the tested angles. However, the dry-out
point is relatively low, meaning that the pipe cannot effectively perform heat transfer at
high temperatures. The samples with Rf = 30% and 40% exhibit the same heat resistance
values at angles of 45◦and 90◦, as shown in Figure 8b,c. Nevertheless, when subjected to a
power exceeding 13 W, the sample with the Rf of 40% exhibits a slightly higher thermal
resistance compared to the sample with the Rf of 30%. Two key requirements for an effi-
cient heat pipe are low thermal resistance and a moderately high dry-out point. According
to these criteria, it can be concluded that this heat pipe exhibits optimum heat transfer
properties when the filling ratio (Rf) of the working fluid is 30%.il As the filling ratio (Rf) of the working fluid rises, there is a proportional increase in
the amount of fluid that undergoes a phase transition into vapor, as well as an increase
in the quantity of fluid that returns back to a liquid state in the condenser section. The
higher initial thermal resistance observed in the condenser section may be attributed to the
presence of residual working fluid, which acts as a liquid barrier. Furthermore, when there
is an extensive amount of fluid, the heat input required to convert the working fluid into
vapor also increases. In this case, the thermal resistance remains high at lower temperatures. As the temperature rises, the liquid block reduces gradually, resulting in an increase in heat
transfer capacity. As it improves, the corresponding value of Qmax increases. EW
10 of 12 Figure 9 shows a schematic diagram illustrating the progressive change in a liquid-
vapor state in a heat pipe. The heat pipe contains a wick with a thickness of 534.7 µm,
which is made of 200 D powder. This transition proceeds as the temperature rises. During
the initial stage, when the evaporation sector is being heated, the heat pipe exhibits a
significant level of thermal resistance until the vapor is generated. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio
e quantity of fluid that returns back to a liquid state in the condenser section. Th
itial thermal resistance observed in the condenser section may be attributed to Subsequently, despite
a rise in temperature and the resulting generation of vapor in the evaporation sector, the
presence of bubble blocks hinders the movement of vapor [16]. As the temperature rises,
these bubble blocks disappear, thereby enabling the possibility of heat transfer. With an increase in the amount of working fluid, it is expected that the dry-out tem-
perature will eventually increase. On the contrary, in order to achieve a low thermal re-
sistance, it is essential to minimize the occurrence of initial bubble blockage caused by an
excessive amount of working fluid. Therefore, it is necessary to maintain the working fluid
at an appropriate level. The study observed that the optimal heat transfer capability was
achieved when the level of working fluid was between 30–40%, which corresponds to re-
sults from previous studies [17–20]. Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45°). 3.4. Effect of the Tilling Angle on Heat Transfer Performance
Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45◦). Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45°). Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45◦). Energies 2024, 17, 1113 10 of 12 10 of 12 Afterwards, at a higher temperature, there is an increase in the amount of vapor
accumulated in the condensation sector, while the amount of working fluid that need to
be transported back to the evaporation sector through capillary force gradually decreases. In the case of a sustained rise in temperature, the working fluid in the evaporation sector
becomes exhausted and the generation of evaporation-latent heat becomes impossible,
leading to a dry-out state. g
y
With an increase in the amount of working fluid, it is expected that the dry-out
temperature will eventually increase. On the contrary, in order to achieve a low thermal
resistance, it is essential to minimize the occurrence of initial bubble blockage caused by
an excessive amount of working fluid. Therefore, it is necessary to maintain the working
fluid at an appropriate level. The study observed that the optimal heat transfer capability
was achieved when the level of working fluid was between 30–40%, which corresponds to
results from previous studies [17–20]. 3.4. Effect of the Tilling Angle on Heat Transfer Performance The comprehensive test results showed that there was an enhancement in heat transfer
capability as the test angle (θ) increased from 0◦to 90◦, regardless of variations in powder
type and wick thickness. This phenomenon can be attributed to the enhanced thermal
distribution enabled by the gravity force, as well as the increased surface area of heat
transfer, leading to higher cooling and heating capabilities. Figure 10 shows a schematic
illustration of the phenomenon of capillary rise in a cylindrical tube, wherein the tilling
angles are denoted by θ. The mathematical representation of the tilting angle requires
the calculation of the cosine of the angle(θ) produced between two vectors. Hence, when
the test angle reaches 90◦, the alignment of capillary force and gravity occurs, leading to
the enhanced movement of the liquid working fluid due to the resultant force. As the
test angle approaches 0◦, the relative alignment of capillary force and gravity undergoes
a transition leading to a decrease in the value of cosθ and a reduction in the rate of the
working fluid’s returning to the evaporator. In the situation of a horizontal orientation, the
force of gravity is negated, thus enabling the controlled flow of the working fluid towards
the evaporation unit. The decrease in pumping capacity causes a decrease in the ultimate
operational threshold [21]. EW
11 of 12 Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. 4 Conclusions
4. Conclusions 4. Conclusions
4. Conclusions This can be attributed to the enhanced thermal distribu-
tion by the gravity force, as well as the expansion of the surface area for heat transfer
due to the enlarged cooling and heating surfaces. Consequently, the heat resistance
exhibits a low value, whereas the Qmax exhibits a high value. Author Contributions: Methodology, I.-N.J.; Formal analysis, I.-N.J. and Y.-S.A.; Investigation, I.-N.J. and Y.-S.A.; Resources, Y.-S.A.; Data curation, I.-N.J.; Writing—original draft, I.-N.J. and Y.-S.A.;
Writing—review & editing, Y.-S.A.; Visualization, I.-N.J.; Supervision, Y.-S.A.; Project administration,
Y.-S.A.; Funding acquisition, Y.-S.A. All authors have read and agreed to the published version of
the manuscript. Funding: This research was financially supported by the Ministry of Trade, Industry, and Energy
(MOTIE), Korea, under the “Development of a Cooling module for the Aircraft Data Transfer System
(DTS)” program (reference number P150200002), supervised by the Korea Institute for Advancement
of Technology (KIAT). Data Availability Statement: All data are contained in the paper. Data Availability Statement: All data are contained in the paper. Data Availability Statement: All data are contained in the paper. Conflicts of Interest: The authors declare no conflicts of interest. Conflicts of Interest: The authors declare no conflicts of interest. References 1. Kim, S.-D.; Kang, H.-K.; Sung, B.-H.; Kim, C.-J. In A Study on a Sintered Metal Wick Heat Pipe; Manufacturing and Inspection. In
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2. Lee, W.H.; Lee, K.W.; Park, K.H.; Lee, K.J.; Noh, S.Y. In Study on a Operating Characteristics of Loop Heat Pipe Using a Brass
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10. 4. Conclusions
4. Conclusions 4. Conclusions
(1) The heat pipe, which was equipped with a sintered wick made from 200 D powder,
exhibited a smaller effective pore radius in comparison to 100 U. As a result, the uti-
lization of 200 D powder resulted in an enhanced capillary force and exhibited im-
proved efficacy in heat transfer. (1)
The heat pipe, which was equipped with a sintered wick made from 200 D powder,
exhibited a smaller effective pore radius in comparison to 100 U. As a result, the
utilization of 200 D powder resulted in an enhanced capillary force and exhibited
improved efficacy in heat transfer. Energies 2024, 17, 1113 11 of 12 11 of 12 (2)
The heat pipes’ wick thicknesses were measured as 902 µm, 534.7 µm, and 179.1 µm,
which correspond to mandrel diameters of 1.5 mm, 2 mm, and 2.5 mm, respectively. The heat pipe with a wick thickness of 534.7 µm exhibited the most efficient heat
transfer performance. The presence of a sufficient thickness of the wick ensures
that an appropriate amount of working fluid is available to reach the region where
evaporation takes place. Conversely, reducing the thickness of the wick results in a
decrease in the amount of working fluid that can be retained in the wick, which can
lead to dry-out, even when operating at low temperatures.i y
p
g
p
(3)
The initial thermal resistance value showed an increase as the filling ratio of the
working fluid increased from 20 wt.% to 50 wt.%. Additionally, it was observed that
the Qmax value exhibited a positive correlation with increasing temperature. (3)
The initial thermal resistance value showed an increase as the filling ratio of the
working fluid increased from 20 wt.% to 50 wt.%. Additionally, it was observed that
the Qmax value exhibited a positive correlation with increasing temperature. (4)
The heat transfer performance showed an enhancement as the tilting angles increased
within the range of 0◦to 90◦. This can be attributed to the enhanced thermal distribu-
tion by the gravity force, as well as the expansion of the surface area for heat transfer
due to the enlarged cooling and heating surfaces. Consequently, the heat resistance
exhibits a low value, whereas the Qmax exhibits a high value. (4)
The heat transfer performance showed an enhancement as the tilting angles increased
within the range of 0◦to 90◦. References Esmaeilzadeh, A.; Silakhori, M.; Nik Ghazali, N.N.; Metselaar, H.S.C.; Bin Mamat, A.; Naghavi Sanjani, M.S.; Iranmanesh, S. Thermal performance and numerical simulation of the 1-pyrene carboxylic-acid functionalized graphene nanofluids in a sintered
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https://openalex.org/W3013297601 | https://run.unl.pt/bitstream/10362/96296/1/M_Luz_Sampaio_The_introduction_of_new_construction_materials.pdf | English | null | The legend of Sardanapalus: From ancient Assyria to European stages and screens | Enlighten: Publications (The University of Glasgow) | 2,019 | public-domain | 5,313 | 1. Introduction ted M
The teaching of engineering and the performance
of their schools is a way to analyse the transmission
of scientific knowledge and the production of an
academic elite, an intelligentsia responsible for
innovation and the circulation of knowledge. One of the materials that would progressively
expand in utilisation throughout construction, was
Portland cement and over the course of the 20th-
century the use of reinforced concrete: this new
material had the advantage of fire resistance; the
possibility of realizing large spans; economy, speed;
and improved quality in the construction (Póvoas,
2015). Accepte
We focus on the Engineering Faculty of Porto
University, through the work of professor Antão de
Almeida Garrett, in order to analyse the
introduction of reinforced concrete in the decade
of 1930, and we concluded that he belongs to a
generation
of
engineering
professors
that
improved the use of concrete and disseminated
technical knowledge within the models created by
education policies since 1911, under the republican
government. Since the second half of the 19th-century progress
in transport and communications onwards ensured
the next century began with a better understanding
of the functioning of materials especially the scope
for concrete and its respective typologies. This
development interlinked with the registering of
numerous
patents
and
other
successful
applications that brought about its adoption for
facades, beams and other structural features. The
development of this new material arose from
various contributions and experiences, especially
those of: Abstract: ript
Through the teaching of engineering, the introduction of new materials into civil construction gained a
privileged mean of circulating knowledge and stimulating the new construction experiences that shaped a
technical intelligence within the scope of which there stood out the professor of the Faculty of Engineering
of the University of Porto, including Francisco Xavier Esteves, Francisco Correia de Araújo and Antão
Almeida Garrett. nuscrip
This chapter’s objective is to analyse the introduction of reinforcing cement and its interconnections with
the study plans for engineering teaching at the University of Porto in the 1920s and 1930s, which were first
structured around the Technical Faculty that later became the Engineering Faculty of Porto University. We
correspondingly opted to identify some of the specific experiences and theoretical reflections around the
application of this new construction material and highlighting the role of Antão Almeida Garrett and his
purposes for advancing with the utilisation of reinforced cement in civil construction, especially in industrial
buildings in Porto. Man
Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable Man
Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable Man
Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable d Ma
nce
on
prefer resistant stonemasonry walls, floors and
roofs in wooden structures, varying in their quality
in accordance with the economic resources
available. The introduction of new construction materials and the
teaching of engineering based on technical intelligence: the
role of Antão Almeida Garrett Maria da Luz SAMPAIO
IHC - Faculdade de Ciências Sociais e Humanas da Universidade Nova de Lisboa,
Lisboa, Portugal
E-mail : mluzsampaio@fsch.unl.pt
ORCID: 0000-0002-9231-4757 Maria da Luz SAMPAIO
IHC - Faculdade de Ciências Sociais e Humanas da Universidade Nova de Lisboa,
Lisboa, Portugal
E-mail : mluzsampaio@fsch.unl.pt
ORCID: 0000-0002-9231-4757 rip
e Araújo and A
t
ti A
2. The utilisation of reinforced
cement in civil construction in the
early decades of the 20th century This process stemmed from the scientific
progress that enabled the provision of different
construction
technologies
coupled
with
experiences associated with the building of large
manufacturing facilities, bridges, channels, garages,
aerodromes, water storage tanks and as well as
platforms, dams and power stations. Already into the 20th century, leading contributions
were made by the French engineer Eugène
Freyssinet, who studied and determined its
characteristics. He patented his ideas in 1928, and
was a structural designer and bridge builder, lacked
the teaching qualities necessary to communicate
his ideas to other engineers (Dinges, 2009),
(Camprubí, 2017). Just like reinforced cement, pre-stressed concrete
also incorporated steel but held a higher load
capacity and thereby endowing greater resistance
and
durability
to
cement
features
and
correspondingly
broadening
their
scope
of
utilisation in civil construction. In Portugal, the 1920s-1930s were years of
experimentation and adaptation to the principles
of Modern Architecture with the application of
modern materials alongside the daring solutions
that only engineers knew how to design (Tostões,
2004). The modern architecture movements would
foster the awareness of the artistry and capacity of
reinforced cement in following the works of
Auguste Perret who encourages the use of
reinforced concrete due to its potentialities to find
new structural systems and aesthetic solutions
(Tostões, 2004). However, materials such as
reinforced cement would only enter in regular use
in the 1950s. Until then only a limited group of
engineers knows how to apply appropriately this
material given its need for unusual calculations and
application manuals (Appleton, 2004). This reality,
more transversal to the entire civil construction
sector, did not prevent the emergence of very
particular experiences in the usage of Portland - as well as the British industrialist and cement
manufacturer Joseph Aspdin (1778-1855), who
obtained the patent for Portland cement in 1824
(Mascarenhas-Mateus, 2018). In 1897, another significant contribution came from
the French François de Hennebique with the use of
iron bars and stirrups inserted in the mass of the
concrete, which developed a construction system
using the iron reinforced concrete that enabled the
construction of spaces with spans of considerable
size, and increased loads (Tostões, 2004). A
2. The utilisation of reinforced
cement in civil construction in the
early decades of the 20th century At the beginning of the 20th century, there
remained the construction practices, techniques
and materials handed down from the 19th century. Limestone, wood (especially pine) applied to floor
and roof structures and as well as forged iron with
steel arriving later. The new materials were used to
improve the construction mainly the connection
between wood and the stonemasonry. (Appleton,
2004). According to Vale (2012) house building in
the early decades of the 20th-century continued to - Louis Vicat (1786- 1861), graduated in engineering
at École Polytechnique de Paris and École Nationale
des Ponts et Chaussées; - Louis Vicat (1786- 1861), graduated in engineering
at École Polytechnique de Paris and École Nationale
des Ponts et Chaussées; - the chemical engineer François Coignet (1814-
1888), deemed the inventor of reinforced cement
applied to building structure (Mascarenhas-
Mateus, 2018); 516 - the German engineer Matthias Koenen (1894-
1924), the first to do structural calculation of
reinforced concrete elements (Moussard et al,
2017). t
cement in as early as the 19th-century and the first
decades of the following century. In Portugal, the
first significant cement construction was the new
building of Moagem do Carmujo [Caramujo Wheat
Mill], built in 1898 (Toscano, 2012) and the Luiz
Bandeira de Sejães Bridge on the EN333-3 over the
river Vouga, dating to 1907, opening up a new
paradigm in the history of construction. (Appleton,
2004). The choice of this material stemmed from
the need to design industrial facilities structured
into large pavilions, capable of bearing significant
loads, providing stable structures and flooring
simultaneously more resistant to fire and high
temperatures. - the German engineer Matthias Koenen (1894-
1924), the first to do structural calculation of
reinforced concrete elements (Moussard et al,
2017). Accepted M
reinforced concrete elements (Moussard et al,
2017). - as well as the British industrialist and cement
manufacturer Joseph Aspdin (1778-1855), who
obtained the patent for Portland cement in 1824
(Mascarenhas-Mateus, 2018). In 1897, another significant contribution came from
the French François de Hennebique with the use of
iron bars and stirrups inserted in the mass of the
concrete, which developed a construction system
using the iron reinforced concrete that enabled the
construction of spaces with spans of considerable
size, and increased loads (Tostões, 2004). Other variants of this product were developed in
the early 20th-century like the pre-stressed
concrete as well as the introduction of asbestos-
cement. 3. The teaching of engineering and
the introduction of reinforced
concrete ript
From 1922 the chair of «Reinforced concrete» was
taught by Theotónio Rodrigues, but in 1932 it
became the responsibility of Antão Almeida
Garrett, (1897-1978), recently graduated in civil
engineering. M
The introduction of this new material is associated
with the reorganisation of engineering education,
especially in civil engineering. Since 1881-82 the
military School had a scientific approach, it became
part of the curricula for the engineers’ training. This
new material was already disseminated in the 19th-
century by the review «Le Betón Armé et ses
Applications» published by Paul Christophe,
engineer of Ponts et Chaussés School and in
Portugal by the Revista de Obras Públicas e Minas
1870-1926, edited by Associação dos Engenheiros
Civis Portugueses [Association of Portuguese Civil
Engineers] (Mascarenhas-Mateus, 2018). uscrip
Graduated in 1925 by the University of Porto, he
became professor-assistant of the First Group: Civil
Constructions in the Faculty of Engineering of the
University of Porto and Manus
recruited in 1932 to the chair of «Reinforced
Concrete». According to the educational traditions
prevailing in engineering schools, he produced an
anthology that included the definitions and
characteristics of this material, its usages as well as
the formulas and calculations for building different
structures and that remained an essential
reference
manual
throughout
many
years. Students, also keeping the tradition, would
annually produce new editions and we highlight the
contributions of the re-edited manual by Pinto
Basto and Lamas Viana, Alfredo Barata da Rocha,
Alberto Fontes, Vicente de Paiva, Torquato Alvares
Ribeiro and as well as the engineer Edgar Cardoso,
who would also be a professor of engineering at
Instituto Superior Técnico, founding in 1944 his own
Laboratory for the Study of Structures and
Foundations. Cardoso had extensive work with the
use of concrete as well as other materials. Among
his projects is the Arrábida Bridge in 1963 and the
S. João Railway Bridge in Porto, opened in 1991. ed M
Under the Republic government, two schools were
founded: the Lisbon Instituto Superior Técnico and
the University of Porto. In the latter, the Technical
Faculty was created in 1915 and was transformed,
in 1926, into the Faculty of Engineering of the
University of Porto. Accepted
y
The Technical Faculty of the University of Porto was
one of the first schools officially to approve this
discipline in the curricular plan. 1 Augusto Pereira Nobre (1865-1946) was a biologist and
professor of Porto University.
2. Diogo Eugénio Cabral was a Porto industrialist and 1st A
2. The utilisation of reinforced
cement in civil construction in the
early decades of the 20th century In the 20th-century,
new facilities came in the 1920s, with Maceira-Liz
factory in Leiria, which began operating in 1923, 517 and under the Estado Novo government was
founded in 1930 the major corporate group: SECIL
– Companhia Geral de Cal e Cimento S.A. In 1934,
Lusalite began the elaboration of fiber-cement,
being an associated company to the group Sommer
that centralised the entire sector. This was the
result of the protectionist and interventionist policy
of Salazar’s government since 1931, but the
changes in the sector only began after World War II
(Costa, Fazenda et al., 2010). the use of Portland Cement also due to its moulding
capacities (Vale, 2012). t
The active participation in public life led Xavier
Esteves to embrace other projects and, in addition
to his short experience in engineering education, he
joined, from December 1917 to June 1918, Sidónio
Pais’ government, as Minister of Commerce
(between December 11, 1917, and March 7, 1918)
and Minister of Finance (between 7 March and 1
June 1918). Later, his business connections led him
to be elected a second term as president of the
Portuense Industrial Association, between 1919
and 1930. A
2. The utilisation of reinforced
cement in civil construction in the
early decades of the 20th century Manuscript
With the proliferation of functional modernism
backed by the ongoing calculations and research,
the technical intelligence of the engineers ensured
the architects recognized this new material for
establishing a new aesthetic language using the
plasticity of this material to project large openings
with extensive glazing, creating a taste for smooth
surfaces and pure volumes (Tostões, 2004). In this
context, there stood out in Lisbon works such as the
Portugália Brewery (1912-1914); the Capitólio
cinema by Cristino da Silva (1896-1976) in 1929; the
Instituto Superior Técnico, designed by Porfírio
Pardal Monteiro in 1927 and completed in 1936. In
Porto, these were accompanied by the São João
Theatre (1910-1918), the Armazéns Nascimento
Department Store (1914-1927) and the Garage for
O Comércio do Porto newspaper designed by the
architect Rogério Azevedo (1899-1983); the Passos
Manuel Garage by the architect Mário Abreu; as
well as the fish fridge building in Massarelos by
Januário Godinho (Tostões, 2004). Other variants of this product were developed in
the early 20th-century like the pre-stressed
concrete as well as the introduction of asbestos-
cement. This process stemmed from the scientific
progress that enabled the provision of different
construction
technologies
coupled
with
experiences associated with the building of large
manufacturing facilities, bridges, channels, garages,
aerodromes, water storage tanks and as well as
platforms, dams and power stations. The introduction of reinforced concrete in Portugal
led to the publication, in 1918, of the Regulatory
Instructions for the employment of Concrete,
carried out based on the French norms and its later
developments. (Appelton, 2004). A new regulation
was published in 1935, establishing the need for
rigorous calculations to meet the needs of
compression, tension and safety of reinforced
concrete
works,
among
other
aspects,
demonstrating a broad field of applications of this
material in civil construction (Decree 25.948 of
October 16, 1935). In parallel, the cement industry underwent
significant expansion. According to Mascarenhas-
Mateus studies “The effective production of natural
cement began in 1866 under the Rasca brand
manufactures in Alcântara, Lisboa, by Francisco
Pereira de Gusman” (Mascarenhas-Mateus, 2018,
p. 905), while the first industrial production unit
had been founded in 1898, Companhia Cimento
Tejo in Allandra by António Teóphilo Araújo Rato
(Mascarenhas-Mateus, 2018). Count of Vizela. 4. The artificial silk factory expansion
plan: Company “Fibra Comercial
Lusitana Lda.” Dissemination
and
experimentation with these new materials were
also much shaped by the founding of the
Laboratory for Testing Construction Materials
under the auspices of the Faculty of Engineering
(established officially as a Cabinet of the school of
engineering in 1915). The Faculty laboratory was
used by the students in practical lessons and to do
their projects, but also as outsourcing services for
official and private entities, carried out a leading
role in testing construction materials. This was
where Professor Antão Almeida Garrett do
experiments with different materials, especially
national woods: maritime pine from Leiria, and
reinforced concrete helicoid beams as well as
testing the fire resistant properties of reinforced
concrete, demonstrating that when slowly exposed
to high temperatures it would inevitably get
destroyed (Garrett, 1938). Many other tests and
studies took place not only in conjunction with the
academic programs but also as a result of studies
requested from industry and official entities, with
the laboratory taking on a determinant role in Man
Three years after licensing the first building for the
artificial silk (rayon) factory, the company advanced
with an investment in its expansion through the
addition of a perpendicular body, with a sizeable
volumetric scale and careful design, surrounded by
a garden that extended as far as the avenue. The calculations for the concrete structures were of
the responsibility of Antão Almeida Garrett who
established the scale, loads and tensions for each
construction component. The new building would
form a typified example of modern architecture
from the early 20th-century, with a regular
composition and flat roofing surface. The imposing
southern facade stands out in this otherwise
classically designed building with its innovation
emerging out of the scale of the vertical openings
that only become feasible due to their reinforced
concrete infrastructure. The flat roof with a terrace
was lined by a row of sheds supported by concrete
trusses. On the inside, space was divided by a
concrete beam-pillar structure that replicated the
design of the metallic structures that were
previously applied to these buildings while ensuring
a wide and very open space with a scalable to cope
with the installation of heavy and large-scale
machinery and equipment. The Descriptive Memory of the project details not
only the calculations as well as the description of
the materials. 3. The teaching of engineering and
the introduction of reinforced
concrete The school board
decided in 1917 to recruit Francisco Xavier Esteves
to be the professor of «Reinforced concrete and
Bridges» (FEUP/Actas do Conselho Escolar, 1917). This teacher obtained a degree in civil engineering
from the Politécnica Academy (Tavares, 2017), and
in 1912 was a managing partner of the Companhia
de Cimentos Tejo, using Portland cement. Among
Xavier Esteves’ works, Livraria Lello (bookshop
Lello) stands out, a 1904 project where the cement
is used in the interior stairs, in the gallery of the
store and the frame of the facade. Xavier Esteves
also signed other works like the 1898 Augusto
Pereira Nobre’s house 1 in the street of Castelo do
Queijo (Foz do Douro) or Diogo Eugénio Cabral’s
residence2 located on Rua Miguel Bombarda and
which received works of expansion in 1927, using
Portland cement (AHMP/CMP, L. O. nº192/1928). It
is important to emphasise that in the case of the
Livraria Lello the neo-gothic facade was built with Like reinforced concrete, pre-stressed concrete was
also introduced in engineering education through
the contacts and missions carried out by another
professor of Porto University, Francisco Sarmento
Correia de Araújo, who graduated in civil
engineering in 1934. He carried out a mission
financed by the Instituto de Alta Cultura at the Gent
University (Belgium) where he worked with Gustaaf
Robert Magnel, professor of reinforced concrete
and founder of the Magnel Laboratory for Concrete
Research one of the great centres of expertise and
knowledge dissemination of reinforced and 518 engineering research. Antão Almeida Garrett would
take over as its director in 1964. prestressed concrete in Europe. Gustave Magnel
gave many lectures in several countries in which he
explained in a simple way the principles of pre-
stressed concrete and wrote the first book of design
in this subject (Dinges, 2009). 4. The artificial silk factory expansion
plan: Company “Fibra Comercial
Lusitana Lda.” This experience ensured Correia de Araújo to
played a decisive role not only in teaching civil
engineering but also in the dissemination the use of
reinforced concrete, participating in the technical
teams for diverse public projects that resulted in
some of the emblematic landmarks of Porto city. His position as head of the Serviços de Obras
Municipais e Habitações Populares (1940-41)
[Town Constructions and Inhabitants Houses
Department] enabled his interventions in the
reinforced concrete project for the Massarelos
Bolsa do Pescado [Massarelos Fishing Market]; the
calculations for the Massarelos bridge to fish fridge;
the inspection, the calculation of the projects of the
construction of the “Abrigo dos Pequeninos”
[Children Shelter]; the new City Council Hall, and
the calculation and inspection of the construction
of the Duque de Saldanha’s local council housing
project, among others. anuscript
From the 1920s, new construction projects of
private entities in the city of Porto allowed for the
emergence of works that marked the introduction
of a modern architecture capable of designing the
necessary interior functionality of the buildings. One of the industrial buildings that used reinforced
concrete was the factory of the company “Fibra
Commercial Lusitana Lda” — designed in 1933 by
the architect Leandro de Morais (1883-?) in a parcel
of land situated in the crossroad between the
avenue of Boavista and the street Coutinho de
Azevedo, neighbouring another textile unit: Fábrica
de Fiação e Tecidos da Boavista owned by William
Graham. This new unit was part of the group of
industrial units located in this new avenue, an
important expansion axis for the city towards the
west allowing the connection of the city centre to
the sea, in particular to Leixões Port, through the
maritime marginal or crossing of the agricultural
suburbs. Accepted M
Within the Porto Faculty of Engineering, the
circulation of knowledge interlinked with the
engineering practices of their professors but also
extended to the missions financed by the Institute
of High Culture (Instituto de Alta Cultura) that
brought an increase of the technical intelligence
able to apply and disseminate these new
construction
materials
sustained
by
their
respective calculations. There thus appeared new
constructions held up by beams, pillars, roofing and
terraces, large-scale architectural projects in their
majority with high functional performance and
resistance
requirements. 4. The artificial silk factory expansion
plan: Company “Fibra Comercial
Lusitana Lda.” In parallel, he
thus defended the use of national woods, referring
to how such materials hold the capacities to
provide solutions to the different demands of
construction systems. Garrett ends his reflections
by expressing the idea that technical progress in
this field does' not yet have given a substantial
improvement on civil construction (Garrett, 1939). M
The article continues with a set of considerations
against the high costs of iron imports for reinforced
concrete, declaring his opposition to the incorrect
employment of reinforced concrete. In parallel, he
thus defended the use of national woods, referring
to how such materials hold the capacities to
provide solutions to the different demands of
construction systems. Garrett ends his reflections
by expressing the idea that technical progress in
this field does' not yet have given a substantial
improvement on civil construction (Garrett, 1939). We highlight that the introduction of concrete was
a gradual process and with Estado Novo regime
(1926-1974) started the regulation and control of
the process of civil construction and housing
projects, framed within the urban growth projects
of the main urban centres. pted
Fig. 2. Project of Shed coverage of the new building
of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/
1936, p. 426. ccepte
This new industrial building is another example of
the complicity established between modern
architecture and engineering, in a partnership
irredeemable for the experimental load that the
new constructive materials imposed. Acc
Antão Almeida Garrett was involved in other
projects. From 1930 and 1939 we found his
signature in projects for water tanks, terraces,
garages, bourgeois dwellings, alterations of
buildings, using always reinforced concrete, namely
for the coverings, pavements, pillars and beams. 5. Antão Almeida Garrett: reflections
and experiences with reinforced
concrete Antão Almeida Garrett had a long career as
professor and engineer, and from the 1940s, he
undertook numerous studies, focusing in particular
in the urban plan of Porto, working in partnership
with national and foreign architects and urban
planners. Antão Almeida Garrett was engaged in the task of
promoting and disseminating new construction
materials and techniques and their impacts on the
construction industry. In 1932, he wrote an article
for the Bulletin of the Civil Engineers Association of
Northern
Portugal,
entitled
“Construction
Processes”, where he details a new process of using
concrete in order to build walls that would enable 4. The artificial silk factory expansion
plan: Company “Fibra Comercial
Lusitana Lda.” In this document, the engineer
Garrett presents the use of a reinforced concrete
skeleton that supports the building from the first
floor to the roof, showing all the calculations for
beams, pillars, sheds and concludes by highlighting 519 cript
homes
to
become
more
insulated
from
temperature variations (Garrett, 1932). Hence, this
engineering professor, driven by his preference for
reinforced
concrete
and
his
capacity
for
experimentation, set up an area to make concrete
moulds at the bottom of his garden. His tests and
studies led him to the production of a unique layout
of moulds, resulting in a concrete beam with two
support frames (Garrett, 1932). In 1938 he
published “O betão armado e o fogo“ [Reinforced
Concrete and the Fire] and he related the
experiences made in concrete, following the
studies and fire tests of the American Professor I. H. Woolson and Professor M. M. Milankovitch from
University of Belgrade, and also from the Station d’
Essais de L’ Office National des Recherches et
Inventions, demonstrating to be aware of the works
in this area in other universities and research
centres. the use of asbestos-cement in the roof (L.O. 1146/1936). Fig. 1: Architectural project of the new building of
the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/
1936, p. 416. Fig. 1: Architectural project of the new building of
the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/
1936, p. 416. pted M
Fig. 2. Project of Shed coverage of the new building
of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/
1936, p. 426. Manuscr
The rationalisation of construction systems was
also a strong subject for this engineer, and he
defended the use of national raw materials for civil
construction. He published an article, in 1939, in
the University of Porto Engineering Journal entitled
“Porque se não deverá empregar tanto betão
armado” [Why we should not employ so much
reinforced concrete] In the opening lines, he
answered by saying that iron is imported; it is
applied where there is no justification, and also
because reinforced concrete is generally poorly
designed and badly executed (Garrett, 1939). M
The article continues with a set of considerations
against the high costs of iron imports for reinforced
concrete, declaring his opposition to the incorrect
employment of reinforced concrete. Acknowledgement: M
This paper was produced under the scholarship FCT
SFRH/BPD/117829/2016, dedicated to the project:
History of engineering education in Portugal: 1901-
1960. M
This paper was produced under the scholarship FCT
SFRH/BPD/117829/2016, dedicated to the project:
History of engineering education in Portugal: 1901-
1960. anu
_____. (1938a). O betão armado e o fogo. In Revista
Faculdade de Engenharia, IV (3), pp. 109-114. Man
Faculdade de Engenharia, IV (3), pp. 109 114. ___. (1938b). Ainda as vigas helicoidais de betão armado
carregadas uniformente. In Revista da Faculdade de
Engenharia, IV (2), pp. 49-51. M
___. (1939). Porque se não deverá empregar tanto betão
armado. In Revista da Faculdade de Engenharia, V,
(4) (dez.), pp. 156-158. 6. Conclusion Cimento Armado: Lições pelo assistente
Engenheiro Antão Almeida Garrett. Porto: FEUP. _____. (1938a). O betão armado e o fogo. In Revista
Faculdade de Engenharia, IV (3), pp. 109-114. _____. (1938b). Ainda as vigas helicoidais de betão armado
carregadas uniformente. In Revista da Faculdade de
Engenharia, IV (2), pp. 49-51. _____. (1939). Porque se não deverá empregar tanto betão
armado. In Revista da Faculdade de Engenharia, V,
(4) (dez ) pp 156 158 d Ma
901-
_____.
_____. 6. Conclusion The first uses of reinforced concrete demonstrate a
progressive knowledge of the properties of new
materials for civil construction, but their diffusion 520 was also due to engineering schools and its
teachers. They have a privileged role in the
circulation of technical knowledge, the diffusion of
new practices and the use of new building
materials. State University. State University. Edgar, C. (1936-1837). Cimento Armado: Lições proferidas
pelo Eng. Antão Almeida Garrett. Porto: FEUP. FEUP. (1959). O laboratório de Ensaios de Materiais da
Faculdade de Engenharia da Universidade do Porto. Porto: FEUP. _____. (1926). Faculdade de Engenharia da Universidade
do Porto: Faculdade Técnica da Universidade do
Porto
(1915-1926). Available:
file:///C:/Users/Utilizador/Downloads/FEUP_-
_Estudo_organico_e_funcional%20(6).pdf
_____. SDI/ARQUIVO - Livro de Actas do Conselho Escolar,
1915 - 1922. Cota: 7(01) ARQ00000006. Porto:
FEUP. The first generations of graduated engineers from
the Faculdade Técnica of the University of Porto,
played an essential role in the dissemination of this
knowledge, especially Antão Almeida Garrett, who
throughout his career as professor improved the
technical intelligence in his disciples and as
engineer designed small-scale projects such as
concrete structures for water tanks, terraces, but
also projects of concrete structures for factory
buildings, houses, making extensive use of
reinforced concrete and even asbestos-cement. file:///C:/Users/Utilizador/Downloads/FEUP_-
_Estudo_organico_e_funcional%20(6).pdf
_____. SDI/ARQUIVO - Livro de Actas do Conselho Escolar,
1915 - 1922. Cota: 7(01) ARQ00000006. Porto:
FEUP. ipt
Fontes, A., Paiva, V. de, Ribeiro, T.A. (1936). Materiais e
Processos gerais de Construção: lições dadas pelo
Ex.mo Senhor Professor Antão Almeida Garrett. Porto: Tipografia Gonçalves & Cª. cript
Garrett, Antão Almeida. (1932). Processos de Construção. In Boletim da Associação dos Engenheiros Civis do
Norte de Portugal, 7, pp. 30-32. Antão Almeida Garrett fostered the study of new
materials, especially the reinforced concrete with
his experimentation and theoretical principles
improving
the
modernisation
of
the
civil
construction, sustained by the development of
engineering. Antão Almeida Garrett fostered the study of new
materials, especially the reinforced concrete with
his experimentation and theoretical principles
improving
the
modernisation
of
the
civil
construction, sustained by the development of
engineering. uscri
_____. (1932-33). Cimento Armado [texto policopiado]:
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assistente Engenheiro Antão Almeida Garrett,
copiadas pelos alunos Germano Venade e Manuel
Arala Chaves. Porto: FEUP. nus
_____. (1935). Cimento Armado: Lições pelo assistente
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https://openalex.org/W4383911025 | https://bmcpediatr.biomedcentral.com/counter/pdf/10.1186/s12887-023-04164-1 | English | null | Think out of the box: association of left congenital diaphragmatic hernia and abnormal origin of the right pulmonary artery | BMC pediatrics | 2,023 | cc-by | 3,818 | Abstract Background We report the occurrence of a severe pulmonary hypertension (PH) in a neonate affected by a left
congenital diaphragmatic hernia (CDH). PH in this patient was associated with an abnormal origin of the right
pulmonary artery from the right brachiocephalic artery. This malformation, sometimes named hemitruncus arteriosus,
has to the best of our knowledge never been reported in association with a CDH. Case presentation A male newborn was hospitalized from birth in the neonatal intensive care unit after prenatal
diagnosis of a left CDH. Ultrasound examination at 34 weeks of gestational age evaluated the observed-to-expected
lung-to-head ratio at 49%. Birth occurred at 38+ 5 weeks of gestational age. Soon after admission, severe hypoxemia,
i.e., preductal pulse oximetry oxygen saturation (SpO2) < 80%, prompted therapeutic escalation including the use
of high frequency oscillatory ventilation with fraction of inspired oxygen (FiO2) 100% and inhaled nitric oxide (iNO). Echocardiography assessment revealed signs of severe PH and normal right ventricle function. Despite administration
of epoprostenolol, milrinone, norepinephrine, and fluid loadings with albumin and 0.9% saline, hypoxemia remained
severe, preductal SpO2 inconsistently greater than or equal to 80-85% and post ductal SpO2 lower on average by
15 points. This clinical status remained unchanged during the first 7 days of life. The infant’s clinical instability was
incompatible with surgical intervention, while chest X-ray showed a relatively preserved lung volume, especially on
the right side. This prompted an additional echocardiography, aimed at searching an explanation of this unusual
evolution and found an abnormal origin of the right pulmonary artery, which was confirmed on computed
tomography angiography subsequently. A change in the medical strategy was decided, with the suspension of
pulmonary vasodilator treatments, the administration of diuretics, and the decrease in norepinephrine dose to
decrease the systemic-to-pulmonary shunt. Progressive improvement in the infant respiratory and hemodynamic
status enabled to perform CDH surgical repair 2 weeks after birth. Full list of author information is available at the end of the article Full list of author information is available at the end of the article © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use,
sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. A train can hide another Arthur Gavotto1,2*
, Pascal Amedro3,4 and Gilles Cambonie1,5 Arthur Gavotto1,2*
, Pascal Amedro3,4 and Gilles Cambonie1,5 © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use,
sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included
in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The
Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available
in this article, unless otherwise stated in a credit line to the data. BMC Pediatrics BMC Pediatrics Gavotto et al. BMC Pediatrics (2023) 23:349
https://doi.org/10.1186/s12887-023-04164-1 Open Access Abstract The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included
in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The
Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available
in this article, unless otherwise stated in a credit line to the data. Think out of the box: association
of left congenital diaphragmatic hernia
and abnormal origin of the right pulmonary
artery A train can hide another Case presentation A male newborn was hospitalized after birth in the neo
natal intensive care unit (NICU) after prenatal diagno
sis of a left congenital diaphragmatic hernia (CDH). The
infant was the second child of consanguineous (first-
degree cousins) and healthy North African parents. The
couple had been referred at the last trimester of preg
nancy to the expert center for CDH in our institution. At
34 weeks of gestational age, prenatal ultrasound showed
left CDH associated with various anomalies: short cor
pus callosum (< 1st centile), palate cleft, azygous venous
return, bilateral cryptorchidism, and intrauterine growth
retardation (< 3rd centile according to the French refer
ence values[11]). Ultrasound examination at 34 weeks
of gestational age evaluated the observed-to-expected
lung-to-head ratio at 49%, and magnetic resonance imag
ing (MRI) at 35 weeks of gestational age measured the
observed-to-expected total fetal lung volume at 33%,
corresponding to a mild-to-moderate severity in terms
of prediction of CDH-related lung hypoplasia [12]. In
addition, MRI showed a persistent portion of the ante
rior diaphragm, which maintained the liver in abdomi
nal position. Standard karyotype and array comparative
genomic hybridization revealed no abnormality. In newborns with CDH, respiratory failure originates
from abnormal lung development, which affects the
alveoli as well as their vascularization. This results in
pulmonary hypoplasia, but also structural and func
tional vascular abnormalities that cause persistent PH
[1]. Underdevelopment and abnormal vasoreactivity
of the pulmonary vasculature result in sustained eleva
tion of pulmonary vascular resistance and low pulmo
nary blood flow, causing right-to-left shunting of blood
across the ductus arteriosus and/or the foramen ovale,
and, ultimately, refractory hypoxemia [2]. Management
mainly consists in supporting respiratory function with
mechanical ventilation, with the aim of maintaining pre
ductal SpO2 > 80% and partial pressure of carbon diox
ide (PCO2) between 50 and 70 mmHg [3]. Treatment of
CDH-associated PH with vasodilator treatments such as
inhaled nitric oxide (iNO), prostacyclin, sildenafil, or mil
rinone should be limited to severe forms after optimiza
tion of alveolar ventilation, control of stress and pain, and
correction of hypovolemia [4, 5].h This standardized support may be unsuitable in very
specific situations, in particular with congenital malfor
mations. According to a recent review, 15% of neonates
with CDH have congenital heart disease, of which 42%
are critical [6]. Anomalous origin of the branches of the
pulmonary artery to the aorta accounts for 0.12% of con
genital heart defects [7]. (2023) 23:349 Page 2 of 6 Gavotto et al. BMC Pediatrics Conclusions This case recalls the interest of systematic analysis of all potential causes of PH in a neonate with CDH, a
condition frequently associated with various congenital malformations. Keywords Congenital diaphragmatic hernia, Congenital heart disease, Pulmonary hypertension, Poiseuille’s law,
Pediatrics Keywords Congenital diaphragmatic hernia, Congenital heart disease, Pulmonary hypertension, Poi
P di
i Background We report the occurrence of a severe pul
monary hypertension (PH) in a neonate affected by a left
congenital diaphragmatic hernia (CDH) associated with
an abnormal origin of the right pulmonary artery from the
right brachiocephalic artery, also named right hemitrun
cus arteriosus. reverse the therapeutic strategy, to restore an adequate
hemodynamic. Discussion Unstable refractory hypoxemia in an infant with CDH
despite apparently appropriate treatment should ques
tion the origin of the PH and make consider multifacto
rial causes. Several unusual data should have drawn our
attention in this observation and, first of all, uncertainty
about pulmonary hypoplasia, the severity of which is
often superimposed on that of PH. In this respect, there
was discrepancy between lung-to-head ratio, which pre
dicted a mild disease and total fetal lung volume, which
predicted a moderate-to-severe disease [12, 13]. In addi
tion, the satisfactory recruitment of the right lung, result
ing in PCO2 measurements regularly below the target
values, were not consistent with severe restrictive respi
ratory insufficiency. This clinical status remained unchanged during the
first 7 days of life, with. The infant’s clinical instabil
ity was incompatible with surgical intervention, while
chest X-ray showed a relatively preserved lung volume,
especially on the right side (Fig. 1). This prompted an
additional echocardiography, aimed at searching an
explanation of this unusual evolution. The pulmonary
veins were in normal position, with no stenosis, and left
ventricle function was normal, with no aortic coarcta
tion. However, the right pulmonary artery was poorly
visualized, and appeared to probably originate from the
right brachiocephalic artery, with significant diastolic
reflux in the descending aorta and increased flow in the
right pulmonary vein. This abnormal origin of the right
pulmonary artery was confirmed on computed tomogra
phy angiography performed 9 days after birth (Fig. 2). fi
Extracorporeal membrane oxygenation (ECMO) is a
rescue support in neonatal CDH with cardio-respiratory
failure, with persistent controversies about patient selec
tion, timing of initiation and timing of surgical repair
[2]. In our patient, the severity of PH and the settings of
high frequency oscillatory ventilation were arguments for
recourse to extracorporeal life support [14]. On the other
hand, the multiple anomalies observed on prenatal ultra
sound as on postnatal examination suggested a genetic
abnormality or syndrome. After sharing this information
with parents, and also taking into account the potential
complications of ECMO,[15] we decided against this
option. A change in the medical strategy was decided, with
the suspension of pulmonary vasodilator treatments, the
administration of diuretics, and the decrease in norepi
nephrine dose to target a minimal mean blood pressure
of 35–45 mmHg to decrease the systemic-to-pulmonary
shunt. Progressive improvement in the infant respiratory Fig. Case presentation In most cases, the right pulmo
nary artery arises from the posterior wall of ascending
aorta, very near the aortic valve, is isolated (e.g., with
out intracardiac malformation), as opposed to left pul
monary artery forms [8]. From the rare cases reported
in the literature, no association with genetic syndromes
has been described in right hemitruncus arteriosus [9]. Without early surgical repair, the patient is exposed to
severe pulmonary hypertension, and, ultimately, cardiac
dysfunction [10]. This malformation has to the best of
our knowledge never been reported in association with
a CDH. Birth occurred at 38+ 5 weeks of gestational age by
cesarean section for fetal bradycardia and membrane
rupture, with a weight of 2670 g (5th centile), a height of
47 cm (8th centile), and a head circumference of 34.5 cm
(55th centile). Apgar scores at 1, 5 and 10 min were,
respectively, 2, 3 and 5. Arterial cord blood pH was 7.21
and cord lactate was 2.5 mmol/L. Nasotracheal intuba
tion was achieved 2 min after birth, and the infant was
transported in the NICU. Clinical examination con
firmed palate cleft, left cryptorchidism with a short penis
(19 mm), and distal arthrogryposis of the hands and
feet. Soon after admission, severe hypoxemia, i.e., pre
ductal pulse oximetry oxygen saturation (SpO2) < 80%,
prompted therapeutic escalation including the use of
high frequency oscillatory ventilation with fraction of
inspired oxygen (FiO2) 100% oxygen and inhaled nitric
oxide (iNO, 20 ppm). Echocardiography revealed signs
of severe PH, with estimated systolic pulmonary artery
pressure of 80 mmHg from peak tricuspid regurgitant
jet velocity, inverted septal curvature, and a predominant
right-to-left shunt in a large persistent ductus arteriosus The challenge of this rare association (left CDH with
an abnormal origin of the right pulmonary artery from
the right brachiocephalic artery) was then to totally Gavotto et al. BMC Pediatrics (2023) 23:349 Page 3 of 6 (2023) 23:349 Gavotto et al. BMC Pediatrics (2023) 23:349 and hemodynamic status enabled to perform CDH sur
gical repair 2 weeks after birth. Then, surgical reimplan
tation of the right pulmonary artery in the trunk of the
pulmonary artery was performed 5 weeks after birth. (PDA) of 4.5 mm of diameter. Case presentation In addition, echocardiog
raphy showed a normal right ventricle function (absence
of dilation, tricuspid annular plane systolic excursion
of 8.5 mm), and confirmed the absence of intracardiac
defect, the absence of inferior vena cava, and the pres
ence of the azygous venous return. Despite administra
tion of epoprostenolol, milrinone, norepinephrine, and
fluid loadings with albumin and 0.9% saline, hypoxemia
remained severe, preductal SpO2 inconsistently greater
than or equal to 80-85% and post ductal SpO2 lower on
average by 15 points. Discussion 1 Chest X-ray at day 1 (left panel) and day 5 (right panel) of life. Chest radiography shows the bowel loops occupying part of the left hemithorax the
1st post-natal day, and a relatively preserved lung volume, especially on the right side, the 5th post-natal day Fig. 1 Chest X-ray at day 1 (left panel) and day 5 (right panel) of life. Chest radiography shows the bowel loops occupying part of the left hemithorax the
1st post-natal day, and a relatively preserved lung volume, especially on the right side, the 5th post-natal day (2023) 23:349 Page 4 of 6 Gavotto et al. BMC Pediatrics (2023) 23:349 Gavotto et al. BMC Pediatrics Fig. 2 3D reconstruction of computed tomography angiography. Reconstruction showing the anomalous origin of the right pulmonary artery from the
right brachiocephalic artery (indicated by the white arrow) Fig. 2 3D reconstruction of computed tomography angiography. Reconstruction showing the anomalous origin of the right pulmonary artery from the
right brachiocephalic artery (indicated by the white arrow) The classical physiology of PH in CDH distinguishes
three main phenotypes: (i) mild or non-existent PH with
normally functional right ventricle; (ii) precapillary PH
with predominant right-to-left PDA and atrial shunts,
possibly associated with right-sided heart failure with
or without secondary left-sided heart failure; and (iii)
post-capillary PH with primary left-sided heart failure,
and predominant right-to-left ductus arteriosus shunt
and left-to-right atrial shunt [2]. According to Poiseuille
equation, pulmonary artery pressure depends on pul
monary blood flow, right ventricular afterload and left
atrial pressure. Thus, assessment of all potential causes
of PH in a patient needs to consider PH associated with
increased pulmonary vascular resistance, as well as with
increased pulmonary blood flow [16].h ultrasound Doppler index to assess precapillary pulmo
nary vascular resistance,[17] and relative shortening of
pulmonary artery acceleration time has been associated
with CDH severity [18]. In our patient, however, this
index was not relevant, as right lung perfusion was sup
plied by the left ventricle, whereas left lung perfusion was
supplied by the right ventricle. Persistence of a right-to-
left flow through a tubular ductus arteriosus, which gen
erally indicates increased right-sided cardiac pressures,
also gave the opportunity, in this hemodynamic situa
tion, to distribute part of the systemic volume flow and
to reduce PH severity of the left lung, as exceptionally
observed in adults [19]. Repeated echocardiography examinations performed
in this patient found no evidence for post-capillary PH. No financial support was received. No financial support was received. References In conclusion, this case reports the importance of
going back to the basics of physiology in complex hemo
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ECMO
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The unexpected occurrence of an increased pulmonary
blood flow in the present CDH infant, led to the search
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tion of an anomalous origin of the right pulmonary artery
from the ascending aorta. The challenge was then to
totally reverse the therapeutic strategy. Our objective was
first to reduce pulmonary blood flow by increasing pul
monary vascular resistance, which involved suspension
of pulmonary vasodilators, elevation of ventilation pres
sures, and permissive hypercapnia. In addition, we aimed
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de Villeneuve Hospital, Montpellier University Hospital, 371 Avenue du
Doyen Giraud, 34295 Montpellier, France
2PhyMedExp, CNRS, INSERM, University of Montpellier, Montpellier, France
3Paediatric and Congenital Cardiology Department, M3C National
Reference Centre, Bordeaux University Hospital, Bordeaux, France
4IHU Liryc, INSERM 1045, Bordeaux University, Bordeaux, France
5Pathogenesis and Control of Chronic Infection, INSERM UMR 1058,
University of Montpellier, Montpellier, France Received: 29 March 2023 / Accepted: 28 June 2023 Fundingi 11. Salomon LJ, Duyme M, Crequat J, Brodaty G, Talmant C, Fries N, et al. French
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published maps and institutional affiliations. |
https://openalex.org/W4255931800 | https://jeatdisord.biomedcentral.com/track/pdf/10.1186/s40337-020-00329-w | English | null | Are weight status and weight perception associated with academic performance among youth? | Research Square (Research Square) | 2,020 | cc-by | 7,884 | RESEARCH ARTICLE Open Access Are weight status and weight perception
associated with academic performance
among youth? Maram Livermore1, Markus J. Duncan1, Scott T. Leatherdale2 and Karen A. Patte1* Maram Livermore1, Markus J. Duncan1, Scott T. Leatherdale2 and Karen A. Patte1* (2020) 8:52 (2020) 8:52 Livermore et al. Journal of Eating Disorders
https://doi.org/10.1186/s40337-020-00329-w * Correspondence: kpatte@brocku.ca * Correspondence: kpatte@brocku.ca
1Department of Health Sciences, Brock University, Faculty of Applied Health
Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S
3A1, Canada
Full list of author information is available at the end of the article ,
l list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if
changes were made. The images or other third party material in this article are included in the article's Creative Commons
licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons
licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain
permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the
data made available in this article, unless otherwise stated in a credit line to the data. Abstract Background: Emerging evidence suggests perceptions of being overweight account for many of the psychosocial
consequences commonly associated with obesity. Previous research suggests an obesity achievement gap, yet
limited research has explored weight perception in association with academic performance. Moreover, underweight
perceptions have typically been excluded from research. The current study examined how BMI classification and
weight perception relate to academic performance in a large cohort of youth. Methods: We used cross-sectional survey data from 61,866 grade 9–12 students attending the 122 Canadian
schools that participated in Year 6 (2017/2018) of the COMPASS study. Mixed effect regression models were used
to examine associations between students’ BMI classification and weight perceptions and their math and English/
French course grades. All models were stratified by sex and adjusted for sociodemographic covariates and school
clustering. Results: For English/French grades, males and females with overweight or underweight perceptions were less likely
to achieve higher grades than their peers with perceptions of being at “about the right weight”, controlling for BMI
and covariates. For math grades, females with overweight perceptions, and all students with underweight
perceptions, were less likely to achieve higher grades than their peers with “about the right weight” perceptions. All
students with BMIs in the obesity range were less likely to report grades of 60% or higher than their peers with
“normal-weight” BMIs, controlling for weight perception and covariates. Overweight BMIs were predictive of lower
achievement in females for English/French grades, and in males for math grades, relative to “normal-weight” BMIs. Results for students that did not respond to the weight and weight perception items resembled those for obesity
BMI and overweight/underweight perceptions, respectively. Conclusions: Overall, this study demonstrates that an obesity achievement gap remains when controlling for
students’ perceptions of their weight, and that both underweight and overweight perceptions predict lower
academic performance, regardless of BMI classification. Results suggest barriers to academic success exist among
youth with larger body sizes, and those with perceptions of deviating from “about the right weight”. Keywords: Obesity, Overweight, Academic achievement, Weight perception, Education, Youth * Correspondence: kpatte@brocku.ca
1Department of Health Sciences, Brock University, Faculty of Applied Health
Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S
3A1, Canada
Full list of author information is available at the end of the article Plain language summary with high BMI in North America than other cultures,
possibly due to differing weight norms and given the
stigma associated with overweight and obesity. Emerging
evidence suggests weight perception—individuals’ sub-
jective appraisal of their body weight—accounts for
many of the psychosocial consequences commonly asso-
ciated with obesity [12–14]. That is, the perception of
being overweight, rather than body weight itself, may ac-
count for risks of lower self-concept and poor mental
health. One of the potential factors linking obesity and
the perception of overweight to adverse outcomes is the
experience of stigma and bias. An individual may need
to perceive themselves as overweight, in order to
internalize the bias associated with overweight/obesity. To date, the relationship between self-perceptions of
weight and academic achievement has been largely over-
looked. To our knowledge, only one study has examined
weight perception as a predictor of academic achieve-
ment [15]. Among US adolescents (ages 14 to 17) par-
ticipating in the 2003 Youth Risk Behavior Study, Florin,
Shultz, and Stettler found that perceived overweight sta-
tus was associated with lower grades, regardless of BMI
classification, and that obesity was no longer associated
with grades when controlling for weight perception [15]. Replication is necessary, particularly in more recent
samples, given potential shifts in social weight norms
(e.g., related to obesity prevalence, body positive move-
ments, and anti-obesity stigma and weight bias efforts). Furthermore, consideration of underweight perceptions
in addition to overweight, and exploration of sex or gen-
der differences, are warranted. Related to thinness and
muscularly sociocultural body ideals, girls/women are
more likely to report perceptions of underweight than
boys/men, while boys/men tend to be split between per-
ceptions of underweight and overweight [16]. Regardless
of body size, both overweight and underweight percep-
tions appear detrimental to mental and physical health
relative to perceptions of being “about the right weight”
[12–14, 16–25]; however, the latter has received rela-
tively limited attention. g
g
y
An obesity achievement gap has been suggested as an
early
contributor
to
later
socioeconomic
disparities
found by weight status. To date, limited research has ex-
amined how sociocultural weight norms contribute to
academic
performance. Emerging
evidence
suggests
weight perception—individuals’ subjective appraisal of
their body weight—accounts for many of the psycho-
social consequences commonly associated with obesity. We sought to determine if body weight and weight per-
ceptions predicted grades in a large sample of Canadian
secondary school students. © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if
changes were made. The images or other third party material in this article are included in the article's Creative Commons
licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons
licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain
permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the
data made available in this article, unless otherwise stated in a credit line to the data. Page 2 of 10 Page 2 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Plain language summary It was hypothesized that per-
ceptions of being at “about the right weight” would pro-
vide a protective effect. Overall, this study demonstrates
that an obesity achievement gap remains when control-
ling for students’ perceptions of their weight, and that
weight perceptions—both underweight and overweight—
predict academic performance, regardless of BMI classi-
fication. Results contribute to a body of research that en-
courages the consideration of both overweight and
underweight perceptions and their potential impact on
adolescent emotional and physical health. Further re-
search is needed to determine the mechanisms under-
lying these relationships, in order to remove barriers to
academic success among youth with larger body sizes,
and those with perceptions of deviating from “about the
right weight”. Weight perception Subjective perception of weight status was determined
using the question, “How do you describe your weight?”
Response options included: “very underweight”, “slightly
underweight”, “about the right weight”, “slightly over-
weight” and “very overweight”. Responses were collapsed
into three categories: underweight, about right, and
overweight. In addition, missing weight perception re-
sponses were included as a fourth category. Introduction About 35% of Canadian children and adolescents are at
risk of having overweight or obesity [1]. Numerous stud-
ies have shown that childhood obesity is associated with
various
physical
health
concerns
[2]. Additionally,
larger-bodied adolescents are at increased risk of adverse
psychosocial outcomes [3]. Strauss and Pollack reported
that children and adolescents face many challenges but
“few problems in childhood have as significant an impact
on emotional development as being overweight” (p.747)
[4]. In fact, children with overweight or obesity report
lower quality of life scores than children diagnosed with
cancer [5]. Previous research also indicates the presence
of an obesity achievement gap for children and adoles-
cents [6, 7]. More specifically, some evidence suggests
students with obesity have poorer academic achieve-
ment, more absenteeism, higher dropout rates [6, 8], and
are less likely to pursue and attain post-secondary edu-
cation [9, 10]. Further examination of a potential weight-related
achievement gap is critical to inform a learning environ-
ment that will enable all youth to thrive. Deterrents to
academic achievement in adolescence have critical impli-
cations for future career opportunities and successful
transitions to adulthood, with school failure and dropout
increasing the risk of later unemployment, poverty,
lower quality life, criminality, violence, and various
health risk behaviors [6, 7, 26]. We sought to determine
if larger-bodied students report lower grades in second-
ary school than their peers with “normal-weight” BMIs. In addition, we explored whether weight perceptions
predicted grades, while controlling for weight status. It
was hypothesized that perceptions of being at “about the A recent meta-analysis by He et al. included 60 studies
of weight status and academic performance and found a
pooled correlation (r = −.111) between higher Body Mass
Index (BMI) and lower grades [11]. The researchers con-
cluded that the relationship between weight status and
academic achievement was moderated by geographical
region, with lower grades more likely to be associated Page 3 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Page 3 of 10 Page 3 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 right weight” would provide a protective effect, and any
relationship between BMI classification and academic
achievement would be reduced when controlling for
weight perception. Design and participants The COMPASS study is a prospective cohort study de-
signed to collect longitudinal and hierarchical health
data from a large sample of grade 9 through 12 students
(ages 14–19) enrolled in Canadian secondary schools. Schools and school boards were purposely selected
based on whether they permitted active-information
passive-consent parental permission protocols, which are
critical for collecting robust data among youth [27]. The
COMPASS student questionnaire (Cq), a self-report
paper-and-pencil survey, is completed once annually by
full school samples during one classroom period. All
grade 9 through 12 students attending participating
schools were eligible to participate and could decline at
any time. A full description of recruitment methods [28]
and the COMPASS study are available in print [29] and
online
(www.compass.uwaterloo.ca). The
COMPASS
study received ethics approval from the University of
Waterloo and Brock University Human Research Ethics
Committee and all participating school boards. Academic performance Academic performance was assessed using student-
reported grades. Participants reported their approximate
overall mark in their current or most recent math and
English (in Ontario, Alberta and BC schools) or French
(in Quebec) courses. Grades were dichotomized as ≥60%
or < 60%
for
both
math
and
English/French
grade
models. p
p
g
We used cross-sectional data from Year 6 (2017–2018
school year) of the COMPASS study, which included 66,
434 students at 122 secondary schools in Ontario (n =
61), British Columbia (n = 16), Alberta (n = 8) and Que-
bec (n = 37). The overall student response rate in Year 6
was
81.85%
of
eligible
students. Student
non-
participation primarily resulted from absences or sched-
uled study-periods during data collection. Participants
with missing outcome, sex, or covariate data were re-
moved, leaving a final sample of 61,866 adolescents. Weight status Student weight status was defined by Body Mass Index
(BMI;
kg/m2)
classification
determined
based
on
student-reported height and weight [30], and the World
Health
Organization
[31]
age-and
sex-adjusted
cut
points (underweight, normal weight, overweight, obes-
ity). A previous study found the weight status measure
to be reliable, valid, and valuable for use when objective
methods are not feasible [30]. Given the prevalence of
missing BMI data, and as missing self-reported weight
data may not be missing at random [32], two separate
categories were created for missing weight status based
on which variables were missing to determine BMI clas-
sification: missing BMI classification due to weight not
being reported, and missing BMI due to missing age,
sex, or height. Covariates Participant-reported
race/ethnicity
(categorized
into
white and, non-white minority, multiethnic, or other)
and school grade (9, 10, 11, 12, other [Secondary I- II in
Quebec]) were entered into the model as covariates. Also, student weekly spending/saving money (catego-
rized into $1–$20, $21–$100, >$100, don’t know) was
included as an indicator of part-time employment and/
or allowance, as proxy for student-level SES in the ab-
sence of data on parental income or education data. Statistical analysis R software [33] was used to conduct frequency descrip-
tive statistics and mixed effect logistic regression models. Separate models explored the association between BMI
status and weight perception with math grades and Eng-
lish/French course grades, stratified by sex and control-
ling for weekly spending money, school grade, and race/
ethnicity. Mixed models were used to account for school
clustering by adding a random intercept at the school
level. No interaction effect between weight status and
weight perception was indicated when tested (results not
reported). Descriptive statistics Descriptive statistics for all variables are described in
Table 1. In this sample, 49.4% of participants identified
as male and 50.6% as female. About two-thirds (66.6%)
of the sample identified as white and one-third as non-
white, mixed, or other race/ethnicity. In terms of weight
status, 5.7, 12.0, 54.7 and 3.6% of the total sample had
BMIs in the obesity, overweight, “normal-weight”, and
underweight categories, respectively, while 19.6% of stu-
dents did not report their weight, and the remaining Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 4 of 10 Page 4 of 10 ti
i i
h i ht d t
t
Table 1 Descriptive statistics for secondary school students in
Year 6 (2017/2018) of the COMPASS study (N = 61,886)
Female
(n = 31,334)
Male
(n = 30,552)
% (n)
% (n)
Grade
9
24.3 (7614)
24 (7332)
10
24.5 (7677)
24.3 (7424)
11
23.3 (7301)
23.1 (7058)
12
14.9 (4669)
15.7 (4797)
Othera
13.0 (4073)
12.9 (3941)
Race/ethnicity
White
66.7 (20889)
66.6 (20355)
Non-white, multietnic, or others
33.3 (10445)
33.4 (10197)
BMI Classifications
Underweight
1.5 (470)
2.1 (642)
“Normal Weight”
56.8 (17798)
50.6 (15459)
Overweight
10.3 (3227)
13.3 (4063)
Obesity
4.1 (1285)
7.4 (2261)
Missing weight
21.7 (6799)
19.4 (5927)
Missing age, sex, or height
5.6 (1755)
7.2 (2200)
Weight Perception
Underweight
11.1 (3478)
21.2 (6477)
“About the right weight”
60.7 (19019)
56.2 (17170)
Overweight
26.5 (8304)
20.6 (6294)
Missing
1.7 (533)
2.0 (611)
Weekly Spending Money
None
14.2 (4449)
17.9 (5469)
$1–$20
25.9 (8116)
24.7 (7546)
$21–$100
25.5 (7990)
22.0 (6721)
>$100
16.9 (5295)
20.4 (6233)
Don’t know
17.5 (5484)
15.0 (4583)
Math Grades
60–100%
51.0 (15980)
51.2 (15643)
0–59%
49.0 (15354)
48.8 (14909)
English/French Grades
60–100%
51.3 (16074)
51.1 (15612)
0–59%
48.7 (15260)
48.9 (14940)
aSecondary I-II in Quebec schools
BMI body mass index Table 1 Descriptive statistics for secondary school students in
Year 6 (2017/2018) of the COMPASS study (N = 61,886) weight” (60.7% versus 56.2%) than males. Just over half
of students (51.0–51.3%) reported math and English/
French grades above 60%. g
The concordance between weight perception and BMI
category is presented in Fig. 1. The weighted Kappa was
0.392 among females and 0.370 among males. The ma-
jority of males (74.9%) and females (81.3%) with BMIs in
the obesity category reported perceptions of overweight. Descriptive statistics Among those with overweight BMIs, most females re-
ported perceptions of overweight (62.2%); whereas more
males reported “about right” weight perceptions (54.5%)
than
overweight
perceptions
(42.4%). Most
males
(64.2%) and females (61.5%) in the underweight BMI
category reported underweight perceptions. In the “nor-
mal weight” BMI category, more males reported under-
weight perceptions (27.5%) than females (12.2%), while
females were more likely to perceive their weight as
“about right” (71.6%) or overweight (15.4%) than males
(65.4%; 5.9%). Students with missing BMI data resembled those with
“normal weight” BMIs, except a higher proportion re-
ported overweight perceptions. About half of students
with missing BMI data reported “about right” weight
perceptions (51.1% males; 55.1% females), over a quarter
reported overweight perceptions (25.1% males; 30.8% fe-
males), and 9.7% of females and 19.0% of males reported
underweight perceptions. Discussion The current study examined whether weight status and
student perceptions of their weight were associated with
academic grades in selected secondary school courses
(math and English/French) in a large population study of
Canadian youth. Results support the links between obes-
ity, as determined by BMI, and lower academic perform-
ance in both males and females. Overweight BMI
classifications were also associated with lower odds of
high grades in English/French courses among females,
and in math classes among male students, relative to
BMIs considered “normal-weight”. Similar to previous
research [15], females with overweight perceptions were
less likely to achieve higher course grades in math, and
both males and females with overweight perceptions had
lower odds of grades above 60% in their English/French
courses, relative to their peers with perceptions of being
at “about the right weight”, controlling for BMI classifi-
cation and covariates. While no effect was found for
underweight relative to “normal-weight” BMI, females
and males with perceptions of being underweight had
lower odds of high grades in math and English/French
courses relative to students with “about the right weight”
perceptions. Results for youth with missing BMI or
weight perception data resembled those for obesity BMI
classifications and perceptions of overweight or under-
weight, respectively. Overall, this study demonstrates Math course grades g
See Table 2 for model results testing BMI classification
and weight perception as predictors of math grades, after
stratifying by sex and controlling for covariates. In males
only, having over $100 a week available for spending or
saving and identifying as nonwhite, mixed, or other
race/ethnicity were associated with lower odds of report-
ing math grades over 60%, relative to males without any
weekly spending money and of white race/ethnicity, re-
spectively. Students with BMIs in the obesity range were
less likely to report a math grade above 60% compared
to those with BMIs considered “normal weight”. In
males only, overweight BMIs were associated with a
lower likelihood of report a math grade above 60% com-
pared to those with “normal-weight” BMIs. No effect re-
sulted for underweight BMI relative to “normal-weight”
BMI. In females only, weight perceptions of overweight
predicted a lower likelihood of reporting math grades
above 60% when compared to perceptions of being
“about the right weight”, controlling for BMI classifica-
tion and covariates. In both males and females, percep-
tions
of
underweight
were
associated
with
lower
likelihood of higher math grades than perceptions of be-
ing “about the right weight”. Student with missing BMI
data either due to not reporting weight or missing
height, age or sex data were more likely to have lower proportion were missing sex, age, or height data to
categorize BMI. Additionally, a total of 23.8 and 58.7%
students reported overweight and “about the right
weight” perceptions respectively, while 1.4% did not re-
spond to the weight perception item. More males re-
ported perceptions of “underweight” than females (21.2%
versus 11.1%), while more females reported perceptions
of overweight (26.5% versus 20.6%) and “about the right Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 5 of 10 Fig. 1 Weight perception and BMI category concordance among female and male secondary school students participating in Year 6 (2017/2018)
of the COMPASS study when compared to those with “about the right weight”
perceptions. math grades when compared to those in the “normal-
weight” BMI category. Similarly, students with missing
weight perception data were more likely to report lower
math grades when compared to those with “about the
right weight” perceptions. English/French course grades
bl
h Table 3 summarizes the resultant model testing BMI
classification, weight perception, and covariates as pre-
dictors of English/French grades by sex. Both males and
females identifying as nonwhite, mixed, or other race/
ethnicity had lower odds of English/French grades above
60% than their counterparts identifying as white. No dif-
ferences in English/French grades resulted by spending
money or grade. Both male and female adolescents with
BMIs in the obesity range, and females with overweight
BMIs, were less likely to report higher grades than their
peers with BMIs considered “normal weight”. Both males and females with weight perceptions of
overweight and underweight were less likely to report
higher grades (above 60%) in their English/French clas-
ses when compared to those with perceptions of being
at “about the right weight”. Students with missing BMI
data due to either not reporting weight, or because of
missing height, age, or sex data, had significantly lower
odds of reporting English/French grades above 60%,
when compared to those with “normal-weight” BMIs. Similarly, students with missing weight perception data
were less likely to have English/French grades above 60% Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 6 of 10 Table 2 Mixed-effect model testing BMI category and weight perception as predictors of Math grades ≥60% among youth
Females (N = 31,334)
Males (N = 30,552)
AOR
95% CI
AOR
95% CI
BMI Category (Reference: “Normal weight”)
Obesity
0.70**
0.59–0.82
0.62**
0.55–0.71
Overweight
0.90
0.80–1.02
0.87*
0.79–0.97
Underweight
0.93
0.70–1.25
0.85
0.68–1.07
Missing weight data
0.56**
0.51–0.61
0.62**
0.57–0.68
Missing sex, age, or height data
0.64**
0.55–0.74
0.65**
0.57–0.74
Weight Perception (Reference: “About the right weight”)
Overweight
0.82**
0.75–0.89
0.91
0.83–1.00
Underweight
0.77**
0.69–0.86
0.90*
0.82–0.97
Missing weight perception
0.64**
0.50–0.83
0.59**
0.47–0.73
Race/ethnicity (Reference: White)
Nonwhite, multiethnic, or other
0.92
0.85–1.00
0.87**
0.81–0.94
Grade (Reference: 9)
10
0.82**
0.74–0.90
0.80**
0.73–0.88
11
0.96
0.87–1.07
0.83**
0.75–0.91
12
0.91
0.81–1.02
0.88
0.79–0.99
Othera
1.10
0.95–1.26
1.14
0.99–1.31
Weekly Spending Money (Reference: None)
$1–$20
0.94
0.84–1.05
0.93
0.84–1.02
$21–$100
0.94
0.84–1.05
0.89
0.80–0.99
> $100
0.94
0.83–1.07
0.86*
0.77–0.95
Don’t know
1.05
0.93–1.19
1.02
0.91–1.14
Note: Cross-sectional data from Year 6 (2017/2018) of the COMPASS study (N = 61,886). The outcome reference category is math grades < 60%. English/French course grades
bl
h Mixed models
were used to account for school clustering by adding a random intercept at the school level
*p < .01
**p < .001
aSecondary I-II in Quebec schools Table 2 Mixed-effect model testing BMI category and weight perception as predictors of Math grades ≥60% among youth accounting
for
overweight
perceptions
[15]. Over-
weight perceptions have been linked to poor mental
health, psychosocial distress, and low self-esteem in
adolescents [26, 34–36], factors that have also been
associated with lower academic achievement [37]. In
fact, researchers have reported perceiving oneself as
overweight to be a stronger predictor of behavioural
issues and mental distress than actual weight status
[12, 36, 38]. Similarly, the current results indicate that
perceptions
of
overweight
significantly
predicted
poorer academic outcomes independent of BMI classi-
fication, with the exception of math grades in males. However, unlike Florin et al. [15], obesity BMI classi-
fications remained predictive of lower grades when
controlling for weight perception. that an obesity achievement gap remains when control-
ling for students’ perceptions of their weight, and that
weight perceptions—both underweight and overweight—
predict lower academic performance, regardless of BMI
classification. Further research is needed to determine
the mechanisms underlying these relationships, in order
to remove barriers to academic success among youth
with larger body sizes, and those with perceptions of de-
viating from “about the right weight”. that an obesity achievement gap remains when control-
ling for students’ perceptions of their weight, and that
weight perceptions—both underweight and overweight—
predict lower academic performance, regardless of BMI
classification. Further research is needed to determine
the mechanisms underlying these relationships, in order
to remove barriers to academic success among youth
with larger body sizes, and those with perceptions of de-
viating from “about the right weight”. To the best of our knowledge, only one previous
study has examined weight perception as a predictor
of academic grades. The current study provides neces-
sary replication and builds on existing literature, by
examining these relationships in a more recent and
larger sample of youth. English/French course grades
bl
h In a sample of approximately
11,000 US adolescents participating in the 2003 Youth
Risk Behavior Study, perceptions of overweight were
found to be a stronger predictor of academic out-
comes than BMI, and obesity was no longer a signifi-
cant
predictor
of
academic
performance
when The current study suggests other factors appear to
contribute to the obesity achievement gap, such as par-
ental education, mental health, or external weight bias. Students with obesity are more likely to experience
weight-based bullying within the school context [15, 35]. Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 7 of 10 Table 3 Mixed-effect model testing BMI category and weight perception as predictors of English/French grades ≥60% among
youth
Females (N = 31,334)
Males (N = 30,552)
AOR
95% CI
AOR
95% CI
BMI Category (Reference: “Normal weight”)
Obesity
0.51**
0.41–0.64
0.63**
0.55–0.73
Overweight
0.71**
0.60–0.85
0.87
0.77–0.99
Underweight
1.04
0.68–1.59
0.93
0.71–1.21
Missing weight data
0.45**
0.40–0.50
0.54**
0.49–0.60
Missing sex, age, or height data
0.49**
0.40–0.59
0.58**
0.51–0.66
Weight Perception (Reference: “About the right weight”)
Overweight
0.76**
0.68–0.85
0.83**
0.75–0.92
Underweight
0.59**
0.51–0.69
0.87*
0.79–0.95
Missing weight perception
0.50**
0.36–0.68
0.66**
0.51–0.84
Race/ethnicity (Reference: White)
Nonwhite, multiethnic, or other
0.67**
0.60–0.75
0.74**
0.68–0.80
Grade (Reference: 9)
10
0.96
0.83–1.10
0.94
0.85–1.05
11
0.87
0.75–1.00
0.94
0.84–1.05
12
1.07
0.90–1.27
1.06
0.93–1.21
Othera
1.19
0.98–1.44
1.12
0.97–1.29
Weekly Spending Money (Reference: None)
$1–$20
0.88
0.75–1.03
1.08
0.97–1.21
$21–$100
0.95
0.80–1.11
1.05
0.93–1.18
> $100
0.88
0.74–1.06
0.93
0.83–1.05
Don’t know
0.99
0.84–1.18
1.09
0.96–1.23
Note: Cross-sectional data from Year 6 (2017/2018) of the COMPASS study (N = 61,886). The outcome reference category is English/French grades < 60%. Mixed
models were used to account for school clustering by adding a random intercept at the school level
*p < .01
**p < .001
aSecondary I II in Quebec schools Table 3 Mixed-effect model testing BMI category and weight perception as predictors of English/French grades ≥60% among
th aSecondary I-II in Quebec schools Also, weight bias has been documented in physical
education teachers [9, 39–41] and given its perva-
siveness across the population [9, 39], may contrib-
ute to educators’ perceptions of students’ academic
abilities. Several studies have indicated that the asso-
ciation between BMI and academic performance was
no longer significant when models adjusted for par-
ental/familial characteristics [42, 43]. For instance,
Datar et al. English/French course grades
bl
h concluded that overweight status is not
a causal factor of lower academic performance, as
weight-related differences in test scores became in-
significant
when
social
and
behavioural
variables,
such as SES and parental time spent with the child
were considered [43]. The authors cautioned that
higher weight
students
may be
labeled as
lower
achievers, as weight is a more obvious marker than
sociodemographic characteristics. the high prevalence of obesity, weight stigma continues
to be problematic. Stereotypes that individuals living
with obesity are lazy, unintelligent, or lack willpower
contribute to stigma and discrimination [39]. Internal-
ized stigma, or self-stigma, occurs when individuals
apply negative stereotypes to themselves and believe that
the stigma is deserved [40], leading to low self-esteem
and psychological distress [39]. Research indicates that
bias toward individuals with overweight and obesity per-
sists in health care, employment, and home settings [9]. Education, however, has received less research attention,
particularly at the secondary school level. It is plausible
that adolescents who perceive themselves as overweight
have lower self-concepts related to internalized weight
stigma, which in turn, contributes to poorer academic
engagement and performance. That is, students who feel
their weight is “about right” may be more likely to suc-
ceed
because
they
have
not
internalized
negative
stereotypes. Adolescents who perceive themselves as overweight
may be at risk of internalizing weight stigma. Despite Page 8 of 10 Page 8 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Students with underweight perceptions also reported
lower grades than those with “about right” perceptions. Interestingly, the effect of underweight perceptions was
more consistent than overweight perceptions in predict-
ing lower grades in both females and males, and across
Math and English/French grades. To our knowledge, no
previous study has examined underweight perceptions in
relation to academic performance. While less studied,
underweight perceptions have been associated with de-
pressive and anxiety symptoms in males [21, 44, 45] and
suicidality and lower health-related quality of life in all
youth [25, 38]. Based on this result, it is plausible that
links between weight perception and academic perform-
ance relate more to deviations from the social norm or
sociocultural body ideals than to weight stigma. Results
are consistent with sociocultural body ideals of thinness
for women and muscularity for men, with more males
reporting underweight perceptions than females. Limitations Several limitations require consideration. First, while the
large sample supports generalizability, the COMPASS
study was not designed to be representative. Second,
cross-sectional data was used to explore relationships. Future longitudinal analysis of COMPASS data will as-
sist in establishing temporality and testing potential
mechanistic
contributors
(e.g.,
mental
health,
self-
concept, bullying victimization, school connectedness). Third, the use of self-reported data carries risks of recall
and social desirability bias. For instance, lower achieving
students may over report their achievement. However, a
review of 37 independent samples found strong response
validity of self-reported grades in high school students
[49]. Similarly, weight status was based on student-
reported height and weight, and as such, results likely
reflect greater concordance between weight perception
and weight status than exists. However, time and cost
constraints preclude the feasibility of obtaining objective
height and weight measures, not to mention the poten-
tial harm of weight measurements in a school-based
study. Also, a strong correlation between measured and
self-reported BMI has been shown in youth [30, 50]. Fourth, the reference point that youth used to answer
the weight perception question is not entirely clear. That
is, it is not known whether respondents were comparing
their weight to their ideal body, their peers, a medical
standard, or some other alternative. For instance, re-
sponses of ‘about the right weight’ may indicate weight
satisfaction rather than youths’ perception of how their
weight compared to an external reference point. Lastly,
as discussed, this study did not assess the contribution
of self-esteem or mental health. Mental health may con-
found the relationship between weight status or percep-
tion and academic achievement. Several studies have
linked poor mental health with lower grades [37], and a
recent intervention promoting positive mental health
and wellbeing significantly improved academic grades in
participating schools [51]. Future studies, using longitu-
dinal designs, standardized test grades, and including
mental health, self-concept, and stigma measures should
be considered. Interestingly, students that did not report their body
weight or weight perception tended to have the lowest
likelihood of achieving higher grades, comparable to the
odds for obesity BMI classification. Far more males and
females with missing BMI data reported perceptions of
overweight than their peers with “normal-weight” BMIs. Adolescents are less likely to report their weight as BMI
increases and if they have poor body image [32, 46]. English/French course grades
bl
h About
one-fifth of males and one-tenth of females reported
underweight perceptions; yet only 1.5 and 2.1% of female
and males had BMIs classified as underweight, respect-
ively. Another plausible explanation is that youth with
underweight perceptions were experiencing weight re-
strictions (e.g., due to food insecurity) and/or had lost
weight, while “normal-weight” by BMI, which in turn
contributed to reduced ability to perform in school. Re-
sults highlight the importance of including weight per-
ceptions across the spectrum in future research. weight-based bullying and promote weight acceptance
are also advised. Previous research suggests bullying
victimization predicts changes from perceptions of be-
ing at “about the right weight” to underweight and
overweight perceptions among youth [48]. Limitations Missing self-reported weight status and perceptions may
be influenced by an awareness of societal norms of thin-
ness/muscularity ideals and weight bias attitudes [46,
47]. Hence, if adolescents with larger body sizes did not
report their weight due to concerns of judgment by
others, results lend support to the theory that negative
perceptions regarding body weights outside of “about
right” contribute to lower academic performance. Future research should explore both internalized
and externalized weight bias, and associated lower
self-concept and mental distress, as possible mecha-
nisms explaining links between higher weight status,
and perceptions of overweight and underweight, with
academic achievement. Upstream strategies targeting
the negative connotations of varying body sizes may
prove valuable, to prevent the adverse psychosocial
outcomes associated with perceptions of being over-
weight or underweight. Enhanced efforts to prevent Consent for publication
N/A Consent for publication
N/A Code availability
R
f R software was used for all analysis. Further details available upon request. R software was used for all analysis. Further details available upon request. 8. Lanza HI, Huang DYC. Is obesity associated with school dropout? Key
developmental and ethnic differences. J Sch Health. 2015;85(10):663–70. References 1. Shentow-Bewsh R, Zuberi D. Reducing the prevalence of obesity in Canada:
a call to action. Soc Work Public Health. 2018;33(6):329–41. https://doi.org/
10.1080/19371918.2018.1482252. 2. Must A, Anderson SE. Effects of obesity on morbidity in children and
adolescents. Nutr Clin Care. 2003;6(1):4–48. 3. Erickson SJ, Robinson TN, Haydel KF, Killen JD. Are overweight children
unhappy? Body mass index, depressive symptoms, and overweight
concerns in elementary school children. Arch Pediatr Adolesc Med. 2000;
154(9):931–5. https://doi.org/10.1001/archpedi.154.9.931. 4. Strauss RS, Pollack HA. Social marginalization of overweight children. Arch
Pediatr Adolesc Med. 2003;157(8):746–52. https://doi.org/10.1001/archpedi. 157.8.746. 4. Strauss RS, Pollack HA. Social marginalization of overweight children. Arch
Pediatr Adolesc Med. 2003;157(8):746–52. https://doi.org/10.1001/archpedi. 157.8.746. 5. Schwimmer JB, Burwinkle TM, Varni JW. Health-related quality of life of
severely obese children and adolescents. JAMA. 2003;289(14):1813–9. https://doi.org/10.1001/jama.289.14.1813. Availability of data and materials 14. Atlantis E, Ball K. Association between weight perception and psychological
distress. Int J Obes. 2008;32(4):715–21. COMPASS study data is available upon request through completion and
approval of an online form: https://uwaterloo.ca/compass-system/
information-researchers/data-usage-application. The datasets used during the
current study are available from the corresponding author on reasonable
request. 15. Florin TA, Shults J, Stettler N. Perception of overweight is associated with
poor academic performance in US adolescents. J Sch Health. 2011;81(11):
663–70. https://doi.org/10.1111/j.1746-1561.2011.00642.x. 16. Patte KA, Laxer RE, Qian W, Leatherdale ST. An analysis of weight perception
and physical activity and dietary behaviours among youth in the COMPASS
study. SSM Popul Health. 2016;2:841–9. https://doi.org/10.1016/j.ssmph.2016. 10.016. Funding
Th COM The COMPASS study has been supported by a bridge grant from the CIHR
Institute of Nutrition, Metabolism and Diabetes (INMD) through the “Obesity
– Interventions to Prevent or Treat” priority funding awards (OOP-110788;
awarded to SL), an operating grant from the CIHR Institute of Population
and Public Health (IPPH) (MOP-114875; awarded to SL), a CIHR project grant
(PJT-148562; awarded to SL), a CIHR bridge grant (PJT-149092; awarded to
KP/SL), a CIHR project grant (PJT-159693; awarded to KP), and by a research
funding arrangement with Health Canada (#1617-HQ-000012; contract
awarded to SL). 11. He J, Chen X, Fan X, Cai Z, Huang F. Is there a relationship between body
mass index and academic achievement? A meta-analysis. Public Health. 2019;167:111–24. https://doi.org/10.1016/j.puhe.2018.11.002. 12. Ter Bogt Tom FM, Van Dorsselaer SA, Monshouwer K, Verdurmen J, Engels
R, Vollebergh W. Body mass index and body weight perception as risk
factors for internalizing and externalizing problem behavior among
adolescents. J Adolesc Health. 2006;39(1):27–34. 13. Roberts RE, Duong HT. Perceived weight, not obesity, increases risk for
major depression among adolescents. J Psychiatr Res. 2013;47(8):1110–7. https://doi.org/10.1016/j.jpsychires.2013.03.019. Acknowledgements 6. Shore SM, Sachs ML, Lidicker JR, Brett SN, Wright AR, Libonati JR. Decreased
scholastic achievement in overweight middle school students. Obesity. 2008;16(7):1535–8. https://doi.org/10.1038/oby.2008.254. g
The authors would like to thank the schools, school boards, and students
that have participated in the COMPASS study, and all COMPASS staff and
team members. 7. Benson R, Von Hippel PT, Lynch JL. Does more education cause lower BMI,
or do lower-BMI individuals become more educated? Evidence from the
National Longitudinal Survey of youth 1979. Soc Sci Med. 2018;211:370–7. https://doi.org/10.1016/j.socscimed.2017.03.042. Received: 25 July 2020 Accepted: 28 September 2020 Received: 25 July 2020 Accepted: 28 September 2020 Received: 25 July 2020 Accepted: 28 September 2020 Conclusion Results support the existence of an achievement gap by
both weight status and weight perception. This study
has widespread implications with over 2 million adoles-
cents at risk of having overweight or obesity in Canada Page 9 of 10 Page 9 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 [1], and over 40% of youth reporting weight perceptions
other than “about right”. Research is needed to further
examine the mechanisms underlying these associations. Academic achievement sets a lifelong trajectory of health
and wellbeing. Lower academic achievement is linked to
increased rates of unemployment, poverty, criminality,
and negative future health outcomes [6, 7, 26, 52]. The
obesity achievement gap has been suggested as an early
contributor to later SES disparities found by weight sta-
tus [53]. The present study contributes to a body of re-
search
that
encourages
the
consideration
of
both
overweight and underweight perceptions and their po-
tential impact on adolescent emotional and physical
health. Upstream strategies to prevent negative connota-
tions associated with body sizes divergent from “about
right” and to promote weight acceptance merit consider-
ation. Further exploration is necessary to inform policies
and interventions that foster a learning environment that
will enable all youth to thrive. Authors’ contributions ML lead the writing of the manuscript. MJD conducted all analysis. STL is the
PI of the COMPASS Study. ML and KAP conceptualized the manuscript study. All authors (ML, MJD, STL, KAP) contributed to manuscript revisions, results
interpretation, and approved the final version. p
9. Puhl RM, Heuer CA. The stigma of obesity: a review and update. Obesity. 2009;17(5):941–64. https://doi.org/10.1038/oby.2008.636. y
2009;17(5):941–64. https://doi.org/10.1038/oby.2008.636. 10. Larsen JK, Kleinjan M, Engels R, Fisher JO, Hermans R. Higher weight, lower
education: a longitudinal association between adolescents’ body mass
index and their subsequent educational achievement level? J Sch Health. 2014;84(12):769–76. https://doi.org/10.1111/josh.12212. Author details
1 1Department of Health Sciences, Brock University, Faculty of Applied Health
Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S
3A1, Canada. 2School of Public Health and Health Systems, University of
Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada. Ethics approval and consent to participate The University of Waterloo Office of Research Ethics (ORE#17264) and
participating school boards approved all procedures. All students attending
participating schools were invited to participate using active-information
passive-consent parental permission protocols. Students could withdraw
from the study at any time. 17. Neumark-Sztainer DR, Wall MM, Haines JI, Story MT, Sherwood NE, van den
Berg PA. Shared risk and protective factors for overweight and disordered
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on the health behaviors of college students. Am J Health Educ. 2016;47(5):
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dietary intake measures in the COMPASS questionnaire: are the self-
reported measures of body mass index (BMI) and Canada’s food guide
servings robust? Int J Behav Nutr Phys Act. 2013;10(1):42. https://doi.org/10. 1186/1479-5868-10-42. 30. Leatherdale ST, Laxer RE. Reliability and validity of the weight status and
dietary intake measures in the COMPASS questionnaire: are the self-
reported measures of body mass index (BMI) and Canada’s food guide
servings robust? Int J Behav Nutr Phys Act. 2013;10(1):42. https://doi.org/10. 1186/1479-5868-10-42. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in
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growthref/en/. Accessed 20 Aug 2019. 31. WHO. Growth reference data for 5–19 years. https://www.who.int/
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review. Obes Rev. 2018;19(8):1141. Publisher’s Note https://doi.org/10.1111/obr.12701. |
https://openalex.org/W4255605386 | https://zeitschrift-suburban.de/sys/index.php/suburban/article/download/346/577 | German | null | Titelbild | Sub\urban | 2,018 | cc-by-sa | 202 | zeitschrift für kritische stadtforschung
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zeitschrift für kritische stadtforschung aufsätze ‚Neue soziale Stadtpolitik‘
in Hamburg als Strategie der
Verbürgerlichung
Moritz Rinn ‚Demenzfreundliche
Kommunen‘ zwischen
sozialstaatlichem Sparmodell
und Emanzipationsgewinn
Mike Laufenberg debatte Die Kritik zerbricht an der
documenta
Tim König
Machtverhältnisse überall
analysieren! Jenny Künkel
Elitenkritik, populare Bündnisse
und inklusive Solidarität
Violetta Bock, Thomas Goes, Lisa Vollmer Elitenkritik, populare Bündnisse
und inklusive Solidarität
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und inklusive Solidarität
Violetta Bock, Thomas Goes, Lisa Vollmer magazin Feministische Klassenpolitiken
in Kämpfen um soziale
Reproduktion
Julia Dück Das BID Reeperbahn+ und die
Kampagne „St. Pauli pinkelt
zurück“
Friederike Häuser rezensionen
Erfolgreiches Scheitern eines
politischen Projekts
Sofrony Riedmann
„Morningside Park: A Civil
Rights Battleground“
Maxi Schreiber
Die logistische Stadt
Fabian Namberger |
https://openalex.org/W4394758381 | https://www.ajtmh.org/downloadpdf/view/journals/tpmd/110/5/article-p1010.pdf | English | null | Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Longitudinal Study | The American journal of tropical medicine and hygiene | 2,024 | cc-by | 3,795 | *Address correspondence to Jeremy D. Keenan, Proctor Foundation,
University of California San Francisco, 490 Illinois St., P.O. Box 0944,
San Francisco, CA 94158. E-mail: jeremy.keenan@ucsf.edu
†These authors contributed equally to this work. Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Lo Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Longitudinal Study
Neha Pondicherry,1† Amza Abdou,2† Boubacar Kadri,2 Beido Nassirou,2 Sun Y. Cotter,1 Nicole E. Varnado,1 Travis C. Porco,1,3
Sheila K. West,4 Thomas M. Lietman,1,3,5,6 and Jeremy D. Keenan1,3*
1Francis I. Proctor Foundation, University of California, San Francisco, California; 2Programme National de Sante Oculaire, Niamey, Niger;
3Department of Ophthalmology, University of California, San Francisco, California; 4Dana Center for Preventive Ophthalmology, Wilmer Eye
Institute, Johns Hopkins University, Baltimore, Maryland; 5Department of Epidemiology & Biostatistics, University of California, San Francisco,
California; 6Institute for Global Health, University of California, San Francisco, California 1Francis I. Proctor Foundation, University of California, San Francisco, California; 2Programme National de Sante Oculaire, Niamey, Niger;
3Department of Ophthalmology, University of California, San Francisco, California; 4Dana Center for Preventive Ophthalmology, Wilmer Eye
Institute, Johns Hopkins University, Baltimore, Maryland; 5Department of Epidemiology & Biostatistics, University of California, San Francisco,
California; 6Institute for Global Health, University of California, San Francisco, California Abstract. Millions of doses of azithromycin are distributed each year for trachoma, yet the treatment efficacy of a
single dose of azithromycin for ocular Chlamydia infection has not been well characterized. In this study, four villages in
Niger received a mass azithromycin distribution for trachoma. All 426 children aged 0–5 years residing in the study
villages were offered conjunctival swabbing every 6 months to test for ocular Chlamydia trachomatis. Among the children
infected with ocular Chlamydia before treatment, 6% (95% CI: 2–15%) tested positive for ocular Chlamydia infection 6
months later, and 15% (95% CI: 7–28%) tested positive 12 months later. The most important predictor of post-treatment
ocular Chlamydia infection was pretreatment ocular Chlamydia infection (relative risk: 3.5, 95% CI: 1.3–9.4). Although the
6-monthly monitoring schedule was suboptimal for testing the treatment efficacy of an antibiotic, these findings are
nonetheless consistent with high treatment efficacy of a single dose of azithromycin and suggest that additional interven-
tions might be most effective if targeted to those children infected prior to treatment. INTRODUCTION each study visit. In addition, one village from each of the four
treatment groups was randomly selected for longitudinal
monitoring, in which the same children were followed up at
each visit (Figure 1). Here, we report results from these four
longitudinally monitored villages for the period after their first
mass azithromycin distribution (i.e., months 0–12 for the two
annually treated villages and months 0–6 for the two biannu-
ally treated villages). Trachoma, the leading infectious cause of blindness world-
wide, is caused by ocular infection with Chlamydia trachomatis. As of July 2023, around 116 million people worldwide remained
at risk.1 The WHO recommends 3–5years of annual mass
azithromycin distributions in districts where $10% of children
aged 1–9years have trachomatous inflammation–follicular (TF),
according to the WHO’s simplified grading system.2 Despite
the millions of doses of azithromycin distributed each year for
trachoma, few studies have assessed the treatment efficacy
of a single dose of azithromycin for an individual child with
ocular Chlamydia infection.3–5 The objectives of the present
study were to estimate the treatment efficacy of a single dose
of azithromycin and to determine factors associated with an
increased incidence of ocular Chlamydia infection. y
g
)
At all monitoring visits, the upper right eyelid was everted
and graded for the presence of TF and trachomatous
inflammation–intense (TI) according to the WHO’s simplified
grading system. Conjunctival swabs of the everted right
superior tarsal conjunctiva were collected without media and
transported to the University of California, San Francisco,
where they were stored at 280C. Swabs were pooled in
groups of five and processed for C. trachomatis with the
AMPLICOR polymerase chain reaction assay (Roche Diag-
nostics, Indianapolis, IN); swabs from positive pools were
subsequently tested individually. Details of swab storage,
transport, and processing are reported elsewhere.6 Log-
binomial regression models incorporating a random inter-
cept for a village were used to estimate incidences and to
assess for risk factors of post-treatment infection at month 6
and month 12. Analyses were performed using R, version
4.1.3 (R Foundation for Statistical Computing) with a signifi-
cance level of 0.05. MATERIALS AND METHODS This study describes a non-prespecified analysis of chil-
dren treated with azithromycin in 2010–2011 at the Niger site
of the cluster-randomized Partnership for the Rapid Elimina-
tion of Trachoma (PRET) trial.6 As part of the PRET trial,
all residents from 48 villages in Matameye District, Zinder
Region, Niger were enumerated on a door-to-door census. In 2010 the prevalence of TF among 0–5-year-olds in the
study area was approximately 25%.6 Villages were subse-
quently randomized in a factorial design to annual versus
biannual mass azithromycin distributions and to standard
(i.e., $80%) versus enhanced (i.e., $90%) antibiotic cover-
age, with coverage targets based on the most recent study
census. During the antibiotic distributions, a single dose of
azithromycin was offered to each community member (1 g
for adults, 20 mg/kg for children). Trachoma monitoring was
performed at biannual study visits, with a new random sam-
ple of 0–5-year-old children selected from each village at Ethical approval was obtained from the Committee on
Human Research at the University of California, San Francisco
and the Comite d’Ethique du Niger. Owing to the high preva-
lence of illiteracy in the study area, the ethical boards approved
verbal consent, which was obtained from community leaders
before randomization and from participants or a caregiver at the
time of antibiotic distribution and examinations. Am. J. Trop. Med. Hyg., 110(5), 2024, pp. 1010–1013
doi:10.4269/ajtmh.23-0540
Copyright © 2024 The author(s) Am. J. Trop. Med. Hyg., 110(5), 2024, pp. 1010–1013
doi:10.4269/ajtmh.23-0540
Copyright © 2024 The author(s) RESULTS The two biannually treated villages
quently received a mass azithromycin distribution at
6 and thus did not contribute data from the month 12
visit for this analysis. In the two annually treated com
ties that did not receive additional azithromycin over t
year 215 of the 257 (84%) children swabbed at b
PRET Trial
48 villages in Niger
Randomized
Annual azithromycin
Enhanced coverage: 12 villages
Standard coverage: 12 villages
Biannual azithromycin
Enhanced coverage: 12 villages
Standard coverage: 12 villages
Randomly selected for longitudinal sampling
2 villages (1 enhanced, 1 standard)
264 children 0-59 months
Randomly selected for longitudinal sampling
2 villages (1 enhanced, 1 standard)
190 children 0-59 months
Swabbed at 6 months
231 children
Swabbed at 6 months
147 children
Swabbed at 12 months
215 children
Swabbed at baseline
264 children
Swabbed at baseline
190 children
Analyzed
231 children at 6 months
215 children at 12 months
Analyzed
147 children at 6 months
0 children at 12 months
Lost to follow-up
6 mos only: 13
12 mos only: 29
6 and 12 mos: 13
Lost to follow-up
6 mos only: 22
Treated at baseline
257 children
Treated at baseline
169 children
Next round of mass azithromycin
Next round of mass azithromycin
FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. PRET Trial
48 villages in Niger Randomized Annual azithromycin
Enhanced coverage: 12 villages
Standard coverage: 12 villages Swabbed at 12 months
215 children Lost to follow-up
6 mos only: 22 Analyzed
147 children at 6 months
0 children at 12 months Analyzed
231 children at 6 months
215 children at 12 months FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. follow-up and those remaining in follow-up (Table 1). Of the
378 children with a month 6 swab, 68 had evidence of
Chlamydia infection at baseline, of whom four were infected
6 months after receiving azithromycin (6%, 95% CI: 2–15%). Conversely,
of
310
uninfected
children
who
received
the baseline azithromycin treatment and participated in
the month 6 monitoring, 11 were infected at month 6 (3%, 95% CI: 1–8%). The two biannually treated villages subse-
quently received a mass azithromycin distribution at month
6 and thus did not contribute data from the month 12 study
visit for this analysis. RESULTS At the baseline visit, 426 children aged 0–59 months from
the four longitudinally monitored villages contributed a con-
junctival swab and then received azithromycin treatment, of
whom 378 (89%) were again swabbed 6 months later. Base-
line characteristics were similar between children lost to 1010 1011 AZITHROMYCIN EFFICACY FOR TRACHOMA up and those remaining in follow-up (Table 1). Of the
hildren with a month 6 swab, 68 had evidence of
ydia infection at baseline, of whom four were infected
ths after receiving azithromycin (6%, 95% CI: 2–15%). rsely,
of
310
uninfected
children
who
received
aseline azithromycin treatment and participated in
onth 6 monitoring 11 were infected at month 6 (3%
95% CI: 1–8%). The two biannually treated villages
quently received a mass azithromycin distribution at
6 and thus did not contribute data from the month 1
visit for this analysis. In the two annually treated com
ties that did not receive additional azithromycin over t
year, 215 of the 257 (84%) children swabbed at b
were again swabbed at month 12 Among these 215 c
PRET Trial
48 villages in Niger
Randomized
Annual azithromycin
Enhanced coverage: 12 villages
Standard coverage: 12 villages
Biannual azithromycin
Enhanced coverage: 12 villages
Standard coverage: 12 villages
Randomly selected for longitudinal sampling
2 villages (1 enhanced, 1 standard)
264 children 0-59 months
Randomly selected for longitudinal sampling
2 villages (1 enhanced, 1 standard)
190 children 0-59 months
Swabbed at 6 months
231 children
Swabbed at 6 months
147 children
Swabbed at 12 months
215 children
Swabbed at baseline
264 children
Swabbed at baseline
190 children
Analyzed
231 children at 6 months
215 children at 12 months
Analyzed
147 children at 6 months
0 children at 12 months
Lost to follow-up
6 mos only: 13
12 mos only: 29
6 and 12 mos: 13
Lost to follow-up
6 mos only: 22
Treated at baseline
257 children
Treated at baseline
169 children
Next round of mass azithromycin
Next round of mass azithromycin
FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. up and those remaining in follow-up (Table 1). Of the
hildren with a month 6 swab, 68 had evidence of
ydia infection at baseline, of whom four were infected
hs after receiving azithromycin (6%, 95% CI: 2–15%). sely,
of
310
uninfected
children
who
received
seline azithromycin treatment and participated in
95% CI: 1–8%). DISCUSSION The treatment efficacy of azithromycin for C. trachomatis
has mostly been studied in the context of sexually transmit-
ted infections. For sexually transmitted Chlamydia, a single
dose of azithromycin is thought to be 90–95% effective
for urogenital infections but only 75% effective for rectal
Chlamydia.7–9 The limited studies that have assessed the
treatment efficacy of azithromycin for ocular Chlamydia have
had variable results, with testing done 2–6 months after drug
administration, suggesting a treatment efficacy between
70% and 94% for single-dose therapy.3,4 The present study,
conducted in a trachoma-mesoendemic setting during an
initial round of mass antibiotic treatments, found that 94% of
infected children tested negative for Chlamydia 6 months
after a single dose of azithromycin and that the most impor-
tant risk factor for being infected with ocular Chlamydia after
a mass antibiotic distribution was ocular Chlamydia infection
prior to treatment. The values in the table are numbers (proportion). CT 5 ocular Chlamydia trachomatis;
LTFU 5 lost to follow-up; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous
inflammation–intense. with 12-month follow-up, 48 were infected at baseline, of
whom 7 also tested positive for Chlamydia at month 12
(15%, 95% CI: 7–28%), and 167 were not infected at
baseline, of whom 7 were infected at month 12 (4%,
95% CI: 2–10%). Post-treatment Chlamydia infection was more common
among younger children and those with TF or TI at baseline,
although the association with these baseline characteristics
did not achieve statistical significance in the present study. The most important risk factor for post-treatment chlamydial
infection in this population was the presence of ocular
Chlamydia infection prior to treatment, a finding consistent
with several previous studies.10,11 Thus, this study provides )
Associations between pretreatment exposures and ocular
Chlamydia outcomes 6 and 12 months after treatment
are shown in Table 2. RESULTS In the two annually treated communi-
ties that did not receive additional azithromycin over the first
year, 215 of the 257 (84%) children swabbed at baseline
were again swabbed at month 12. Among these 215 children 1012 PONDICHERRY, ABDOU, AND OTHERS TABLE 1
Baseline characteristics of children who participated in follow-up
visits and of those lost to follow-up at the 6-month and
12-month study visits
Pretreatment
Exposure
6 Months after Treatment
in Four Villages
12 Months after
Treatment in Two Villages
Participated
(n 5 378)
LTFU
(n 5 48)
Participated
(n 5 215)
LTFU
(n 5 42)
Age
,1 year
49 (13%)
9 (19%)
25 (12%)
5 (12%)
1 year
69 (18%)
11 (23%)
46 (21%)
3 (7%)
2 years
79 (21%)
12 (25%)
50 (23%)
15 (36%)
3 years
97 (26%)
8 (17%)
52 (24%)
10 (24%)
4 years
84 (22%)
8 (17%)
42 (20%)
9 (21%)
Sex
Female
186 (49%)
21 (44%)
109 (51%)
16 (38%)
Male
192 (51%)
27 (56%)
106 (49%)
26 (62%)
TF
Absent
274 (72%)
43 (90%)
149 (69%)
29 (69%)
Present
104 (28%)
5 (10%)
66 (31%)
13 (31%)
TI
Absent
340 (90%)
45 (94%)
192 (89%)
39 (93%)
Present
38 (10%)
3 (6%)
23 (11%)
3 (7%)
CT
Negative
310 (82%)
41 (85%)
167 (78%)
30 (71%)
Positive
68 (18%)
7 (15%)
48 (22%)
12 (29%)
Sibling with CT
Yes
237 (63%)
31 (65%)
117 (54%)
26 (62%)
No
141 (37%)
17 (35%)
98 (46%)
16 (38%)
The values in the table are numbers (proportion). CT 5 ocular Chlamydia trachomatis;
LTFU 5 lost to follow-up; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous
inflammation–intense. post-treatment ocular Chlamydia infection was pretreatment
ocular Chlamydia infection, which conveyed a relative risk
of 1.6 (95% CI: 0.5–4.7; P 5 0.43) at 6 months and 3.5
(95% CI: 1.3–9.4; P 5 0.01) at 12 months. None of the other
potential exposure variables (e.g., sex, age, presence of TF
at baseline, presence of TI at baseline, or presence of an
infected sibling at baseline) had significant associations with
post-treatment ocular Chlamydia. TABLE 1 Baseline characteristics of children who participated in follow-up
visits and of those lost to follow-up at the 6-month and
12-month study visits statistics
associations with P
0.05.
* Odds ratio estimated with Firth’s penalized logistic regression because of complete separation. CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface
statistics
associations with P ,0 05 CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–
statistics 5 associations with P ,0.05. CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model;
statistics 5 associations with P ,0.05. R 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 tracho
tatistics 5 associations with P ,0 05 CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface
statistics 5 associations with P ,0.05. zed logistic regression because of complete separation. DISCUSSION The most important predictor of TABLE 2
Associations between pretreatment exposures and ocular Chlamydia infection at 6 and 12 months after a single dose of azithromycin
Pretreatment Exposure
6 Months after Treatment, n 5 4 Communities (N 5 378 children)
12 Months after Treatment, n 5 2 Communities (N 5 215 children)
CT1/Total
PR (95% CI)
CT1/Total
PR (95% CI)
Age
,1 year
3/49 (6%)
Reference
3/25 (12%)
Reference
1 year
0/69 (0%)
0.1 (0–0.1.0)*
1/46 (2%)
0.2 (0–1.7)
2 years
6/79 (8%)
1.2 (0.3–5.1)*
3/50 (6%)
0.5 (0.1–2.3)
3 years
4/97 (4%)
0.6 (0.15–3.0)*
4/52 (8%)
0.6 (0.2–2.7)
4 years
2/84 (2%)
0.4 (0.1–2.2)*
3/42 (7%)
0.6 (0.1–2.7)
Sex
Female
11/186 (6%)
Reference
10/109 (9%)
Reference
Male
4/192 (2%)
0.3 (0.1–1.0)
4/106 (4%)
0.4 (0.1–1.3)
TF
Absent
10/274 (4%)
Reference
9/149 (6%)
Reference
Present
5/104 (5%)
1.4 (0.5–3.8)
5/66 (8%)
1.3 (0.4–3.6)
TI
Absent
13/340 (5%)
Reference
11/192 (6%)
Reference
Present
2/38 (4%)
1.7 (0.4–7.3)
3/23 (13%)
2.3 (0.7–7.6)
CT
Negative
11/310 (4%)
Reference
7/167 (4%)
Reference
Positive
4/68 (6%)
1.6 (0.5–4.7)
7/48 (15%)
3.5 (1.3–9.4)
Sibling with CT
Yes
6/237 (3%)
Reference
7/117 (6%)
Reference
No
9/141 (6%)
2.2 (0.8–6.3)
7/98 (7%)
1.2 (0.4–3.3)
CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface AZITHROMYCIN EFFICACY FOR TRACHOMA 1013 Financial support: This study was supported by the Bill & Melinda
Gates Foundation (grant OPP48027). Financial support: This study was supported by the Bill & Melinda
Gates Foundation (grant OPP48027). some evidence that additional interventions may be most
effective if targeted to children with chlamydial infection prior
to mass drug administration. Randomized trials are starting
to test this hypothesis. In one trial set in a hyper-endemic
area of Ethiopia, triannual azithromycin distributions were
targeted only to those 0–5 years old with Chlamydia infection
prior to a round of mass azithromycin treatment. Although
this strategy was not found to be effective, the prevalence of
ocular Chlamydia among older children not eligible for tar-
geted treatments was high and likely led to increased trans-
mission.12 Targeted treatments may be more effective if
given as a supplement to routine annual mass azithromycin
distributions. An ongoing trial is testing such a strategy
(clinicaltrials.gov NCT03335072). Authors’ addresses: Neha Pondicherry, Sun Y. Cotter, Nicole E. Varnado, Travis C. Porco, Thomas M. Lietman, and Jeremy D. DISCUSSION Keenan,
University of California, San Francisco, CA, E-mails: neha.pondicherry@
ucsf.edu, sun.cotter@ucop.edu, nvarnado@stanford.edu, travis.porco@
ucsf.edu, tom.lietman@ucsf.edu, and jeremy.keenan@ucsf.edu. Abdou
Amza, Boubacar Kadri, and Beido Nassirou, Programme Nationale de
Sante Oculaire, Niamey, Niger, E-mails: dr.amzaabdou@gmail.com,
boubacarkadri@gmail.com, and nasbeido@yahoo.fr. Sheila K. West,
Dana Center for Preventive Ophthalmology, Johns Hopkins School of
Medicine, Baltimore, MD, E-mail: shwest@jhmi.edu. This is an open-access article distributed under the terms of the
Creative Commons Attribution (CC-BY) License, which permits
unrestricted use, distribution, and reproduction in any medium, pro-
vided the original author and source are credited. (
g
)
This study has limitations. Treatment efficacy was esti-
mated based on ocular Chlamydia monitoring performed
6 and 12 months after treatment. The infrequency of visits
may have increased the chances of misclassification as
some children may have cleared their infection after receiving
antibiotics but then been reinfected in the intervening
6 months, and others may have failed to clear their infection
after treatment but nonetheless had spontaneous resolution
of infection. However, prior longitudinal studies have sug-
gested that the median duration of an ocular chlamydial
infection is approximately 17weeks, increasing the chances
that a negative post-treatment test represents treatment suc-
cess as well as the plausibility that an infection observed 6
months after treatment represents treatment failure.13 Geno-
typic results might have been useful to differentiate treatment
failures from reinfections, and antimicrobial susceptibility
results could have been useful to determine the likelihood of
treatment failure, but neither was performed as part of this
study. Although baseline characteristics were similar, it is
possible that rates of reinfection could have been different for
the approximately 10–15% of children lost to follow-up. Poly-
merase chain reaction tests, although highly sensitive and
specific, are not perfect. The results are representative of the
larger sample of villages enrolled in PRET and likely generaliz-
able to other trachoma-endemic areas of Niger but may not
be generalizable to areas with a different endemicity of tra-
choma or different patterns of trachoma transmission.6 REFERENCES 1. World Health Organization, 2023. WHO Alliance for the Global
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Hygiene and Tropical Medicine, International Trachoma Initiative,
2006. Trachoma Control: A Guide for Programme Managers. Geneva, Switzerland: WHO. 3. Schachter J et al., 1999. Azithromycin in control of trachoma. Lancet 354: 630–635. 4. Andreasen AA, Burton MJ, Holland MJ, Polley S, Faal N,
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Guy R, Bradshaw C, Hocking JS, 2014. Azithromycin versus
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59: 193–205. 8. Dombrowski JC, Wierzbicki MR, Newman LM, Powell JA, Miller
A, Dithmer D, Soge OO, Mayer KH, 2021. Doxycycline versus
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atic rectal Chlamydia trachomatis. N Engl J Med 384: 2418–
2427. This study found that 94% of children infected at baseline
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a single dose of azithromycin. The most important risk factor
for ocular Chlamydia infection after a mass azithromycin
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ments are instituted to further interrupt Chlamydia transmis-
sion (e.g., supplemental antibiotic treatments), one approach
might be to focus on those most likely to have pretreatment
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mycin for trachoma: when is one round enough? Results
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AW, Foster A, Bailey RL, Mabey DC, 2005. Infection with
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https://openalex.org/W4299956070 | https://scholarworks.wm.edu/cgi/viewcontent.cgi?article=1091&context=vimsarticles | English | null | Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature | Carolina Digital Repository (University of North Carolina at Chapel Hill) | 2,010 | cc-by | 12,734 | W&M ScholarWorks
W&M ScholarWorks
VIMS Articles
Virginia Institute of Marine Science
2010
Evolutionary Characters, Phenotypes and Ontologies: Curating
Evolutionary Characters, Phenotypes and Ontologies: Curating
Data from the Systematic Biology Literature
Data from the Systematic Biology Literature
Wasila M. Dahdul
et al W&M ScholarWorks
W&M ScholarWorks Virginia Institute of Marine Science Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/vimsarticles Part of the Marine Biology Commons Part of the Marine Biology Commons Recommended Citation
Recommended Citation
Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes
and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708.
doi:10.1371/journal.pone.0010708 This Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M
ScholarWorks. It has been accepted for inclusion in VIMS Articles by an authorized administrator of W&M
ScholarWorks. For more information, please contact scholarworks@wm.edu. Abstract doi:10.1371/journal.pone.0010708 Received November 12, 2009; Accepted April 6, 2010; Published May 20, 20 ovember 12, 2009; Accepted April 6, 2010; Published May 20, 20 Copyright: 2010 Dahdul et al. This is an open-access article distributed under the terms of the Creative Commons Attributi
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors thank National Science Foundation (DBI 0641025), National Institutes of Health (HG002659), and the National Evolutionary Synthesis
Center (NSF EF-0423641) for the support of this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of
the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: wasila.dahdul@usd.edu (WMD); pmabee@usd.edu (PMM) Wasila M. Dahdul1,2*, James P. Balhoff2,3, Jeffrey Engeman1, Terry Grande4, Eric J. Hilton5, Cartik
Kothari2,3, Hilmar Lapp2, John G. Lundberg6, Peter E. Midford2, Todd J. Vision2,3, Monte Westerfield7,
Paula M. Mabee1* Wasila M. Dahdul1,2*, James P. Balhoff2,3, Jeffrey Engeman1, Terry Grande4, Eric J. Hilton5, Cartik
Kothari2,3, Hilmar Lapp2, John G. Lundberg6, Peter E. Midford2, Todd J. Vision2,3, Monte Westerfield7,
Paula M. Mabee1* 1 Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America, 2 National Evolutionary Synthesis Center, Durham, North
Carolina, United States of America, 3 Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America,
4 Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America, 5 Department of Fisheries Science, Virginia Institute of Marine Science,
College of William and Mary, Gloucester Point, Virginia, United States of America, 6 Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America,
7 Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America Recommended Citation
Recommended Citation Recommended Citation
Recommended Citation
Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes
and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708. doi:10.1371/journal.pone.0010708 s Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M This Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M
ScholarWorks. It has been accepted for inclusion in VIMS Articles by an authorized administrator of W&M
ScholarWorks. For more information, please contact scholarworks@wm.edu. PLoS ONE | www.plosone.org Abstract Background: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations
of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage
to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are
amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing
the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. Methodology/Principal Findings: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic
studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of
integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish,
http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these
publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ
formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies
(Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology
(Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were
developed in response to the challenges that were evident from two annotation experiments and from feedback from
curators. Conclusions/Significance: The challenges we encountered and many of the curation standards and methods for improving
consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is
because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype,
among individual humans, or across the diversity of species, requires a process by which a precise combination of terms
from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed
in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss
some ramifications of EQ representation for the domain of systematics. Citation: Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the
Systematic Biology Literature. PLoS ONE 5(5): e10708. Introduction For
example, a query with the term dorsal fin will also return dorsal fin
ray because of its part_of relationship to dorsal fin. The Entity-
Quality (EQ) formalism, which combines ‘entity’ terms from an
anatomical or other ontology (e.g., ontologies that describe
observable organism features such as behavior), with non-taxon-
specific ‘quality’ terms from the Phenotype and Trait Ontology
(PATO) [9,10,11] has been employed in phenotype descriptions of
model organism mutants, where it has been shown to facilitate the
identification of biologically similar phenotypes in different species
[12]. Ontologies and the EQ formalism have also recently been
applied to the standardization of taxonomic descriptions [13]. While the curation of data from the literature, and the annotation
or tagging of those data using ontology terms, may be practices
that are less familiar to evolutionary biologists than those in
molecular genetics communities, they are nonetheless closely
analogous to the curation of museum specimens and their
associated metadata, such as locality. Figure 1. A systematic character and state, compared to a
phenotype represented by Entity-Quality syntax. In EQ syntax,
the entity being described is represented by a term from an anatomical
ontology, and the variable (‘‘characteristic’’) aspect of the entity is
represented using a term chosen from a quality ontology. Note that the
‘‘shape’’ attribute is an explicit part of the systematic character but is
expressed only implicitly within the quality term. doi:10.1371/journal.pone.0010708.g001 As part of the Phenoscape Project (http://www.phenoscape. org), which aims to integrate model organism with evolutionary
phenotype data using ontologies, we mounted a large-scale
initiative to curate a significant data set of evolutionarily-varying
phenotypes from the phylogenetic systematic literature. Specifi-
cally, we curated 4,617 characters pertaining to a monophyletic
group of teleostean fishes, the Ostariophysi (catfishes, characins,
knifefishes, carps, and minnows; [21]), which also includes the
model organism, zebrafish (Danio rerio). There are many decisions
and details involved in the implementation that are not necessarily
intuitive or straightforward; these decisions affect how the
annotated data can be used. As a result of this experience, we
recommend standards and procedures that will enable more
consistent and efficient translation of complex phenotype descrip-
tions into computable data. These in turn will enable accurate
character and phenotype comparisons and integration on a much
broader scale. Introduction tions exist almost exclusively in a free-text or natural language
format that is not amenable to computational processing. For
example, the diverse ways of describing the shape of the first
infraorbital bone in fishes (‘‘lacrymal bone … flat’’ [4]; ‘‘lacrimal
… triangular’’ [5]; ‘‘first infraorbital (lachrimal) shape…flattened’’
[6]) _msocom_3might seem obviously similar to a human but
would not be recognized as similar by a computer. Natural
language, although allowing the expressive and precise description
of biological form, has serious limitations for comparing or Variation in observable features, or phenotypes, is intensely
studied and richly documented within and between species in the
literature of systematic biology (e.g., [1]_msocom_2), between
wild-type and mutant lines in model organism databases (e.g., [2]),
and among genetic phenotypes of humans (e.g., [3]). Although
fundamentally important to our understanding of genetics,
development, and evolutionary relationships, phenotypic descrip- PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 1 Curation of Evolutionary Data Figure 1. A systematic character and state, compared to a
phenotype represented by Entity-Quality syntax. In EQ syntax,
the entity being described is represented by a term from an anatomical
ontology, and the variable (‘‘characteristic’’) aspect of the entity is
represented using a term chosen from a quality ontology. Note that the
‘‘shape’’ attribute is an explicit part of the systematic character but is
expressed only implicitly within the quality term. doi:10.1371/journal.pone.0010708.g001 integrating data across studies, linking to genetic databases, and
data mining. To facilitate comparison and integration of phenotypes across
organisms, model organism communities have spearheaded the
representation of mutant phenotypes using ontologies and formal
semantics [7]. An ontology extends the notion of a controlled
vocabulary by associating names with formally defined entities,
which include classes and relationships among those classes (c.f.,
[8]). Here we use ‘term’ to refer to those names associated with
classes, in contrast to names of relationships. The application of
ontologies to the curation of phenotype data from the model
organism literature and sharing of these annotations in community
databases
has
promoted
clarity
in
communication
among
researchers and allowed for integration of large quantities of data. In addition to facilitating interoperability among databases,
ontologies allow users to query using very specific or broad
anatomical terms and obtain organized groups of annotations. Introduction The EQ formalism has been suggested
as a means to integrate data across systematic studies and with
phenotypes and genetics of model organisms [15,16,17]. For
example,
a
character
may
describe
how
a
structure
(e.g.,
supraorbital bone) and its attribute (e.g., shape) vary among taxa
(Figure 1); the character states specifying the value of the attribute
(e.g., sigmoid). In comparing EQ syntax to systematic characters, the
quality term represents the character state and, by implication
through the subtype relationships of the quality ontology, the
attribute of the character (e.g., sigmoid is a subtype of shape, Figure 1). S f
l
ifi
h
f d
b i
d h Introduction The principles and best practices for the curation of
complex phenotypes that we have developed from this exercise are
generally applicable, as are the challenges inherent in aligning rich
textual descriptions with ontologies and syntactic relations. Phenotypic variability across species has been documented in rich
natural language in the comparative literature of evolutionary
biology and most formally in phylogenetic systematics. This
variability is described in systematic characters, which consist of
two or more character states contrasting some aspect (e.g.,
morphology, behavior) of the taxa under study [14]. Character
states are assigned to taxa in a character-by-taxon matrix that is
analyzed
with
phylogenetic
methods
to
infer
hypotheses
of
evolutionary relationships. The EQ formalism has been suggested
as a means to integrate data across systematic studies and with
phenotypes and genetics of model organisms [15,16,17]. For
example,
a
character
may
describe
how
a
structure
(e.g.,
supraorbital bone) and its attribute (e.g., shape) vary among taxa
(Figure 1); the character states specifying the value of the attribute
(e.g., sigmoid). In comparing EQ syntax to systematic characters, the
quality term represents the character state and, by implication
through the subtype relationships of the quality ontology, the
attribute of the character (e.g., sigmoid is a subtype of shape, Figure 1). Software tools specific to the type of data being curated have
proven to be a critical ingredient of an efficient annotation
workflow (e.g., for journal articles using Textpresso [18]; or gene
structures using Apollo [19]). To link ontology terms with
phenotypic systematic characters and taxa, we developed the
Phenex curation tool [20]. Upon launch, Phenex automatically
downloads the most recent versions of the required anatomy,
quality, taxonomy, and other ontologies. Phenex allows curators to
use EQ syntax to represent evolutionary characters [16,17]. Using
Phenex, this simple combinatorial EQ syntax can be elaborated,
for example, to accommodate multiple related entities and to
describe complex entities. Phenotypic variability across species has been documented in rich
natural language in the comparative literature of evolutionary
biology and most formally in phylogenetic systematics. This
variability is described in systematic characters, which consist of
two or more character states contrasting some aspect (e.g.,
morphology, behavior) of the taxa under study [14]. Character
states are assigned to taxa in a character-by-taxon matrix that is
analyzed
with
phylogenetic
methods
to
infer
hypotheses
of
evolutionary relationships. Curator training, curation experiments, and quality
control Curator training, curation experiments, and quality
control Curation of the complex phenotypic descriptions contained in
systematics publications required the input of domain experts who
were knowledgeable on the anatomy of the target taxa. Curation
was done by five ichthyologists under the direction of a lead
curator (W. Dahdul). Curators were trained one-on-one by the
lead curator at annotation workshops or remotely by conference
calls. A Guide to Character Annotation was maintained on the
Phenoscape wiki [69] that kept curators up-to-date on the
developing best practices for curation. The phenoscape-curators
mailing list [70] was used for discussion and communication of
data curation issues, solutions, and progress. Participation in and
discussion of issues on several OBO Foundry [22] community
mailing lists, particularly obo-discuss [71] and obo-phenotype
[72], also contributed to the development of standards for the
curation process. Selection of ontology terms for taxa. The Materials list
and character matrix of each systematics publication contain
names of the taxa and individual specimens (voucher specimens)
that were examined by the authors. These form the basis of
observations for phylogenetic characters. Taxon names from the
Materials list and matrix were linked to currently accepted
(according to the Catalog of Fishes, CoF, [25]) taxon names from
the TTO by undergraduate student workers using Phenex. A
taxonomic expert then reviewed the taxon list and, after verifying
taxonomic status in the CoF, requested addition of names or
synonyms missing from the TTO using the SourceForge term
request tracker [74]. Unknown or unidentified species were added
to the TTO with reference to the publication in parenthesis (e.g.,
Akysis sp. 1 (de Pinna 1996) TTO:10000093, Akysis sp. 2 (de Pinna
1996) TTO:10000094). Most synonyms were added to the TTO
with a scope of RELATED (rather than BROAD, NARROW or
EXACT), indicating that the relationship between the synonym
and its primary term was not known. Species names incorrectly
spelled by an author were added to the TTO as synonyms with a
scope of EXACT and an associated synonym category of
‘misspelling.’ The eleven misspellings and missing taxon names
discovered in the CoF through this process were communicated to
the CoF administrators for correction or addition. As part of our curation quality control, we conducted two
annotation experiments at Phenoscape project workshops to identify
areas of improvement in curator training, ontology development,
and software tools. Curator training, curation experiments, and quality
control We wanted to determine how often, and for
what reasons, curators choose divergent EQ statements for the same
character and character states. Curator training consisted of a
hands-on group annotation exercise, and at least one full day of
individual work on each curator’s own publications with assistance
from the lead curator and other project personnel. The Guide to
Character Annotation [69], with examples of character types
commonly encountered in the fish systematic literature, was also
provided to the curators. In both curation experiments, the same 10
characters sampled from the ichthyological literature were annotat-
ed by 4 or 5 curators in parallel. Some publications partially or wholly replicated the species
names from the Materials list in the phylogenetic matrix. However, many publications used higher-level taxa (e.g., genus,
family) for the taxonomic units represented in the matrix. Because
we recorded phenotypes as properties of species unless specifically
asserted to a higher-level taxon by an author, any higher-level
taxon used in a matrix was replaced by all the species within that
taxon as listed in the Materials list. This procedure sometimes
required contacting a taxon expert for assistance in assigning
species to the correct higher-level taxon in the matrix. Curation of Evolutionary Data Curation of Evolutionary Data standard that permits systematic data to be tagged with ontology
terms [25]. experts, the use of specialized curation software (Phenex), online
tools, and community input. Free text entry. Free-text data were manually entered into
Phenex by undergraduate student workers. The data entered
included character and character state descriptions, taxon names,
phylogenetic
matrices,
and
specimen
collection
numbers. Although a few matrices were obtained from authors, most were
transcribed
by
undergraduate
students
from
the
original
publications using Mesquite [73], and subsequently imported as
NEXUS files into Phenex. Matrices for our publications of interest
had not been deposited into public data repositories such as
TreeBASE
(http://treebase.org),
an
online
source
of
user-
contributed phylogenetic matrices. Literature selection and collection An initial list of 420 studies, including published species
descriptions,
taxonomic
revisions,
phylogenetic
studies,
and
unpublished theses and dissertations, was compiled from sugges-
tions by 10 experts on the morphology of ostariophysan fishes and
close relatives. These experts helped prioritize the list to emphasize
studies on higher-level groups for broad taxonomic coverage, and
studies that included data matrices for the efficient annotation of
phenotypic characters. We describe here the results of curation of
all characters reported in a total of 47 studies on ostariophysans,
their clupeomorph relatives, and some euteleosts (percomorphs
and salmoniforms). These studies were published between the
years 1981–2008. They included 26 peer-reviewed publications
[4,6,21,26–48], 12 book chapters [49–60], eight Ph.D. disserta-
tions [5,61–67], and one M.S. thesis [68]. Because this collection
of studies spans the decades prior to the widespread availability of
publications in electronic format, we obtained electronic versions
from numerous sources: approximately half (23) were scanned
from hard copies with text translated by Optical Character
Recognition (OCR), 19 were obtained online from institutional
libraries, two hard-copies were acquired through Interlibrary
Loan, one was purchased from ProQuest UMI Dissertation
Publishing, one was downloaded from the Biodiversity Heritage
Library, and one was obtained from the corresponding author. Curation software and ontologies g
For annotation of the 47 studies from the fish phylogenetic
literature with EQ syntax, we used Phenex [20], the annotation
software that we developed for evolutionary biologists to link
phenotype descriptions (characters and character states) with
ontology terms. Phenex can be configured to load any ontology in
OBO (Open Biological and Biomedical Ontologies; [7]) format. We configured it to load the Teleost Anatomy Ontology (TAO)
[15] and Teleost Taxonomy Ontology (TTO) (Midford et al., in
prep), in addition to several other shared community ontologies
including the Phenotype and Trait Ontology (PATO), Gene
Ontology (GO), Spatial Ontology (BSPO), Relations Ontology
(RO), Evidence Code Ontology (ECO), and Unit Ontology (UO). These ontologies are available for download from the OBO
Foundry [22]. A list of museum codes [23] derived from the
Catalog of Fishes [24] was also loaded into Phenex. Phenex files
were saved in NeXML format, a phylogenetic data exchange Software tools specific to the type of data being curated have
proven to be a critical ingredient of an efficient annotation
workflow (e.g., for journal articles using Textpresso [18]; or gene
structures using Apollo [19]). To link ontology terms with
phenotypic systematic characters and taxa, we developed the
Phenex curation tool [20]. Upon launch, Phenex automatically
downloads the most recent versions of the required anatomy,
quality, taxonomy, and other ontologies. Phenex allows curators to
use EQ syntax to represent evolutionary characters [16,17]. Using
Phenex, this simple combinatorial EQ syntax can be elaborated,
for example, to accommodate multiple related entities and to
describe complex entities. PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 2 PLoS ONE | www.plosone.org Curation workflow We recorded
phenotype descriptions as properties of species, and these were
assigned one of three evidence codes based on the type of evidence
given by an author. These codes are part of the Evidence Codes
Ontology
[78],
which
is
used
by
the
broader
biological
community. A phenotype description that is explicitly tied to a
specimen was assigned IVS (Inferred from Voucher Specimen);
these referenced an institutional catalog number. A phenotype
description in which the author does not reference a specimen was
given one of two weaker evidence codes (NAS, Non-traceable
Author Statement, or TAS, Traceable Author Statement); no
catalog number could be associated. NAS is used for statements
that an author makes with no results or citation presented. TAS is
used for author statements that are attributable to another source. This same methodology was extended to statements about higher-
level
taxa. Here,
species-level
phenotype
annotations
were
generated for every species included in the higher-level taxon (as
listed in the Materials list). In this case, these particular species
were given a strong evidence code (such as IVS) with catalog
numbers attached. When the author did not reference the species
that were observed to make character assertions about higher-level
taxa, the higher-level taxa were assigned a weaker evidence code. The phenotypes described in most of the publications that we
curated were based on observations of voucher specimens and so
merited the strong IVS evidence code. Granularity of curation. To maximize curation consistency
among curators and to meet the needs of the larger purpose of our
work, which is to integrate the phenotypic data of evolutionary
morphology with phenotype descriptions of zebrafish mutants, we
did a ‘first pass’ curation of the characters to a coarse level of
granularity. By coarse, we mean that we selected higher-level
terms, or those with less specificity, for quality and sometimes
entity. Coarse-level qualities from the Phenotype and Trait
Ontology (PATO) are those at the attribute level such as size,
shape, and composition (i.e., those terms in blue font in Figure 3). The
supraorbital bone, for example, is described as having a sigmoid
shape in some characiform fishes [48]. The coarse-level EQ
annotation
for
this
phenotype
is
E:supraorbital
bone,
Q:shape, whereas the fine-level annotation is E:supraorbital
bone, Q:sigmoid (Figure 4). Curation workflow The workflow for curation of publications (Figure 2) required
the coordinated activities of students, taxonomic and anatomical PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 3 Curation of Evolutionary Data Figure 2. Workflow for the curation of phenotypic characters from systematic studies. doi:10.1371/journal.pone.0010708.g002
Curation of Evolutiona Figure 2. Workflow for the curation of phenotypic characters from systematic studies. doi:10.1371/journal.pone.0010708.g002 Selection of anatomy ontology terms for representation of
character states. When curators encountered a term in the
literature that was not in an ontology, they first assessed its use and
context in the publication to determine whether it was a new term
or a synonym of an existing term (synonyms include misspellings). This involved reading all uses of the term in the paper and
checking figures to see whether the author provided further
information. Sometimes
this
also
required
searching
the
referenced literature pertaining to the term. If it was deemed to
be a new term, the curator wrote a corresponding genus-
differentia definition [7] and proposed the relationships of that term to other terms in the ontology. For example, a term was
requested for the hypomaxilla, a bone of the upper jaw in
clupeomorph fishes. The request included a proposed definition,
‘‘Dermal bone found in the anterior margin of the upper jaw,
posterior to the premaxilla,’’ and proposed relationships to other
terms
(is_a
dermal
bone,
part_of
palatoquadrate
arch,
part_of
dermatocranium). The curator submitted this request through the
TAO SourceForge Term Tracker [75], which triggered an
automated email to the community mailing list [76]. The
ontology administrator closed the request after the conclusion of
mailing list discussion, and then updated the ontology to include PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 4 Curation of Evolutionary Data author’s assertion that a change in some aspect of shape is evident
between species. Annotations at this coarse level, i.e., shape, allow
aggregation of all entities and species that have experienced an
evolutionary change in shape. After curation of the 47 papers at a
coarse level was complete, we did a ‘second pass’ of finer-scale
curation of qualities by selecting a more specific child term and
finer-scale curation of some entities by using post-composition. the requested change and associated community comments. Curation workflow A
similar term request procedure was followed for quality terms
needed for PATO. An alternative to adding terms to an ontology is to create a new
term at the time of annotation by post-composition, which is the
process of combining terms from one or more ontologies to create
a new term ([77]; also see Guide to Character Annotation in Text
S1). Frequently, curators needed terms for the processes, margins,
and regions of specific structures. Rather than adding these
directly to an ontology, relevant terms from the spatial ontology
(e.g., anterior margin) and anatomy ontology (frontal bone) can be
joined by a relation (part_of) to create a post-composed term (the
anterior margin that is part_of the frontal bone). Generally, terms were
post-composed when they were not expected to be used repeatedly
in annotation. Those known to exist in multiple species and
referenced repeatedly in the literature were added to the anatomy
ontology (e.g., supraoccipital process). Evidence codes for phenotype observations. We recorded
phenotype descriptions as properties of species, and these were
assigned one of three evidence codes based on the type of evidence
given by an author. These codes are part of the Evidence Codes
Ontology
[78],
which
is
used
by
the
broader
biological
community. A phenotype description that is explicitly tied to a
specimen was assigned IVS (Inferred from Voucher Specimen);
these referenced an institutional catalog number. A phenotype
description in which the author does not reference a specimen was
given one of two weaker evidence codes (NAS, Non-traceable
Author Statement, or TAS, Traceable Author Statement); no
catalog number could be associated. NAS is used for statements
that an author makes with no results or citation presented. TAS is
used for author statements that are attributable to another source. This same methodology was extended to statements about higher-
level
taxa. Here,
species-level
phenotype
annotations
were
generated for every species included in the higher-level taxon (as
listed in the Materials list). In this case, these particular species
were given a strong evidence code (such as IVS) with catalog
numbers attached. When the author did not reference the species
that were observed to make character assertions about higher-level
taxa, the higher-level taxa were assigned a weaker evidence code. The phenotypes described in most of the publications that we
curated were based on observations of voucher specimens and so
merited the strong IVS evidence code. Evidence codes for phenotype observations. Curation workflow Coarse annotation meets the
immediate use of linking to zebrafish genetic phenotypes in the
Phenoscape Knowledgebase (http://kb.phenoscape.org), because
most of the zebrafish phenotypes are currently annotated to a
coarse level by ZFIN. In addition, the coarse-level annotations,
though lacking the detail that free-text provides, do express the Review
of
annotations
for
consistency
among
curators. Annotation
summary
reports
in
the
form
of
a
spreadsheet containing annotations for all 47 publications were
generated regularly from the Phenoscape Knowledgebase to review
annotation consistency. Additionally, Phenex can export files in Figure 3. Attribute-level quality terms from the Phenotype and Trait Ontology used to curate systematic characters. Terms in blue
font represent the higher-level concepts used to describe phenotypic variation at a coarse level (see Figure 4). Qualities are divided into those that
inhere in a single entity (quality of single physical entities; green fill) and those that inhere in multiple entities (quality of related physical entities; red fill). Examples of children of some terms are also shown. doi:10.1371/journal.pone.0010708.g003 Figure 3. Attribute-level quality terms from the Phenotype and Trait Ontology used to curate systematic characters. Terms in blue
font represent the higher-level concepts used to describe phenotypic variation at a coarse level (see Figure 4). Qualities are divided into those that
inhere in a single entity (quality of single physical entities; green fill) and those that inhere in multiple entities (quality of related physical entities; red fill). Examples of children of some terms are also shown. doi:10.1371/journal.pone.0010708.g003 May 2010 | Volume 5 | Issue 5 | e10708 PLoS ONE | www.plosone.org 5 Curation of Evolutionary Data Figure 4. Comparison of coarse-level and fine-level phenotype annotations for the observation of a sigmoid-shaped supraorbital
bone. doi:10.1371/journal.pone.0010708.g004 Figure 4. Comparison of coarse-level and fine-level phenotype annotations for the observation of a sigmoid-shaped supraorbital
bone. doi:10.1371/journal.pone.0010708.g004 Excel format, so that consistency can be checked for individual files. We developed a series of review tasks that checked for proper EQ
syntax and consistent annotation of different character types. Curation workflow These
include checking that a related entity was recorded when a relational
quality was used; checking that a related entity was not recorded
with a quality of a single entity; checking for incomplete annotations
(e.g., only one state annotated); and checking that post-composed
terms were nested correctly (e.g., process (part_of (anterior region (part_of
(maxilla)))) versus process (part_of (anterior region))((part_of (maxilla))) and
created with logically correct relations (e.g., part_of, connected_to,
overlaps_with, adjacent_to and spatial relations such as anterior_to). Undergraduate student workers also proofread the curated files to
check for the correct transcription of data matrices and numerical
values of counts. characters, taxa, specimens, and matrices were presented in the
different studies. These led to the creation of annotation guidelines
(summarized in Text S1; [69]). The standards and the variation
encountered in the literature also drove the development of our
annotation software (Phenex). (
)
Character and character states and EQ annotation. The
curation of 4,617 characters, or 10,512 character states, resulted in
12,861 ontology-based phenotypes or Entity-Quality statements. Characters and character states were divided among several
categories in the process of EQ annotation. First we distinguished
among characters and states that involved a single entity vs. those
that involved two or more entities, terminology that follows the
division of quality terms in PATO [11]. For example, a character
might involve a single anatomical structure, such as the shape of
the dorsal fin (‘‘dorsal fin … acuminate’’ [49]) versus a character
that involves the relationship between two structures (‘‘dorsal fin
origin anterior to that of pelvic fin’’ [49]). Selection of specific
entities from the appropriate ontology was generally the next step
in the curation process (described further in Discussion). The third
step was to determine the particular quality, initially at the
attribute level, that is required to represent the phenotype
described in the character state. If a single entity is involved, a
monadic quality (quality of a single physical entity; Figure 3), i.e., one
that inheres in a single entity is required. If two (or more) entities
are involved in the phenotype, frequently a relational quality
(quality of related physical entities; Figure 3), i.e., one that inheres
between multiple entities, is required. Size comparisons among
entities require special consideration, and involve monadic
qualities (see Text S1). Last, we considered whether a character
state contained single or multiple logical qualities and thus
required
single
(non-composite
characters)
or
multiple
(composite characters) EQ statements. Curation workflow Frequently we found that
several different attribute qualities (e.g., color and shape; Figure 3)
were required for the annotation of composite characters (see
Systematic Character Types and Application of EQ Formalism). Author contact and verification. fter the curation of each
publication was completed and verified for consistency, the
primary author was notified by email that their published data
had been curated for inclusion in the Phenoscape Knowledgebase. Authors were sent a spreadsheet with the original character and
taxonomic data and its ontological representation (e.g., free-text
character descriptions vs. EQ phenotypes; published vs. currently
accepted taxonomic names). Authors were invited to send
suggestions or corrections prior to upload of the data to the
public version of the Phenoscape Knowledgebase. Two authors
returned corrections to their published data. Author contact and verification. fter the curation of each
publication was completed and verified for consistency, the
primary author was notified by email that their published data
had been curated for inclusion in the Phenoscape Knowledgebase. Authors were sent a spreadsheet with the original character and
taxonomic data and its ontological representation (e.g., free-text
character descriptions vs. EQ phenotypes; published vs. currently
accepted taxonomic names). Authors were invited to send
suggestions or corrections prior to upload of the data to the
public version of the Phenoscape Knowledgebase. Two authors
returned corrections to their published data. Data upload to Phenoscape Knowledgebase. Phenotypes
and corresponding matrix information were loaded into the
Phenoscape Knowledgebase, a relational database built on the
Ontology-Based Database (OBD) schema, in which all data are
represented as semantic links between ontology terms (Kothari et
al., in preparation). The deductive reasoning and the query
interface of OBD support analyses of the anatomical and
taxonomic disposition of phenotypic annotations at any level of
granularity that is present within the logical structure of the
ontologies. In addition to the Knowledgebase itself, we created a
web interface (http://kb.phenoscape.org/) that allows users to
browse and query the phenotype data in ways that exploit the
ontological context. Taxonomic names. From the 47 publications, we curated
phenotype data to 3,449 taxa (mostly species), of which 2,682 were
nonredundant names, of which there were a corresponding 2,410
valid names (according to the Catalog of Fishes, CoF [24]). Of the
2,682 names, 729 are now invalid or were misspelled. Curation workflow The invalid
names were annotated to the currently valid name as listed in CoF
using the TTO, or the invalid or misspelled name was added as a
synonym, if not already present in CoF. Three hundred and ten
taxon names were added to the TTO as unknown, uncertainly
identified, or unnamed taxa (out of 36,895 taxonomic terms total). PLoS ONE | www.plosone.org Discussion Higher-level taxa appeared in 35 of the 45 published data
matrices. These taxa were expanded to the species level to
represent the particular species examined in a publication. As
mentioned previously, this was not always straightforward because
some authors did not indicate which species belong to these
higher-level taxa used in the matrix. For example, one author [63]
categorized species by family in the Materials list, but additionally
used subfamilies in the matrix. In this case, curation of species to
the correct matrix subfamily (and thus to the correct phenotype
descriptions) required personal communication with an expert
taxonomist. Additionally, some authors (e.g., [65]) organized
species in the Materials list by higher-level taxa proposed in their
own study (and reflected in their matrices) instead of by currently
recognized higher-level taxa. Again, curation of species to the
correct matrix taxon, and thus to the correct character data,
required personal communication with an expert taxonomist. Our experience in successfully transforming a large collection
(10,512 character states) of legacy systematic character data into
the ontology-based EQ syntax resulted in a recognition of several
distinct systematic character types with respect to the logical
categorization enforced by ontologies. It also contributed to the
growth and improvement of several domain and community
ontologies, and it resulted in the development of standards and
best practices for phenotype curation. Moreover it offers a new
view of morphological characters that is valuable for practicing
systematists. Curation effort The time required for curation of the chosen papers [4–
6,21,26–68] to the level described herein was approximately 5
person-years. This
included
significant
time
investment
by
personnel in software development, testing and improvement,
initiation of new ontologies, and development of curation
standards and workflow. Character-by-taxon matrices. Forty-five of the 47 curated
publications included data matrices. From the two publications
that lacked them, one was supplied by the author [4] and the other
was reconstructed from the text [21]. Some matrices contained
numerical character states that were not textually described. We
annotated EQ statements for only those character states that were
documented. Curation of Evolutionary Data Curation of Evolutionary Data We included reference to the author(s) and year in the term name
for these 310 publication-specific taxa (e.g., Akysis sp. 1 (de Pinna
1996), TTO:10000093). proportion of characters were annotated correctly to the higher-
level quality term (Figure 3) although only two of the 10 characters
were annotated identically among curators for the more specific
child term. The overall variability in annotation consistency
resulted from different interpretations of shape and size descrip-
tors, inexperience and unfamiliarity with the ontologies and
software, difficulties in creating post-compositional terms, and lack
of adequate terms in the ontologies, particularly for shape
descriptors. Specimens and materials examined. In most of the
publications (42 of the 47) a list of materials was presented,
giving the provenance and other information about the particular
specimens that were examined. Synthesis papers [55] or book
chapters [51,52] frequently did not include a Materials list, but
specimen collection numbers were sometimes provided in figure
captions (e.g., [36]). We obtained a list of materials examined from
the authors of these papers where possible. Some authors referred
to previous publications for a full list of materials (e.g., [28,59]),
and where feasible, we curated specimens from these. Specimens and materials examined. In most of the
publications (42 of the 47) a list of materials was presented,
giving the provenance and other information about the particular
specimens that were examined. Synthesis papers [55] or book
chapters [51,52] frequently did not include a Materials list, but
specimen collection numbers were sometimes provided in figure
captions (e.g., [36]). We obtained a list of materials examined from
the authors of these papers where possible. Some authors referred
to previous publications for a full list of materials (e.g., [28,59]),
and where feasible, we curated specimens from these. Systematic character types and application of EQ
formalism Systematists use the expressiveness and richness of natural
language to describe precisely the morphological variation that
they observe among species. These phenotype descriptions are
represented in a somewhat formalized way as characters and
character states in the systematic literature [14]. EQ formalism
provides a rigorous yet flexible syntax for these data; it is to some
extent, a ‘natural fit’. As previously described (Figure 1), systematic
characters typically consist of a short character header (e.g.,
maxilla shape) denoting the relevant structure(s) (entity: maxilla)
and attribute (high-level quality: shape) that varies among taxa,
followed by several character states that specify the value of the
quality (round, rectangular, triangular, etc…). Many systematic
characters, however, do not follow this format (see [14] for review),
and a standardized logical framework, consistent with EQ
formalism, has been recently proposed [14]. In systematic
characters, entities and qualities can be found in the character
description, in the character state description, or in both. Irrespective of this, the morphological descriptions of variants
among species in the literature conform to the general formalism
of EQ syntax and semantics. From the breadth of our curation
work emerged standards and recommendations for deploying this
formalism, and we relate these below and in our Guide to
Character Annotation ([69]; Text S1). Ontology growth As a result of literature curation, the ontologies that we used
grew in number of new terms, synonyms, definitions, and
relationships among terms. The TAO more than doubled its
skeletal terms, from 253 in version 1 [15] to 644 skeletal terms of
2,662 total in the most recent version (March 2010). The TTO
grew to 36,895 taxon terms, including 154 fossil taxa (from an
initial 36,080 terms with no fossil taxa), 43,215 synonyms (from an
initial 38,269), 30,865 species, 5,107 genera, and 551 families. Our
curators contributed 16 terms, four synonyms, three name
changes, and one relationship change to PATO. We added four
terms (parental care, oral incubation, adult foraging behavior, foraging by
probing substrate) to the Biological Process hierarchy of the Gene
Ontology (GO-BP), and 41 terms and six synonyms to the Spatial
Ontology. Museum codes were based on the CoF list [79] (479
entries) that was enhanced with 37 additional codes identified
during the process of paper curation. PLoS ONE | www.plosone.org Characteristics of the data reported in the source
publications From our comprehensive undertaking to represent complex
phenotype data using ontologies, patterns emerged in how May 2010 | Volume 5 | Issue 5 | e10708 6 Curation of taxa Our finding that more than one quarter (729 of 2,682) of the
species names used in the 47 curated publications were outdated
was unexpected, given the recency of these publications (1981–
2008). These fishes may present an unusual case, however,
because two of the groups that we curated (catfishes and
cypriniforms) have undergone extensive recent taxonomic revi-
sion. Given that some taxa will be revised more frequently than
others, the rapid turnover in taxonomic names draws attention to
the need for adaptable resources such as taxonomy ontologies like
the TTO, that record the relationships among not only current,
but also synonymous, taxonomic names thus supporting compar-
isons across studies in the literature. Ontologies provide the
capability to accommodate the needs of the specific literature or
type of data under curation. Systematic characters are sometimes framed such that different
character states involve different logical qualities (e.g., absent and
shape). For example, variation in the spermatophoral gland in
brachiopods (a phylum of invertebrates) is described with three
states
[81]:
‘‘Absent,
Simple,
Composite’’. Although
some
systematists have previously raised concerns about the logical
structure of these characters, it does not pose a problem for
phenotype annotation from a practical standpoint, e.g., the EQ
statements for these character states are: E:spermatophoral
gland, Q:absent; E: spermatophoral gland, Q:simple;
E: spermatophoral gland, Q:composite (see Text S1 for
discussion of the semantics for absent and present). From the
standpoint of reasoning with ontologies within a database,
presence can be implied by an annotation to any quality term
(e.g., tubular or lamellar) other than absent. Phenotypes are recorded from observations on individual
organisms in both model organism genetics and evolutionary
biology. Curation
of
the
evolutionary
literature,
however,
presented a special challenge because it required distinguishing
between author statements that were based on direct observation
of specimens and generalizations to higher-level taxa. We
discovered that authors represented species observations using
one or more higher-level taxa in more than 75% of the published
data matrices that we curated. Generalizing to a higher-level taxon
from observations on a single or only a few exemplar species is in
fact common practice in systematic studies of many taxonomic
groups. Curation experiments and curator consistency ‘‘fused medial and proximal anal-fin
radials’’, which is a complex entity not named in the literature,
we annotated this as a relational character using the qualities fused
with and separated from to describe the relationship between two
separate entities (state 0: E:medial anal-fin radial, Q:fused
with, RE:proximal anal-fin radial; state 1: E:medial
anal-fin radial, Q:separated from, RE:proximal anal-
fin radial). The advantage of representing this using two
separate recognized and defined entities is that they can thereby be
linked to other annotations of these entities. Character states were generally translated into a single EQ
statement, but not uncommonly we noted that multiple aspects of a
structure or multiple structures are described within a single
character state, requiring the annotation of multiple EQ statements. This may reflect an investigator’s observation that the structures co-
vary, and perhaps an assumption that they are non-independent and
thus represent a single character state. We termed these ‘composite’
character states. For example, variation in the pectoral fin is
described as follows [26]: ‘‘Pectoral fin size. 0: pectoral fin large and
pigmented; more than 43% head length; membrane infused with
numerous
small
chromatophores;
1:
pectoral
fin
small
and
unpigmented; less than 43% head length; membrane without
chromatophores.’’ Here each character state corresponds to two
phenotypes (e.g., state 0, EQ1: E:pectoral fin, Q:size‘in-
creased_in_magnitude_relative_to (E:pectoral fin in_
taxon X) and EQ2: E:pectoral fin, Q:pigmented). Dividing
the distinct logical components (size and color in this case) into
multiple EQ statements is necessary for reasoning with them
independently using ontologies – and possibly, but not necessarily,
for phylogenetic character construction. By recording separate EQ
statements, one may query on independent logical qualities of a
character state (e.g., size) and expect to find similar annotations. However, if a systematist separates them into separate characters, it
results in increasing the weight of potentially non-independent
characters in the phylogenetic analysis. On the other hand,
representing them as a single character may underrepresent them
in the analysis. The process of dissociating the states of some characters
(composite) into multiple, distinct EQ statements, and the states of
other characters into EQ statements with different logical values
has implications for their potential use in phylogenetic analysis. Characters are the units of homology in phylogenetic analysis, and
the alternative character states have been judged by the researcher
to be homologues of one another. Curation experiments and curator consistency In the first curation experiment, only one of 10 characters was
annotated identically among four curators. The reasons for this
variability among curators included curation software bugs,
difficult aspects of the ontologies (e.g., lack of appropriate quality
terms from PATO), lack of standardized guidelines for unusual
cases, and differing interpretations of the text descriptions. For the
second experiment, curators were told to curate characters to a
coarse level of granularity for quality. In this experiment, a greater Systematists typically represent only one aspect of a structure in
a character state. An example from bird systematics involves
variation in the shape of the external naris in stem rollers: ‘‘ovoid
(0); triangular with a flat ventral margin (1)’’ [80]. Here each
character state corresponds to a single phenotype: state 0, for
example, corresponds to the EQ: E:external naris, Q:ovoid. Occasionally, however, authors represent observations in ways
that may be interpreted as either monadic or relational. An May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 7 Curation of Evolutionary Data ischiac process: small or posteriorly elongate (0); falciform (1);
falciform and strongly developed (2).’’ To represent ‘‘small or
posteriorly elongate’’ using PATO qualities, the qualities size‘de-
creased_in_magnitude_relative_to(E in_taxon X) and elongated are
applied. However, the parent of these two terms is size, not shape. A consequence of this mismatch between natural language and the
ontology is that querying the resulting annotations for ‘‘pelvic
bone’’ and ‘‘shape’’ will not return annotations corresponding to
the author’s state 0. Thus applying mutually exclusive terminology
to annotate these aspects from a morphological description can be
difficult and possibly result in misrepresentation of an author’s
intention. Many investigators, however, would recognize that
many aspects of size variation also relate to shape and vice versa. Size and shape terms were a frequent source of inconsistency
among curators. In cases such as the example above, we
recommended that curators annotate coarsely to shape. example from fishes [48] is a character involving two elements of
the anal fin described as: ‘‘Presence or absence of fusion of medial
and proximal anal-fin radials: (0) absent; (1) present.’’ Rather than
annotate this as a monadic character by adding a new term to the
anatomy ontology, i.e. Curation experiments and curator consistency To the extent that they are
atomized using EQ, they may lose their genealogical connection. On the other hand, the task of homologizing complex phenotypic
characters across different studies and taxa has proved difficult to
impossible for phylogeneticists thus far, and it may be the case that
EQ statements provide the broad initial grouping of characters
and character states that facilitate subsequent broader-scope
phylogenetic evaluation. PLoS ONE | www.plosone.org Curation of phenotypes in the legacy literature:
challenges and feasibility The
solutions that we suggest and have at least partially implemented
are generally useful for other phenotype efforts, and they are
described below. New attempts to curate phenotypes from the legacy literature of
other taxonomic groups (phylogenetic treatments or not) will
require overcoming the initial hurdle of creating new ontologies or
expanding existing ones for the inclusion of terms required to
represent the diversity of organism features and taxonomy under
consideration. In our experience, we found it efficient to build
from existing ontologies where available. We used, for example,
the existing PATO ontology for annotation of qualities, and we
built the Teleost Anatomy Ontology (TAO) from the Zebrafish
Anatomical Ontology [15]. As we annotated the literature, we
concurrently added required terms and relationships to these and
other ontologies. In this way, ontology growth and development
was driven by active curation of the literature. For example, in the
course of curating evolutionary phenotypes for the fishes in this
study, we more than doubled the number of primary terms (not
including synonyms) for the skeletal system axis of the TAO. In
contrast, no new terms were proposed for cell types, embryonic
structures, or the immune system, because no evolutionary
variants of these anatomical structures were documented in the
literature we curated. As a consequence, ontologies might appear
to be incomplete or missing basic terms, and may not provide the
encyclopedic knowledge that some may expect of an anatomy
ontology. Although terms, definitions, and relationships can be
supplied at any time, the effort required for curators to break away
from direct annotation and turn to ontology development is
significant; 15–50% of an individual curator’s time might be spent
on ontology development. In particular, curation of publications
covering taxa that have not been previously annotated require the
addition of new taxonomy and anatomy terms and is thus more
time consuming. We anticipate that future curation of the fish
literature will be more time efficient because of our significant
refinement and enlargement of the core ontologies (TAO, TTO,
PATO). For new efforts in different taxonomic domains, once the
respective ontologies have been populated, the curation of
additional publications will require less time. In summary, term
addition to shared ontologies broadened their scope and provided
greater utility to others in the community. Curation of phenotypes in the legacy literature:
challenges and feasibility familiarity with the tools, ontologies, and syntax for creation of
phenotypes. Consistency improved as curators gained familiarity
with the ontologies, acquired experience using curation software
and tools, became more aware of the developing annotation
standards, and were restricted in their term choices. The almost
daily updated documentation of annotation problems, examples,
and standards in the Guide to Character Annotation [69] was
important in promoting these annotation standards. High-level
oversight of the process and manual and automated consistency
checks by the lead curator before making the data public were
critical
to
maintaining
consistency
and
data
quality,
and
contributed to improvements in consistency. The
rich
literature
that
documents
the
similarities
and
differences among taxa goes back several centuries, spans many
languages, and at first appearance, seems almost insurmountably
large
to
render
computable
using
ontology-based
curation
methods. By initially focusing on large-scale treatments where
phenotypic descriptions are most formalized, i.e., the phylogenetic
studies, we reduced the number of papers for more than 8,000
species of ostariophysan fishes to approximately 50. This struck us
as
surprisingly
few
such
papers;
however,
given
that
the
phylogenetic approach has been mainstream only over the past
30+ years, and that morphological treatments of this sort may take
an author 6–10 years to produce, the number may well be
representative for other taxonomic groups. If this is the case, with
annotation software and ontologies in place at the outset, we
estimate that similar phenotype annotation projects can be done in
possibly half the time (approximately 2.5 person years). Addition-
ally,
by
incorporating
semi-automated
methods
to
extract
character states from the literature and associate ontology terms,
the time involved could be further reduced. A significant level of
phenotypic data, however, remains in non-phylogenetic studies,
e.g., species descriptions, and methods for efficient EQ curation of
this literature remain a critical challenge. The results of our curation experiments and subsequent work
with individual curators pinpointed several general problems that
required improvement in curation procedures and software tools
to increase curator consistency and efficiency. Importantly, we
discovered that curators had a difficult time navigating large
ontologies to determine whether an appropriate term was present. This is almost certainly a general problem in annotation of
phenotype descriptions and not specific to systematic biology
literature. The absence of the correct ontology term led to
inconsistent use of existing terms by curators or a time-consuming
change of focus to the process of term addition and definition. Curation of phenotypes in the legacy literature:
challenges and feasibility A i
ifi
l
h ll
f
l
bli h d
i To help remediate the navigation of large ontologies problem,
we implemented software restrictions to reduce the number of
terms available for use in annotations. For example, if only the
skeleton is being annotated, then a ‘slim’ version of the TAO
containing only terms from the skeletal system might be made
available. Restricting which terms are available is particularly
important in large community ontologies (e.g., the Gene Ontology)
that contain many terms not applicable to the particular data
under curation. We, for example, implemented a ‘slim’ version of
the Relations Ontology, with only a small subset of relations (such
as part_of, towards, etc.) available for use by our curators. We found
that it is critical for relations to be restricted for use in post-
composition. Curators, for example, improperly used left_of rather
than in_left_side_of and contained_in rather than located_in. In the
future we feel it will be useful to further restrict availability of
particular terms and relations, depending on the literature under
curation, so that for example, the relation connected_to is the only
one available for use when annotating the relation of scales to the
body of fishes. Thus a curator would be forced to annotate scale
connected_to
head
versus
(incorrectly)
scale
part_of
head. Such
restrictions are expected to decrease the effort required by a
curator to find an appropriate term or relation, and increase
significantly the consistency of curation and thus the logical value
of the annotations. The second part of the curation problem is that after a curator
determined that a term was truly missing from an ontology (versus
in some part of the ontology that they may not have browsed), they
then needed to request that a new term be added to the ontology. This was a significant interruption in the curation process, as
curators turned their attention from the phenotype description to
composing a new term definition. To help expedite the term
addition process for curators, we provided easy links to term
trackers on the Phenoscape wiki [69] for different ontologies. We
also encouraged curators to provide basic definitions that could
later be improved upon by community feedback on the term
request mailing list [15]. A significant general challenge for newly established curation
projects is the consistent annotation of phenotypes among
curators. Curation of taxa Sometimes an author explicitly asserts in the correspond-
ing text that a particular phenotype pertains to all species included
in a higher level taxon, but other times using a higher-level taxon
in a matrix is simply shorthand for reference to the species that
were actually examined. To compare data across multiple studies,
however, it is critical to interpret appropriately the meaning of the
author’s use of these higher-level taxa. The natural language used in the original description of
systematic characters sometimes corresponds to a term in an
ontology that is different from the author’s intent; in other words,
there is a mismatch between an author’s free-text description and
the literal match to an ontology term. For example, authors
sometimes describe variability in the shape of a structure using
terms that are not types of shape in the quality ontology. Variation
in the pelvic bone, for example, is described as [29]: ‘‘Shape of May 2010 | Volume 5 | Issue 5 | e10708 8 Curation of Evolutionary Data PLoS ONE | www.plosone.org Curation of Evolutionary Data appropriate fine-scale quality term in PATO, mainly due to the
incomplete development of this ontology (i.e., the term was
missing). This led to individual curators choosing different, fine-
scale terms that approximated the author’s intent, but did not fully
or adequately represent it. Rather than expedite the term addition
process here, we used the Phenex software to restrict term choices
primarily to higher-level attribute qualities (Figure 3). Consistency
and efficiency improved as a result. Additionally, term restriction
had an educational and training value in that our curators learned
to abstract quickly the essence of the varying quality from complex
descriptions. The negatives of this approach are that the PATO
ontology did not grow at the leaf-node level, at least initially, as a
result of our work, and that queries across qualities cannot be
made at a fine scale. That is, querying for all ‘elongate’ jaws, for
example, would return jaws of all shapes because all descriptions of
jaw shape variation are annotated to the high level term shape. The
cost of further annotation refinement must be judged against the
intended use of the annotations. ways that investigators describe their observations makes it difficult
to combine or compare data across studies, and renders the
observations vulnerable to misinterpretation. Many of the issues
we encountered in curation (different terminologies, noncompa-
rable
attributes
among character
states)
could be
avoided
prospectively if systematists are provided access to data collection
tools that link to community anatomy, quality, and taxonomic
ontologies. Use of ontologies for complex phenotype descriptions
has the potential to clarify the identity of structures under
consideration, allow comparison of similar phenotypes, and
facilitate
the
application
of
characters
across
studies
and
taxonomic groups. Moreover, use of a mapping to EQ syntax
during the course of a study can generally promote higher levels of
standardization. Curated data that a computer can understand and reason with
facilitates the aggregation and comparison of data on a scale that is
unmanageable for individual researchers. The expressiveness,
creativity, and precise descriptions possible with natural language,
however, are not easily replaced, despite the promise and
advantages of computational methods. The inherent human
ability to describe and interpret complex phenotypes will always
be an essential element in biological fields that involve compar-
isons of the visible phenotype. These, however, are complemented
by computational tools such as ontologies that promote clarity and
communication among researchers and interoperability of data. Conclusions The benefits of using an ontology in communication in any
discipline include standardization of terminology, explicit defini-
tions of concepts, logical relations among concepts, and the
creation of structured and precise representations of information
that
facilitate
computability. From
a
practical
standpoint,
communities benefit because communication is clearer and less
ambiguous. Using multiple ontologies to describe more complex
concepts such as phenotypes can promote similar benefits at a
broader level and to a broader community, promote comparisons
of phenotypes across studies and taxonomic groups, and allow
interoperability with different data types. Currently the multiple Supporting Information Text S1
Phenoscape Guide to Character Annotation. We
describe our standard practices for annotation of entities and
qualities in the Guide to Character Annotation. Our online
version describes more specialized cases and issues (https://www. phenoscape.org/wiki/Guide_to_Character_Annotation). Found
at:
doi:10.1371/journal.pone.0010708.s001
(0.09
MB
DOC) Text S1
Phenoscape Guide to Character Annotation. We
describe our standard practices for annotation of entities and
qualities in the Guide to Character Annotation. Our online
version describes more specialized cases and issues (https://www. phenoscape.org/wiki/Guide_to_Character_Annotation). Curation of Evolutionary Data It is a significant remaining challenge to curate complex
phenotype descriptions using EQ syntax fully. This challenge
extends beyond systematic biology to all curation efforts (e.g.,
Human Phenotype Ontology; http://www.human-phenotype-
ontology.org) that seek fine-scale representation of phenotypes,
including those that compare human genetic phenotypes to those
of model organisms. This is because full or fine-scale curation of
complex phenotype descriptions (e.g., the antero-dorsally project-
ing process of the posterior maxilla is located posterior to the
laterally projecting and bent knob of the ethmoid in species X)
requires elaborate post-compositional combinations of ordered sets
of terms from multiple ontologies. All efforts to represent complex
phenotypes will require multiple ontologies and post-composition,
and they will thus experience the same general problems. Although the Phenex software supports such compositions [20],
and although sophisticated and biologically relevant reasoning
across these compositions is feasible [77], the curatorial burden of
accurate and consistent annotation at this scale is high. Our work
to reduce the burden of curation of these phenotypes by
developing standards, restricting ontology terms available for
annotation, and making it easier to add new terms, represents a
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thank the two anonymous reviewers for their helpful comments on the
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W1985455137.txt | https://arthritis-research.biomedcentral.com/counter/pdf/10.1186/ar2373 | en | What do we know about communicating risk? A brief review and suggestion for contextualising serious, but rare, risk, and the example of cox-2 selective and non-selective NSAIDs | Arthritis research & therapy | 2,008 | cc-by | 10,605 | Available online http://arthritis-research.com/content/10/1/R20
Research article
Open Access
Vol 10 No 1
What do we know about communicating risk? A brief review and
suggestion for contextualising serious, but rare, risk, and the
example of cox-2 selective and non-selective NSAIDs
R Andrew Moore1, Sheena Derry1, Henry J McQuay1 and John Paling2
1Pain
Research and Nuffield Department of Anaesthetics, University of Oxford, Oxford Radcliffe NHS Trust, The Churchill, Headington, Oxford OX3
7LJ, UK
2Risk Communication Institute, 5822 NW 91st Boulevard, Gainesville, Florida 32653, USA
Corresponding author: R Andrew Moore, andrew.moore@pru.ox.ac.uk
Received: 4 Apr 2007 Revisions requested: 22 May 2007 Revisions received: 6 Dec 2007 Accepted: 7 Feb 2008 Published: 7 Feb 2008
Arthritis Research & Therapy 2008, 10:R20 (doi:10.1186/ar2373)
This article is online at: http://arthritis-research.com/content/10/1/R20
© 2008 Moore et al.; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background Communicating risk is difficult. Although different
methods have been proposed – using numbers, words, pictures
or combinations – none has been extensively tested. We used
electronic and bibliographic searches to review evidence
concerning risk perception and presentation. People tend to
underestimate common risk and overestimate rare risk; they
respond to risks primarily on the basis of emotion rather than
facts, seem to be risk averse when faced with medical
interventions, and want information on even the rarest of adverse
events.
Methods We identified observational studies (primarily in the
form of meta-analyses) with information on individual nonsteroidal anti-inflammatory drug (NSAID) or selective
cyclooxygenase-2 inhibitor (coxib) use and relative risk of
gastrointestinal bleed or cardiovascular event, the background
rate of events in the absence of NSAID or coxib, and the
likelihood of death from an event. Using this information we
present the outcome of additional risk of death from
gastrointestinal bleed and cardiovascular event for individual
NSAIDs and coxibs alongside information about death from
other causes in a series of perspective scales.
Introduction
Many factors contribute to an incomplete understanding and
evidence base for risk and risk presentation. We should not be
surprised when both patients and professionals are confused
about risk, about competing risks, and about comparing risks
with benefits. Decisions are based on facts and emotions,
both of which may be manipulated, and it may well be that
emotions dominate the facts. This is important in the frame-
Results The literature on communicating risk to patients is
limited. There are problems with literacy, numeracy and the
human tendency to overestimate rare risk and underestimate
common risk. There is inconsistency in how people translate
between numbers and words. We present a method of
communicating information about serious risks using the
common outcome of death, using pictures, numbers and words,
and contextualising the information. The use of this method for
gastrointestinal and cardiovascular harm with NSAIDs and
coxibs shows differences between individual NSAIDs and
coxibs.
Conclusion Although contextualised risk information can be
provided on two possible adverse events, many other possible
adverse events with potential serious consequences were
omitted. Patients and professionals want much information
about risks of medical interventions but we do not know how
best to meet expectations. The impact of contextualised
information remains to be tested.
work of medical decision-making and specifically in the choice
of pharmacological and interventional therapies for individuals.
Risk has two main components. One is that of chance, the
pure statistical likelihood that an event will happen (probability). The other is that of a bad outcome – danger, injury, harm
or loss – together with an indication of severity. To some extent
the term is used commonly to process or communicate the
Coxibs = selective cyclooxygenase-2 inhibitors; NSAIDs = non-steroidal anti-inflammatory drugs.
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product of probability and severity, and the complexities have
been reviewed elsewhere [1].
from gastrointestinal bleeding or cardiovascular events with
NSAIDs and coxibs might be presented by using this method.
We can recognise three main areas that have to be considered to help professionals understand their patients' risk, and
patients to understand their own risk. Broadly these can be
aggregated under the headings of perception (influences on
how individuals and populations relate to risk information),
presentation (how information – data – can be conveyed, and
possibly manipulated, for clarity or impact), and pertinent facts
(accurate data with clear, decisive relevance to the matter in
hand, and which may be used as the basis of future outcomes). These broad areas are not independent of each other,
but it helps understanding to try to organise the many different
facets of risk.
The only certainty is that there is uncertainty. We wish to
emphasise that these explorations are not intended to be
definitive; indeed, they cannot be without extensive testing.
However, given the growing emphasis of patient involvement
in decision-making, methods have to be developed that can
deliver risk information effectively.
'Everything is poison, there is poison in everything. Only the
dose makes a thing not a poison.' Paracelsus might have been
intrigued by the controversy that has arisen over the cardiovascular adverse effects that have lately been associated with traditional NSAIDs and selective cyclooxygenase-2 inhibitors
(coxibs) [2]. Traditional NSAIDs have long been associated
with upper gastrointestinal bleeding, renal impairment, and
congestive heart failure, and, more recently, with injury to the
lower bowel. The only expected benefit of coxibs over NSAIDs
was reduced levels of upper gastrointestinal bleeding.
NSAIDs and coxibs have become some of the most studied
drugs ever, with at least 145,000 patients enrolled in randomised trials [3], and with up to 3.5 million patients in observational studies [4]. There is unprecedented information on
different adverse events associated with particular drugs,
especially for the outcomes of upper gastrointestinal bleeding
and cardiovascular risk.
Different drugs, even within a class, can have different rates of
particular adverse events. For NSAIDs there are large differences between drugs and between different doses of the
same drug in terms of upper gastrointestinal bleeding. Individual patient meta-analysis showed that low-dose ibuprofen was
not different from non-use, whereas high-dose naproxen had
an odds ratio of 16 [5]. In observational and other studies of
NSAIDs there were large differences between drugs [6]. Similarly, differences between individual coxibs are apparent for
gastrointestinal bleeding [7], and between individual coxibs
and NSAIDs for myocardial infarction [4,3,8].
This review set out to do three things: to examine the background to our understanding and perception of risk; to examine how risk can be presented, and explore the possibility of
using a common outcome, death, and contextualising information on non-medical life risks with a presentation involving
numbers, words, and pictures, based on visual aids introduced
by Paling [9]; and to explore how competing risks of death
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Materials and methods
We initially searched PubMed using a number of free-text
terms for the particular area of interest. Thus for literacy, for
instance, we sought articles with literacy in the title. Other
searches were aimed at numeracy, risk, and risk presentation
or perception. An iterative search process was then applied to
identify additional studies; this involved checking the 'Web of
Knowledge Cited References', and the 'Related Articles' link in
PubMed using details of retrieved studies from the initial
search. When the iterative process indicated alternative
search terms, we repeated searches using these new terms.
Terms were generally restricted to title only, at least initially, to
avoid impossibly large numbers of references using words
with many other common meanings (such as relative risk). We
also checked the bibliographies of any relevant studies, risk
websites (see [10], for instance) and books, reviews and articles on risk presentation. We looked for full journal-published
articles without language restrictions.
Results
Background to risk perception
Literacy and numeracy
An inability to handle words or numbers at an appropriate level
(literacy and numeracy skills) are fundamental to communicating risk probability or severity. Illiteracy in patients is known to
be a barrier to communication. In a survey of 127 rheumatology patients in Glasgow [11], 3 were unable to read and 18
were functionally illiterate, so that 17% (1 in 6) would at best
struggle with patient education material and 1 in 20 could not
read prescription labels. An identical value of 17% with limited
reading ability was found in 999 diabetic patients in primary
care in Vermont [12].
Health numeracy has been provided with a set of definitions
[13]. Using three simple questions to test for numeracy,
Sheridan [14,15] showed that 5% (1 in 20) of US medical students and 71% (7 in 10) of patients at an internal medicine
clinic could answer only one or none correctly. Half (1 in 2) of
patients attending an anticoagulation clinic in North Carolina
had numeracy and literacy skills that would limit their understanding [16].
Risk information that people want
A large study of 3,500 adults in Kansas indicated that 90% of
them wanted information on all adverse events (not just
Available online http://arthritis-research.com/content/10/1/R20
serious adverse events) occurring in at least one person in
every 100,000 [17]. This standard, if real, poses challenges in
obtaining and communicating information on risk.
How the general public responds to risk information
People consistently overestimate rare risk and underestimate
common risk. This was first shown for estimates of mortality
three decades ago [18], and has been confirmed more
recently [19] to demonstrate that the trend is common
throughout society, although more educated and perhaps
older people with more life experience have more accurate risk
beliefs.
Where causes of death involved fewer than 10 deaths a year
in the USA (fireworks, measles, botulism), overestimation was
by almost two orders of magnitude [19]. Where causes of
death involved many deaths a year (100,000 to 700,000
deaths: stroke, cancers, heart disease), underestimation was
almost one order of magnitude. At the extremes, then, people
overestimate rare risks by 100-fold or more, whereas they
underestimate common risks by a factor of 10. The degree of
overestimation or underestimation is startling.
Interestingly, both studies [18,19] showed that people were
likely to judge the level of risk correctly when the risk was associated with about 1,000 deaths per year in the USA. It is also
worth noting that different societies can have very different
perceptions of the same risk. An important determinant may
well be the state of technological development [20]. How this
societal attitude relates to or affects individual attitude is not
understood.
In some circumstances, patients can be very risk averse, as a
study of patients attending an emergency department in Boston demonstrated [26]. They were presented with a scenario
in which they had come to hospital with chest pain that could
not be diagnosed by standard procedures, and doctors asked
them to participate in a trial using a safe and approved test
involving a small amount of radioactivity that might help make
a diagnosis. The study was about whether using the test in the
emergency room rather than elsewhere in the hospital was
acceptable, given that it had a very small level of risk. The trivial
level of risk was presented in various ways, like being equivalent to 20 chest X-rays, smoking a small number of cigarettes,
driving 150 miles, or breathing radon in a house for 2.5 years
while living in Boston. Between 40% and 60% of patients
would have refused to have the test in the emergency room,
with more refusing than accepting it, however the risk was presented. Yet the additional risks were not only small, but equivalent to those they accepted as part of their life in any event,
because they smoked, drove, or lived in Boston.
Dimensions of risk
Risk has a number of dimensions (Figure 1), with extremes that
make a risk more or less tolerable. There is no good evidence
about which dimensions are most important, how they affect
patient or professional judgement, and in what circumstance
they might do so.
Attitudes to risk, at least to drug therapy, can be affected by
direct-to-consumer
advertising.
Examining
consumer
responses to a US survey indicated that such advertising was
associated with a greater willingness to talk with doctors
about advertised drugs in those with a chronic condition, and
that advertising made prescription drugs appear harmless
[21]. US Food and Drug Administration research is quoted as
showing that patients and physicians believe that consumerdirected advertising frequently overstates the benefits of
drugs and understates the risks [22].
It is generally assumed that risks over which individuals have
no control are less acceptable than those over which they do
have control, or that novel risks have greater impact than those
with which we are familiar. Man-made risks appear to be worse
than natural risks. For instance, the risks of radiation are often
posed as a major concern, yet in the USA in 2002 there were
no deaths from radiation, compared with 66 from lightning, 63
from cataclysmic storm, 31 from earthquake or other earth
movements, and 9 from flood. There were 767 deaths of pedal
cyclists in the USA in 2002 [27]. Some risks are not highly
related to demographic variables such as sex or age (road traffic accidents, for example). Others, such as the risk of death
by choking, are so related; here annual risk is lowest at 1 in
1,000,000 in children aged 5 to 18 years, but approaches 1
in 1,000 in the over-90s.
How patients respond to risk information
A number of small studies have assessed what patients think
about risk and the effectiveness of interventions. There is a
tendency for patients to overestimate the risk of something
bad happening [23]. For instance, 65% (2 in 3) of women
either overestimated or grossly overestimated their own
chance of breast cancer [24]. Women also tended to overestimate the chance of harm with hormonal contraceptives and
underestimate their effectiveness [25]. For other methods of
contraception, women could overestimate effectiveness
(female sterilisation or female condom) or underestimate it
(hormonal implants and intrauterine devices).
These are trivial compared with the top two causes of death in
the USA in the same year: heart disease and cancer [28]. Considerable research has shown that modifiable lifestyle factors
such as diet, exercise, and refraining from smoking and being
overweight can exert a massive reduction, but most people
ignore this advice. The US Nurses' Study exemplified how big
the beneficial effect of healthy living can be [29]. The greater
the number of low-risk lifestyle factors women had, the lower
their risk of heart attack or stroke was. The implications are
that, in women, 82% (95% confidence interval 58 to 93%) of
heart attacks and 74% (95% confidence interval 55 to 86%)
of heart attacks or strokes are preventable by having a good
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Figure 1
Antecedents and consequences
How individuals assess and process risk information is
dependent on their circumstances or medical condition at that
time. Attitudes and choices about an intervention depend on
the state of illness as well as on the perceived benefits that
accompany the risk. For instance, adherence to statins or lowdose aspirin for cardioprotection is low. In the USA it is estimated that only about 50% (1 in 2) of patients continue at 6
months, and 30 to 40% (1 in 3) at 1 year [31], and in the UK
50% (1 in 2) of patients prescribed low-dose aspirin have discontinued within a year [32]. This low adherence may be a
combination of low expectation of personal benefit for therapies that are measures of prevention, combined with an
adverse event that crosses a consequential boundary for the
individual.
Where benefit is greater and more tangible, adherence is likely
to be higher, even if adverse events are common. Thus in renal
transplant patients, only 15% (1 in 7) were non-adherent to
immunosuppressants under stringent criteria [33]. The consequence of non-adherence, rejection of a transplanted kidney,
was particularly significant, with an absolute risk increase averaging 26% (1 in 4) over a number of studies.
Some dimensions and qualities of risk and risk decisions.
decisions
lifestyle. Despite widespread advice about healthy living, four
out of five US citizens have lifestyles that put them at increased
risk of heart attack and stroke [30].
When the number of deaths from heart disease (684,000 in
the USA in 2003) and stroke (158,000) is so large, the implication is that people in general are content with large numbers
of avoidable deaths from some causes, which are well known,
largely within their control, and perhaps 'natural'. Yet the same
people can cavil over extremely remote risks from nuclear
power plants, electricity power lines or mobile phones, over
which they have, or believe they have, no control, and which
are man-made. New risks need to be put into perspective, and
this might be considered an important aspect of evidencebased decision-making that has, as yet, received little
attention.
The lesson is that, in practice, patients' response to risk is
influenced by more than just hard facts. It may be that if risks
were presented in an appropriate context, people's attitudes
to risk or behaviour might change.
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At face value, the idea of placing a catheter in the epidural
space alongside the spinal cord does not seem to be a good
one, because of the possibility of direct physical damage, indirect physical damage from a haematoma, or infection, any of
which could result in transient or permanent neurological damage. Yet 2.4 million of the 4 million births in the USA every year
involve epidural analgesia, a procedure accepted because the
benefits of pain relief are immediate and great, the risk is small
(persistent neurological injury 1 in 240,000; transient 1 in
6,700 [34]), and not all risks are directly connected with the
epidural. Childbirth is common, women may have experienced
an epidural themselves or be familiar with the experience of
others, and all these antecedents influence the acceptance of
a low risk.
Perhaps one of the most striking examples of antecedent
effects on risk behaviour is smoking cessation. In primary care,
nurse interventions for smoking cessation had no effect, with
about 4% (1 in 25) quitting with or without intervention by a
nurse. In hospital settings and patients after cardiac surgery,
heart attack, or with cancer there were high quit rates (25%; 1
in 4) without intervention by a nurse, and even higher rates
(32%; 1 in 3) with an intervention [35]. The difference
between the presence and the absence of serious illness
changed attitudes of smokers towards quitting and therefore
changed the effects of intervention to help stop smoking. Attitudes to risk and measures of prevention seem to change
when an event becomes a more immediate problem.
Available online http://arthritis-research.com/content/10/1/R20
Presenting risk
To find studies of any description regarding risk perception
and presentation, a number of broad, free-text searches were
undertaken with PubMed (up to September 2006). Combinations of words, for instance 'risk AND presentation', or 'risk
AND communication' were used, and any original studies or
reviews likely to be pertinent were obtained, in as much as they
related to communicating medical risks. Bibliographies were
examined to uncover other relevant studies, because electronic searching alone is inadequate [34,36].
Studies found were used to inform thinking about risk and risk
communication, rather than to constitute a formal systematic
review. The wide range of issues relating to risk perception
and presentation, and the fragmented and often sparse
research literature, rules out a conventional systematic review.
Frequency, probability, and words
Probability, in terms of simple frequencies or odds, is often
used to describe or communicate risk, sometimes in numbers,
often with associated verbal descriptors (common, rare, negligible), and sometimes also with graphical presentations.
Some of the more commonly used risk scales have been
reviewed by Adams and Smith [37]. There is an assumption,
perhaps unstated, that we can couple the numbers and words
externally so that their relationship remains fixed.
Patients are known to respond differently to how adverse
events are presented. For instance, the patients estimated the
likelihood of an adverse event as three to nine times greater
with verbal rather than numerical information [38]. Similar differences can be seen in professionals. Graduate students and
healthcare professionals in Singapore were asked to match
frequency with one of six phrases, from very common to very
rare, when a hypothetical situation about adverse events of an
influenza vaccine was presented to them in either a probability
format (5%) or a frequency format (1 in 20) [39]. With either
format of numerical presentation, a risk of 1 in 20 was
described verbally from rare to very common, with somewhat
more consistency for frequency format than probability.
The European Union has guideline descriptors for the frequency of an adverse event, with verbal descriptors linked to
frequency. Thus very common is more than 10% (or greater
than 1 in 10) and very rare is less than 0.01% (less than 1 in
10,000). Four studies involving more than 750 people demonstrate that people invariably grossly overestimate frequency
from these verbal descriptors [40]. Overestimation occurred
at all frequencies, but for the very rare adverse events they
were overestimated by at least 400-fold.
The way in which we perceive and process numbers seems to
be very different from how we perceive and process words,
and different in different people. Moreover, different numbers
are linked to similar words in different scales; for instance, the
European Union descriptors are not the same as those proposed by Calman [41] or others (Table 1).
Framing risk for patients
When patients are provided with information about drug therapy or surgery, the way in which information is provided can
affect patient decisions in a major way, and the extensive literature has been reviewed, especially in terms of benefits or
losses, situation, and context [42]. Our knowledge of the
extent of framing effects on patients and outcomes is limited
by small numbers of relatively small studies [43].
Patients respond very differently depending on how data
about benefits of therapy are framed. Hypertensive patients
only rarely would have refused hypertensive therapy when
information about efficacy was presented as relative risk
reduction, but refusal rose to 23% (1 in 4) for absolute risk
reduction, 32% (1 in 3) for number needed to treat, and 56%
(6 in 10) with information presented as patient-specific probability of benefit [44]. The choice between having surgery or a
cast for a fracture [45], or different types of surgery [46], is
Table 1
Risk frequency and various verbal descriptors
Frequency range (1 in)
EU descriptors
Calman verbal scale
1–9
Very common
10–99
Common
High
100–999
Uncommon
Moderate
1,000–9,999
Rare
Low
10,000–99,999
Very rare
Very low
Calman descriptive scale
Paling perspective scale
Very high
Frequent, significant
High
Moderate
Tolerable, reasonable
Low
Very low
100,000–999,999
Minimal
Acceptable
Minimal
1,000,000–9,999,999
Negligible
Insignificant, safe
Negligible
Data are taken from [41] and other sources. EU, European Union.
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influenced by framing effects of different types of data
presentation, verbal renderings of outputs such as relative risk
reduction, or number needed to treat.
It is not only patients who respond differently to data depending on presentation or framing. A number of studies have documented the fact that relative presentation (like relative risk
reduction) has a much greater influence on professionals'
decision-making than absolute risk difference or number
needed to treat. This is true for purchasers [47], hospital doctors [48], general practitioners [49,50] and pharmacists [51].
Although a systematic review of randomised trials supports
this general finding, it also indicates that framing is susceptible
to modification by other factors [52].
Pictorial representation of risk
Calman and Royston [53] reviewed a number of different ways
of explaining risk, including pictorial representations involving
logarithmic scales, expressing results in terms of distance, or
population, and the use of visual presentation. Paling [54] had
already suggested a visual presentation of risk with logarithmic
scales, and later expanded risk presentation with a number of
different presentations into the clinical, rather than the predominantly environmental, field [55,56]. Other types of representation have been suggested, based, for instance, on number
needed to treat [57], although women favoured simple bar
charts for the presentation of absolute lifetime risks [58].
Figure 2
Early attempt to contextualise risk [63].
[63] Cigs, cigarettes.
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Other suggestions have expanded use of the scales, with some
contextualising information [59], into mainly anaesthetic [37] or
obstetric and gynaecological risks [60]. The utility of logarithmic
scales such as the Paling scale in delivering better information
about risk has been tested at least once [61]: both visual and
comprehensive written information on transfusion risks improved
patient knowledge to the same extent. This agrees with a systematic review, which also showed that decision aids improved
patient involvement, knowledge, and realistic expectation of benefits and harms[62].
Visual risk scales have not been used extensively. Scales might
be made more relevant by adding contextualising information to
medical risk (Figure 2) [63]; contextualising anchors were chosen
only because they seemed useful at the time, and they can be criticised for not necessarily being relevant to the specific risks arising from the intervention. Although the risks may be
contextualised, the wrong context was used.
It is difficult to obtain good information for all grades of risk or
adverse event, with their various dimensions. Population data are
available, though, on death from various causes. Serious but rare
adverse events are often associated with death. Myocardial infarction, gastrointestinal bleeding, and rhabdomyolysis, for example, can be fatal or non-fatal, and the fatality rate is known. It is
therefore possible to link the risk of death associated with an intervention to other, common risks that we face as individuals.
Available online http://arthritis-research.com/content/10/1/R20
A series of examples follow, using a vertical form of the Paling
Perspective Scale, populated with numerical and verbal
descriptors of risk, together with information on the risk of
death from various causes taken from US data in 2002
[27,28]. The contextualising examples include high mortality
risk from heart disease (about 1 in 400 per year for US adults,
although obviously skewed to older people), and death from
any accident (about 1 in 2,000). Low risks include death from
an automobile accident (about 1 in 20,000) or from any fall
(about 1 in 70,000). Very low risks include death from firearm
(about 1 in 300,000) or in a cataclysmic storm or lightning
(about 1 in 3,000,000).
Figure 3
Data on risk of mortality from medical interventions were taken
from systematic reviews or large observational studies, and, if
needed, mortality was calculated from the rate of the adverse
events and the known or estimated mortality rate from that
event. The examples are as follows:
1. Risk of serious skin reactions with coxibs [64]. Because
these data come from adverse event reporting they almost certainly underestimate the true risk, but from these data the risks
varied between 1 in 300,000 for valdecoxib, to 1 in 1,000,000
for celecoxib, and 1 in 1,700,000 for rofecoxib (Figure 3).
2. Risk of muscle adverse events of statins, including rhabdomyolysis and death from rhabdomyolysis [65]. The risk of
death from rhabdomyolysis is about 1 in 300,000 a year (Figure 4).
3. Risk of cardiac adverse events, including death, associated
with use of propofol anaesthesia [66]. Here the risk of death
from asystole was estimated at about 1 in 70,000 (Figure 5).
4. Risk of hip fracture associated with use of proton pump
inhibitor for 1 year or more in people aged over 65 years. Data
from the UK General Practice Database suggesting a
doubling of risk [67] are supported by evidence of an
increased risk seen in Denmark [68]. The risk of death from hip
fracture while using a proton pump inhibitor is 1 in 4,500 (Figure 6).
5. Risk of death from gastrointestinal bleeding with NSAID or
full-dose aspirin for 2 months or longer [69]. This gave a risk
of death of 1 in 1,200 (Figure 7).
The presentation of risk with these methods – a common outcome of death, and the Paling Perspective Scale – requires
that a body of evidence is available to allow the appropriate
calculations. As the rather disparate examples in Figures 3 to
7 show, it is unusual to have a coherent set of data available
for a single topic because the amount or extent of evidence is
not available. A notable exception is the case of NSAIDs and
coxibs, and the outcomes of gastrointestinal and cardiovascular events, which have been the subject of extensive investiga-
Risk of serious skin reactions with coxibs [64].
[64]
tion in both randomised trials and a retrospective metaanalysis of them, and meta-analyses of substantial numbers of
observation studies examining the use of NSAIDs and coxibs
in the community.
Death from gastrointestinal and cardiovascular events
with NSAIDs and coxibs
Systematic reviews and meta-analyses of observational studies published since 2000 reporting either upper gastrointestinal bleeding or cardiovascular events with particular NSAIDs
and/or coxibs were used for relative risk estimates. For upper
gastrointestinal bleeding, we also used individual observational studies published since 2000, because searching
uncovered only a single systematic review [6], which was
devoid of information on coxibs.
The search strategy avoided meta-analyses of randomised trials, because many of the data in those came from trials with
higher than licensed doses of coxibs, and maximum daily
doses of NSAIDs. This does not reflect clinical practice, in
which guidance is to use the lowest dose possible for the
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Figure 4
Figure 5
Risk of [65]
statins
myopathy, rhabdomyolysis and death from rhabdomyolysis with
statins [65].
Risk of cardiac
propofol
anaesthesia
adverse
[66]
events, including death, associated with use of
propofol anaesthesia [66].
shortest possible time. By contrast, observational studies
reflect actual clinical practice, including dose, more
accurately, and also have the benefit of being larger, with many
more events.
Data on event rates for individual NSAIDs and coxibs
Table 2 summarises the main findings. One systematic review
and meta-analysis of upper gastrointestinal bleeding [6] collected information from observational studies of NSAIDs in the
1990s but was devoid of coxib data. Data on coxibs and additional NSAIDs were available in four individual studies published subsequently [5,7,70,71]. Estimates of relative risk
were generally in good agreement. The influence of duration of
use was uncertain; one individual study found higher risk with
short-term versus long-term use [5], although no relationship
between increased event rate and duration was evident in a
systematic review [6].
We also sought studies that would provide information on
background rates of upper gastrointestinal bleeding or cardiovascular events in the absence of use of NSAIDs or coxibs, initially from studies in the original search, but supplemented
with additional searches and the use of bibliographies. In addition, we required information on the likely mortality rate for
upper gastrointestinal bleeding and cardiovascular events to
provide a suitable and consistent context. The background
rate of events, the relative risk with NSAID or coxib, and the
probability of dying could then be used to calculate the additional risk of death from gastrointestinal and cardiovascular
events associated with the use of particular NSAIDs and
coxibs.
Two systematic reviews provided essentially identical estimates of relative risk for cardiovascular events [4,8] (Table 2).
One further systematic review [72] was without pooled estimates for individual drugs.
We used figures for relative risk of upper gastrointestinal
bleeding from the meta-analysis for NSAIDs, and an average
figure from observational studies for coxibs. We used relative
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Figure 6
Figure 7
Risk of hip fracture associated with proton pump inhibitor [67].
[67] Use for
1 year or more in people aged over 65 years.
Risk of [68]
aspirin
death from gastrointestinal bleeding with NSAID or full-dose
aspirin [68]. Use for 2 months or longer.
risks for cardiovascular events from the meta-analysis with the
largest body of data [4]. Results of both systematic reviews
were broadly in line with a pooled analysis of cardiovascular
events in randomised trials [3], namely a significant difference
between coxibs and placebo in trials of colorectal polyps (but
not dementia or arthritis trials, in which background event rates
are higher), and an increase with doses of rofecoxib above 25
mg a day.
As regards non-users of NSAIDs, Mamdani and colleagues
[74] reported a rate of myocardial infarction of 8.2 per 1,000
person years. This is in line with reports of the incidence of
acute myocardial infarction without including pre-admission
deaths from Holland [75] and England [76].
Background rates of events without NSAID or coxib
The main patient-specific influences on the background incidence of both gastrointestinal bleeding and myocardial infarction are age and sex.
For serious upper gastrointestinal bleeding or perforation in
non-users of NSAIDs, a systematic review of epidemiological
studies [73] suggests a rate of 1 in 1,000 persons a year,
although at age 60 years a higher rate of about 2 or 3 per
1,000 would apply, similar to that of a large survey in Spain
[71]. A cohort study in Canada [7] showed matched nonusers (mean age 75 years) to have a rate of 2.2 per 1,000.
We used background rates of 2.2 per 1,000 for gastrointestinal bleed and 8.2 per 1,000 for myocardial infarction as being
typical of non-users of NSAIDs or coxibs selected as controls
in large observational studies.
Mortality from upper gastrointestinal bleeding and
cardiovascular events
Gastrointestinal bleeding carries a risk of death of about 6%
according to a large, recent, Spanish observational study with
most patients aged over 60 years [77], up to 14% in a recent
Dutch study [78], and in the range of 6 to 12% in a meta-analysis combining randomised trials and observational studies
[69].
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Table 2
Relative risk (95% confidence interval) for serious upper gastrointestinal bleed or myocardial infarction
Information source
Relative risk compared with non-use of coxib or NSAID
Ibuprofen
Naproxen
Diclofenac
All NSAIDs
Upper GI bleed [6]
1.9 (1.6–2.2)
4.0 (3.5–4.6)
3.3 (2.8–3.9)
4.2 (3.9–4.6)
Upper GI bleed [5]
1.7 (1.1–2.5)
9.1 (6.0–14)
4.9 (3.3–7.1)
Celecoxib
Rofecoxib
Hospital admission [7]
4.0 (2.3–6.9)
1.0 (0.7–1.6)
1.9 (1.3–2.8)
Upper GI bleed [70]
3.3 (2.4–4.4)
1.3 (0.7–2.8)
2.1 (1.2–3.5)
Upper GI bleed [71]
4.1 (3.1–5.3)
7.3 (4.7–11.4)
3.1 (2.3–4.2)
5.3 (4.5–6.2)
1.0 (0.4–2.1)
2.1 (1.1–4.0)
CV events [4]
1.07 (1.02–1.12)
0.98 (0.92–1.05)
1.44 (1.32–1.56)
1.09 (1.06–1.13)
0.96 (0.90–1.02)
1.26 (1.17–1.36)
CV events [8]
1.07 (0.97–1.18)
0.97 (0.87–1.07)
1.40 (1.16–1.70)
1.10 (1.00–1.21)
1.06 (0.91–1.23)
1.35 (1.15–1.59)
Results for NSAIDs and coxibs were compared with non-use, from observational studies. These did not, or were unable to, produce dose-specific
results. Bold lines represent relative risks or equivalent from systematic reviews and meta-analyses. Coxib, cyclooxygenase-2 inhibitor; NSAID,
non-steroidal anti-inflammatory drug; GI = gastrointestinal; CV = cardiovascular.
About 1 in 3 people who have a heart attack die before they
reach hospital [79,80]. Mortality within 30 days of a hospital
admission with myocardial infarction was 11% in a recent
Danish study of people aged 30 to 74 years [81]. However,
sudden cardiac death rate before hospital admission is higher
than this, with overall 28-day mortality, including sudden cardiac death outside hospital, of about 40% [76]. In Finland the
28-day case mortality rate for men was 34% and for women it
was 20% [82].
To estimate mortality for risk calculations we chose to use
rounded estimates of 10% mortality for gastrointestinal bleeding and 30% for myocardial infarction.
Calculating competing risks
Table 3 shows calculations of risk for individual NSAIDs and
coxibs compared with non-use, using the background rates of
2.2 per 1,000 for gastrointestinal bleed and 8.2 per 1,000 for
myocardial infarction [4,15]. It provides an indication of the
Table 3
Additional gastrointestinal bleeding events and myocardial infarction associated with using NSAIDs and coxibs
Event and drug
Relative risk
Additional events per 1,000
Additional deaths per 1,000
Frequency (1 in)
Gastrointestinal bleeding (background rate 2.2 per 1,000)
Ibuprofen
1.9
1.98
0.20
5,051
Naproxen
4.0
6.60
0.66
1,515
Diclofenac
3.3
5.06
0.51
1,976
All NSAIDs
4.2
7.04
0.70
1,420
Celecoxib
1.1
0.22
0.02
45,455
Rofecoxib
2.0
2.20
0.22
4,545
Myocardial infarction (background rate 8.2 per 1,000)
Ibuprofen
1.07
0.57
0.17
5,807
Naproxen
0.98
-0.16
-0.05
-20,325
Diclofenac
1.44
3.61
1.08
924
All NSAIDs
1.09
0.74
0.22
4,517
Celecoxib
0.96
-0.33
-0.10
-10,163
Rofecoxib
1.26
2.13
0.64
1,563
Any dose of drug was allowed in the data, and the table additionally shows the rate and frequency of additional events. The calculations used a
mortality rate of 10% for gastrointestinal bleeding and 30% for cardiovascular events. NSAID, non-steroidal anti-inflammatory drug; coxib,
cyclooxygenase-2 inhibitor.
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Figure 8
Figure 9
Additionalevent
vascular
risk of
with
dying
ibuprofen
from an upper gastrointestinal bleed or cardiovascular event with ibuprofen. GI, gastrointestinal.
Additional
vascular
event
risk of
with
dying
naproxen
from an upper gastrointestinal bleed or cardiovascular event with naproxen. For representational purposes an additional risk of 1 in about 100,000 was assumed where there was no
numerically increased cardiovascular risk. GI, gastrointestinal.
likely risks for an average patient. The calculations were for
additional number of events, the likely number of additional
deaths, and the frequency of those deaths.
For example, for gastrointestinal bleeding with a background
rate of 2.2 bleeds per 1,000 patients per year, use of ibuprofen would result in 1.98 extra bleeds (calculated as (2.2 × 1.9)
-2.2, or 4.18 -2.2, or 1.98). With a death rate of 10%, this
would mean 0.2 additional deaths per 1,000 per year, at a frequency of 1 in 5,051 (calculated as 1,000 ÷ (1.98 ÷ 10)).
Results for other drugs or outcomes were derived similarly.
Where there was no significant difference between use of
NSAID or coxib and non-use, a risk frequency of 1 in 100,000
was assumed.
Presenting contextualised risks
Figures 8 to 10 show the additional risk over background of
dying with an upper gastrointestinal bleed or cardiovascular
event for users of ibuprofen, naproxen and diclofenac, respectively. Figures 11 and 12 show the same information calculated for celecoxib and rofecoxib. In these representations, the
events have been described as gastrointestinal bleeding or
heart attack, for simplicity, and to be less technical to facilitate
possible use with patients rather than professionals.
The figures show that additional risks can vary from moderate
(gastrointestinal bleeding with naproxen and cardiovascular
risk with diclofenac) through to very low or negligible (gastrointestinal bleeding with celecoxib and cardiovascular risk with
naproxen and celecoxib). There are considerable differences
between the five drugs.
An alternative version of the scale (Figure 13) presents the five
drugs, together with all NSAIDs combined, on a single, horizontal, version. This might allow easier comparison, both
between drugs and with some acceptable level of risk provided by contextualising information.
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Figure 10
Figure 11
Additionalevent
vascular
risk of
with
dying
diclofenac
from an upper gastrointestinal bleed or cardiovascular event with diclofenac. GI, gastrointestinal.
Additionalevent
vascular
risk of
with
dying
celecoxib
from an upper gastrointestinal bleed or cardiovascular event with celecoxib. For representational purposes an additional risk of 1 in about 100,000 was assumed where there was no
numerically increased risk, here for either risk. GI, gastrointestinal. GI,
gastrointestinal.
Discussion
It is important to recognise that the method of presenting risk
outlined in this paper is only one way in which the relative consequences of treatment might be shown. Whether the method
is useful to patients or professionals in some of the contexts
shown is not known, and we stress that it still has to be evaluated. The value of the method is also dependent on the quality
and quantity of evidence about risk in any given situation.
That said, patient-led healthcare means that patients need to
be supported in making choices about, and taking control of,
their health and healthcare. Not only must services evolve to
provide personalised care by listening and responding to
patients, but information also needs to be provided to them to
help in decision-making. Patients react adversely to hypothetical risk [83], and providing information about a rare but serious risk of treatment may lead them to make different
judgements. When asked, patients want to know about even
rare risks of adverse events [17].
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Most adverse events are mild, reversible and predictable,
although common. They pose some prospect of discomfort
and may lead to drug discontinuation if they cannot be tolerated, but they are not dangerous. More problematic are those
adverse events that are serious, irreversible and unpredictable.
They will be rare because no drug could be marketed if these
adverse events were also common. It is these rare but serious
events that attract attention. Paradoxically, more effective and
widely used medicines are more likely to attract pressure for
bans based on adverse events [84]. This is because with only
a few hundred or a few thousand people using a drug, a rare
but serious adverse event at the 1 in 100,000 level would
never attract attention. By contrast, use in 2 million people
would result in 20 events that could well attract attention.
Where a medical intervention is performed for major life-saving
or life-enhancing purposes (such as cardiac revascularisation
or joint replacement), possible adverse events are offset by
Available online http://arthritis-research.com/content/10/1/R20
Figure 12
Figure 13
An alternative version of the Paling Perspective Scale
Scale. It puts the five
drugs from Figures 8 to 12 together with all NSAIDs combined, on a
single, horizontal, version. GI, gastrointestinal; NSAID, non-steroidal
anti-inflammatory drug; coxib, cyclooxygenase-2 inhibitor.
Additionalevent
vascular
risk of
with
dying
rofecoxib
from an upper gastrointestinal bleed or cardiovascular event with rofecoxib. GI, gastrointestinal.
significant, important and largely immediate benefit; only major
adverse events, such as mortality, are likely to form a part –
and perhaps only a small part – of decision-making. By contrast, where an intervention delivers less immediate benefits or
where there are alternative therapies available, the risk of
avoidable adverse events becomes a more significant part of
decision-making.
Herein lies the problem. Rare risks of major, irreversible, consequences are by their nature difficult to measure precisely. To
this uncertainty must be added the uncertainty of how information on the risk can be presented in a way that is understood.
This is especially true when there is a background rate in the
population, which we must know or guess, and we then have
to apply an imprecise relative risk, to make judgements about
the severity of different outcomes. It all makes for complex
mental arithmetic, and a representation of the additional risk
faced compared with other risks we assume in life has obvious
benefits, especially when the event is common to all.
Figures 3 to 7 present a series of risks of death associated
with treatments in the range (roughly) of 1 in 1,000,000 to 1
in 1,000, all of which would be regarded are rare. The information about life events regarded as rare allows that to be interpreted and judged, and to provide a context in which individual
decisions can be made. Any judgement will depend not just on
the level of risk but also on the benefits. The fact that a rare
death from a cutaneous adverse event from valdecoxib (Figure
3) is judged differently from a similar risk of death from rhabdomyolysis from a statin (Figure 4) is not necessarily
inconsistent.
There are few easy cases when it is possible to say that a proposed therapy is universally effective or safe, and especially
both effective and safe. Most situations are complex, and none
apparently more so than that of choice of NSAID or coxib for
chronic pain. The examples here have considered only additional risk of death from gastrointestinal bleeding or cardiovascular events, compared with different background rates
without drug therapy. Other levels of risk could have been chosen, including non-fatal outcomes. Moreover, we have deliberately ignored renovascular events, congestive heart failure,
lower bowel problems, anaemia, hypertension and other
adverse events, more and less severe, that might have been
included, especially from individual patient meta-analysis of
randomised trials [85].
In any therapeutic area there are competing risks and benefits
of alternative therapeutic interventions. This paper explores
ways in which risk of just two possible adverse events can be
displayed for several NSAIDs and coxibs that display numerically quite different risks from each other. We have no evidence about how best to convey these to patients in a way
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Moore et al.
that will be fully comprehended, nor have we the evidence to
personalise risk presentation for the individual, so we have to
rely on average results. This is an important omission, because
consequences of treatment are likely to differ for individual
patients, and this now has theoretical underpinning with
regard to coxibs [86].
There are other ways in which risk may be presented. A large
observational study of more than 500,000 over-65s in Canada
[87] examined both myocardial infarction and gastrointestinal
bleeding to produce a combined estimate of risk. It used a different method, but for individual drugs and for patients taking
or not taking low-dose aspirin. Alternatively, data from metaanalyses of randomised trials have been used to present annualised risk estimates for placebo, pooled NSAIDs, and coxibs
[88].
Attitudes of individuals presented with information about possible risks and benefits of treatments will differ as they see the
possible consequences for themselves differently. The product of information presented, their own experience, and emotional factors results in widely differing choices between
individuals [89,90]. All communicated facts will finally be filtered by emotions before a decision is made. We have to
acknowledge that there is a danger of focusing more on how
to calculate and present numerical conclusions about risk,
while ignoring our ignorance of other aspects of decision-making.
There are a number of possible next steps. Contextualised risk
presentations such as these need to be refined. It may well be
that other forms of presentation, or different contextualising
risks, would make them clearer and more relevant for professionals and patients. Risk presentation methods are likely to
have different degrees of success with people of different
backgrounds, languages and cultures. We might consider
whether it is possible to develop risk presentations with
greater utility for physicians. An example is the Joint British
Societies coronary risk prediction charts found in every copy
of the British National Formulary.
Conclusion
We suggest one way of communicating information about the
risk of rare adverse events that can result in death, by combining words, numbers, pictures and context. The area of risk
communication requires significantly more research because
the communication of risk has a limited knowledge base, irrespective of whether it is common or rare, serious or
inconsequential.
ties and government sources at various times. RAM is the
guarantor. JP earns his living from teaching about and consulting on risk communication with doctors, healthcare organisations and pharmaceutical companies. As part of his services,
JP offers special visual aid formats for licensing by commercial
organisations. However, free web-based programs enable
unrestricted access to all parties to build and print customised
versions of JP's main decision aids for non-commercial purposes such as all individual doctor-patient communications
and for trial and evaluation (see http://www.riskcomm.com/
introvisualaids.html). No author has any direct stock holding in
any pharmaceutical company.
Authors' contributions
RAM was involved with the original concept, planning the
study, searching, analysis and preparing a manuscript. SD and
HJM were involved with planning, data extraction, and writing.
JP was involved with planning, writing and visual aids formats
to explain risks. All authors read and approved the final
manuscript.
Acknowledgements
Pain Research is supported in part by the Oxford Pain Research Trust,
and this work was also supported by an unrestricted educational grant
from Pfizer Ltd. Neither organisation had any role in the design, planning
or execution of the study, or in writing the manuscript. The terms of the
financial support from Pfizer included freedom for authors to reach their
own conclusions, and an absolute right to publish the results of their
research, irrespective of any conclusions reached. Pfizer did have the
right to view the final manuscript before publication, and did so.
The use of Paling Perspective Scale for purposes beyond use or dissemination of this article are subject to copyright; see http://www.riskcomm.com. These decision aids are made freely available for authors in
all academic publications provided that the Risk Communication Institute's copyright is always legibly shown on each graphic. With permission of the Risk Communication Institute http://www.riskcomm.com.
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RAM and HJM have received research grants, consulting, or
lecture fees from pharmaceutical companies, including Pfizer,
MSD, GSK, AstraZeneca, Grunenthal, Menarini and Futura.
The authors have also received research support from chari-
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| |
https://openalex.org/W2959540299 | https://digital.library.adelaide.edu.au/dspace/bitstream/2440/126296/3/hdl_126296.pdf | English | null | Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal | Water | 2,019 | cc-by | 5,557 | Received: 11 June 2019; Accepted: 8 July 2019; Published: 10 July 2019 Abstract: This study aims to determine the diversity of pathogenic bacteria in the Bagmati River,
Nepal, during a one-year period. A total of 18 river water samples were collected from three sites
(n = 6 per site) along the river. Bacterial DNA, which were extracted from the water samples, were
analyzed for bacterial 16S rRNA genes by next-generation sequencing for 13 of 18 samples, and by
quantitative PCR targeting Arcobacter for all 18 samples. The 16S rRNA sequencing identified an
average of 97,412 ± 35,909 sequences/sample, which were then categorized into 28 phyla, 61 classes,
and 709 bacterial genera. Eighteen (16%) genera of 111 potential pathogenic bacteria were detected
with abundance ratios of >1%; Arcobacter, Acinetobacter, and Prevotella were the dominant genera. The Arcobacter abundance ratios were 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at
the upstream, midstream, and downstream sites, respectively. Arcobacter was detected in 14 (78%)
of 18 samples tested, with concentrations ranging from 6.7 to 10.7 log10 copies/100 mL, based on
quantitative PCR. Our results demonstrate the poor bacterial quality of the Bagmati River water,
suggesting a need for implementing more measures to reduce fecal contamination in the river water. Keywords: Arcobacter; next-generation sequencing; pathogenic bacteria; quantitative PCR; river water Prevalence of Arcobacter and Other Pathogenic
Bacteria in River Water in Nepal Rajani Ghaju Shrestha 1
, Sarmila Tandukar 2
, Dinesh Bhandari 3,4
, Samendra P. Sherchan 5,
Yasuhiro Tanaka 6, Jeevan B. Sherchand 3 and Eiji Haramoto 1,* Rajani Ghaju Shrestha 1
, Sarmila Tandukar 2
, Dinesh Bhandari 3,4
, Samendra P. Shercha
Yasuhiro Tanaka 6, Jeevan B. Sherchand 3 and Eiji Haramoto 1,* 1
Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu,
Yamanashi 400-8511, Japan 2
Department of Natural, Natural, Biotic and Social Environment Engineering, University of Yamanashi,
4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 2
Department of Natural, Natural, Biotic and Social Environment Engineering, University of Yamanashi,
4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 3
Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu 1524, Nepal
4
School of Public Health, The University of Adelaide, Adelaide, South Australia 5005, Australia
5
Department of Global Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100,
New Orleans, LA 70112, USA 3
Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu 1524, Nepal
4
School of Public Health, The University of Adelaide, Adelaide, South Australia 5005, Australia
5
Department of Global Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100,
New Orleans, LA 70112, USA 6
Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu,
Yamanashi 400-8510, Japan *
Correspondence: eharamoto@yamanashi.ac.jp; Tel.: +81-55-220-8725 Water 2019, 11, 1416; doi:10.3390/w11071416 water water water water www.mdpi.com/journal/water 1. Introduction Industrial pollution load, poor sewage and wastewater treatment facilities, inadequate water
pollution control laws, and rapid urbanization have all contributed to the increased degradation of
the river water environment in developing countries [1,2]. The Bagmati River, which flows from the
northern boundary southwards across the urban areas of the Kathmandu Valley in Nepal, is suffering
from chemical, biological, and solid waste pollution [1,3–9]. Arcobacter, which is widely recognized as an emerging waterborne and foodborne pathogen [10–12],
has been detected in river water samples in Japan, Nepal, and Spain [4,13–16]. Arcobacter in river water
samples has been linked to fecal contamination from animal or human sources [11,13]. In Nepal, only
a few studies using next-generation sequencing (NGS) and quantitative PCR (qPCR) have detected
Arcobacter in the river and groundwater samples [4,14]. The abundance ratios and concentrations of
Arcobacter were highest in river water samples in these studies [4,14]. NGS has been a useful tool in Water 2019, 11, 1416; doi:10.3390/w11071416 www.mdpi.com/journal/water Water 2019, 11, 1416
Water 2019, 11, x FOR 2 of 9
2 of 8
d obtaining large numbers of sequences to determine microbial diversity and community structure, as
explained in a previous study that was conducted by Caporaso et al. (2012) [17]. community structure, as explained in a previous study that was conducted by Caporaso et al. (2012)
[17]. A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream) A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream), Thapathali
(midstream), and Chovar (downstream)) reported that the microbiological quality of the river water
upstream was less degraded when compared to those at the other two sites [9]. Indicator bacteria,
potential index viruses, and human-fecal markers were more frequently detected than protozoa and
human enteric viruses at all three Bagmati River sites. However, it is essential to also understand
the bacterial community of river water at these sites. Therefore, this study aimed to determine the
bacterial diversity and quantify Arcobacter at three Bagmati River sites. A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream),
Thapathali (midstream), and Chovar (downstream)) reported that the microbiological quality of the
river water upstream was less degraded when compared to those at the other two sites [9]. Indicator
bacteria, potential index viruses, and human-fecal markers were more frequently detected than
protozoa and human enteric viruses at all three Bagmati River sites. 2.1. Collection of River Water Samples and Extraction of Bacterial DNA
2.1. Collection of River Water Samples and Extraction of Bacterial DNA As previously described [9], the Bagmati River water samples were collected every two months
from the upstream, midstream, and downstream regions during a one-year period between November
2015 and September 2016, as shown in Figure 1. The sampling sites were selected based on population
density in three regions of the Bagmati River basin, where the population density is lower in the
upstream region when compared to the midstream and downstream regions, and also to observe the
difference in bacterial community in start and end point of the Bagmati River flowing through the
urban area of the Kathmandu Valley. The water samples were collected in 100-mL sterile plastic bottles
and transported to the laboratory in dry ice, kept at 4 ◦C, and then processed within 4 h. As previously described [9], the Bagmati River water samples were collected every two months
from the upstream, midstream, and downstream regions during a one-year period between
November 2015 and September 2016, as shown in Figure 1. The sampling sites were selected based
on population density in three regions of the Bagmati River basin, where the population density is
lower in the upstream region when compared to the midstream and downstream regions, and also
to observe the difference in bacterial community in start and end point of the Bagmati River flowing
through the urban area of the Kathmandu Valley. The water samples were collected in 100-mL sterile
plastic bottles and transported to the laboratory in dry ice, kept at 4 °C, and then processed within 4
h Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Ten milliliters of the river water samples were filtered through a 0.22-µm filter paper, which was
used to extract the bacterial DNA using CicaGeneus DNA Extraction Reagent (Kanto Chemical,
Tokyo, Japan). Briefly, the membrane filter containing the microorganisms was resuspended in 5 mL
of Tris-EDTA buffer (pH 7.4) into a 50 mL plastic tube. Bacterial DNA was extracted from the mixture
Ten milliliters of the river water samples were filtered through a 0.22-µm filter paper, which
was used to extract the bacterial DNA using CicaGeneus DNA Extraction Reagent (Kanto Chemical,
Tokyo, Japan). 1. Introduction However, it is essential to also
understand the bacterial community of river water at these sites. Therefore, this study aimed to
determine the bacterial diversity and quantify Arcobacter at three Bagmati River sites. 2.3. Quantification of Total Bacteria and Arcobacter Total bacterial 16S rRNA genes were quantified by qPCR while using the 515F and U806R
primers [19,20]. The qPCR mixture components were as follows: 2.0 µL of template DNA, 0.1 µL of
50 pmol/µL each of the forward and reverse primers, and 12.5 µL of SYBR Premix Ex TaqII (Tli RNaseH
Plus) (Takara Bio, Otsu, Japan), with a final volume of 25.0 µL. The thermal cycling conditions were at
95 ◦C for 30 s, followed by 35 cycles at 94 ◦C for 15 s, 55 ◦C for 30 s, and 72 ◦C for 20 s, as previously
described [4]. Arcobacter spp. were quantified by SYBR Green-based qPCR using a reaction volume of 25 µL
containing 2.0 µL of template DNA, 12.5 µL of a MightyAmp for Real Time (SYBR Plus) (Takara Bio),
0.1 µL of 50 pmol/µL each of Arco-F and Arco-R-rev primers [14]. The thermal conditions were as
follows: at 98 ◦C for 2 min, followed by 35 cycles at 98 ◦C for 10 s, at 55 ◦C for 30 s, and at 68 ◦C for
40 s, and finally at 95 ◦C for 15 s, at 60 ◦C for 30 s, and at 95 ◦C for 15 s to identify a specific single peak
melting temperature (Tm) [14]. 2.4. Statistical Analysis The Pearson’s correlation coefficient test was performed with Microsoft Excel 2016 (Microsoft
Corporation, Redmond, WA, USA) to determine the relationship of Arcobacter with fecal indicator
bacteria, human-fecal markers, and index viruses [9]. Differences were considered to be statistically
significant if the resulting p value was <0.05. 2.1. Collection of River Water Samples and Extraction of Bacterial DNA
2.1. Collection of River Water Samples and Extraction of Bacterial DNA Briefly, the membrane filter containing the microorganisms was resuspended in 5 mL of
Tris-EDTA buffer (pH 7.4) into a 50 mL plastic tube. Bacterial DNA was extracted from the mixture Water 2019, 11, 1416 3 of 9 using the CicaGeneus DNA extraction kit after shaking and vortex mixing at 50 ◦C with a speed of
300 rpm (Kanto Chemical). Bacterial DNA that were extracted from the river water samples were used
both in a study that was conducted by Tandukar, et al., in 2018 as well as in this study [9]. 2.2. NGS for the Characterization of Bacterial Communities Of the 18 samples collected, 13 samples, excluding five of six samples from Sundarijal in which
bacterial DNA concentrations were not enough high, were subjected to metagenomics sequencing
using a MiSeq gene sequencer (Illumina, San Diego, CA, USA) as previously described [18]. Briefly, the
16S rRNA library was prepared, and the sequence data were analyzed after purification, amplification,
library quantification, normalization, and pooling. Operational taxonomic units were analyzed at
the bacterial domain, phylum, family, and genus levels. A genus was considered to be a potentially
pathogenic bacterium if any one species of the genus was categorized as biosafety level 2 or 3 by
the American Biological Safety Association (https://my.absa.org/tiki-index.php?page=Riskgroups),
as previously described [4]. The raw sequences were registered in the National Center for Biotechnology
Information (NCBI) Sequence Read Archive under the accession number PRJNA547952. 3.1. Characterization of Bacterial Community by NGS At Sundarijal, Thapathali, and Chovar, the abundance ratios
of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected
at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios
of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected
at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Figure 2. Distribution of bacterial phyla. i
b
f b
l l
0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Actinobacteria
Bacteroidetes
Firmicutes
Proteobacteria
Fusobacteria
Others
0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Bacteroidia
Betaproteobacteria
Clostridia
Epsilonproteobacteria
Gammaproteobacteria
Flavobacteriia
Others
Figure 2. Distribution of bacterial phyla. Figure 2. Distribution of bacterial phyla. Figure 3. Distribution of bacterial classes. 0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Actinobacteria
Bacteroidetes
Firmicutes
Proteobacteria
Fusobacteria
Others
0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Bacteroidia
Betaproteobacteria
Clostridia
Epsilonproteobacteria
Gammaproteobacteria
Flavobacteriia
Others
Figure 3. Distribution of bacterial classes. Figure 2. Distribution of bacterial phyla. 0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Bacteroidia
Betaproteobacteria
Clostridia
Epsilonproteobacteria
Gammaproteobacteria
Flavobacteriia
Others
Figure 2. Distribution of bacterial phyla. Figure 3. Distribution of bacterial classes. 0
20
40
60
80
100
May 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
Abundance (%)
Bacteroidia
Betaproteobacteria
Clostridia
Epsilonproteobacteria
Gammaproteobacteria
Flavobacteriia
Others
Figure 3. Distribution of bacterial classes. 3.1. Characterization of Bacterial Community by NGS Thirteen water samples that were collected from three Bagmati River sites were subjected to
the Illumina MiSeq sequencing, where the average number of 16S rRNA gene sequences obtained
was 97,412 ± 35,909 per sample. As shown in Figure 2, among the 28 phyla identified, Proteobacteria
(59–80%) was the most dominant in all of the samples, followed by Bacteroidetes (10–25%) and Firmicutes
(6–15%). Epsilonproteobacteria (29–57%) was dominant in nine river water samples among the 61 classes
that were detected, whereas Betaproteobacteria (27–32%) was dominant in four river water samples, as
shown in Figure 3. The abundance ratios of classes Gammaproteobacteria and Bacteroidia in all of the
samples tested ranged from 6–24% and 5–15%, respectively. Of the 111 potential pathogenic bacteria
identified, 18 genera were detected at abundance ratios of >1% in at least one of the 13 samples tested,
as summarized in Table 1. Arcobacter was the most dominant genus at all three sites, with abundance
ratios of 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at Sundarijal, Thapathali, and 4 of 9
4 of 8
4 of 8 Water 2019, 11, 1416
Water 2019 11 x FOR
Water 2019, 11, x FOR Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were
10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of
5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios
of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected
at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios
of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected
at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were
10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of
5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. 3.1. Characterization of Bacterial Community by NGS Thapathali
Figure 3 Distribution of bacterial classes
Figure 3. Distribution of bacterial classes. 5 of 9 Water 2019, 11, 1416 Table 1. Abundance ratios of potential pathogenic bacteria. Table 1. Abundance ratios of potential pathogenic bacteria. Table 1. Abundance ratios of potential pathogenic bacteria. Genus
Abundance Ratio (%)
Sundarijal (n = 1)
Thapathali (n = 6)
Chovar (n = 6)
Acidovorax
2.2
1.0 ± 0.8
1.1 ± 0.6
Acinetobacter
10.3
5.3 ± 5.3
5.0 ± 3.9
Arcobacter
28.6
31.3 ± 15.8
31.8 ± 17.2
Bacteroides
1.7
2.6 ± 0.9
2.3 ± 1.1
Blautia
0.4
0.8 ± 0.4
0.7 ± 0.6
Burkholderia
0.3
0.5 ± 0.6
0.5 ± 0.2
Chromobacterium
0.4
0.4 ± 0.3
0.6 ± 0.5
Chryseobacterium
1.4
0.9 ± 0.6
1.5 ± 1.0
Clostridium
0.3
0.7 ± 0.2
0.7 ± 0.3
Comamonas
2.1
1.1 ± 1.4
1.0 ± 0.7
Escherichia
1.1
0.4 ± 0.2
0.3 ± 0.1
Flavobacterium
4.7
3.0 ± 4.3
3.4 ± 3.9
Mycobacterium
0.1
0.2 ± 0.1
0.4 ± 0.8
Parabacteroides
0.4
0.8 ± 0.7
1.1 ± 0.9
Plesiomonas
2.2
1.2 ± 0.6
1.5 ± 0.7
Prevotella
5.9
6.8 ± 2.4
4.6 ± 1.5
Pseudomonas
1.6
1.6 ± 0.9
1.8 ± 1.0
Sphingobacterium
1.9
0.1 ± 0.0
0.2 ± 0.1
3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples
Water 2019, 11, x FOR PEER REVIEW
Chryseobacterium
1.4
0.9 ± 0.6
1.5
Clostridium
0.3
0.7 ± 0.2
0.7
Comamonas
2.1
1.1 ± 1.4
1.0
Escherichia
1.1
0.4 ± 0.2
0.3
Flavobacterium
4.7
3.0 ± 4.3
3.4
Mycobacterium
0.1
0.2 ± 0.1
0.4
Parabacteroides
0.4
0.8 ± 0.7
1.1
Plesiomonas
2.2
1.2 ± 0.6
1.5
Prevotella
5.9
6.8 ± 2.4
4.6
Pseudomonas
1.6
1.6 ± 0.9
1.8
Sphingobacterium
1.9
0.1 ± 0.0
0.2
3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples
3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples
3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples As shown in Figure 4, the total bacteria and Arcobacter levels in six river water samples
each from Sundarijal, Thapathali, and Chovar were quantified using qPCR. The minimum and
maximum concentrations of total bacteria at the three sites were 7.1 and 10.5 log10 copies/100 mL,
respectively. 3.1. Characterization of Bacterial Community by NGS In Sundarijal, Thapathali, and Chovar, Arcobacter was detected in two (33%), six (100%),
and six (100%) river water samples, with concentrations of 6.7–10.4, 9.0–10.4, and 8.4–10.7 log10
copies/100 mL, respectively. As shown in Figure 4, the total bacteria and Arcobacter levels in six river water samples each from
Sundarijal, Thapathali, and Chovar were quantified using qPCR. The minimum and maximum
concentrations of total bacteria at the three sites were 7.1 and 10.5 log10 copies/100 mL, respectively. In Sundarijal, Thapathali, and Chovar, Arcobacter was detected in two (33%), six (100%), and six
(100%) river water samples, with concentrations of 6.7–10.4, 9.0–10.4, and 8.4–10.7 log10 copies/100
mL, respectively. Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. 6
8
10
12
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Nov. 2015
Jan. 2016
Mar. 2016
May 2016
July 2016
Sep. 2016
Sundarijal
Thapathali
Chovar
log copies/100 mL
Total bacteria
Arcobacter
Arcobacter
(-)
log10 copies/100 mL
Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. Total bacteria
Arcobacter
Arcobacter Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. 4 Discussion
4. Discussion 4. Discussion
Diverse groups of potential pathogenic bacteria, such as Arcobacter, Acinetobacter, and Prevotella,
were detected by NGS in all three regions of the Bagmati River during a one-year sampling period. In this study, the abundance ratio of the class Epsilonproteobacteria was higher than that of class
Diverse groups of potential pathogenic bacteria, such as Arcobacter, Acinetobacter, and Prevotella,
were detected by NGS in all three regions of the Bagmati River during a one-year sampling period. In this
study, the abundance ratio of the class Epsilonproteobacteria was higher than that of class Betaproteobacteria, Water 2019, 11, 1416 6 of 9 whereas Gammaproteobacteria had the highest abundance ratio in previous studies [4,14]. This may be
attributed to differences in the time and place of sample collection. Although the bacterial community
in the upstream Sundarijal sample was identified, the results of sequencing of only one sample will not
be enough to represent a one-year sampling period, unlike Thapathali and Chovar. Among the potential pathogenic bacterial 16S rRNA genes detected by NGS, those of Arcobacter
were found in the highest abundance ratio. Comparable results have been reported in previous studies,
although a limited number of river water samples were tested [4,14]. During a year of water sampling,
Arcobacter was detected in all sampling months at Thapathali and Chovar. In a previous study, the
highest Arcobacter concentration was found in a river water sample (9.1 log10 copies/100 mL) among
the 13 Arcobacter-positive samples that were collected from shallow dug wells, deep tube wells, and a
river [14]. The detection of Arcobacter in wastewater samples, irrigation water, sludge, drinking water,
surface water, groundwater, and seawater [10,12] shows the bacterium’s capability to survive and
multiply in water with a broad range of qualities. p y
g
q
People living in the Kathmandu Valley are highly dependent on groundwater use [21]. However,
the poor availability of the required volume of water in the valley for domestic purposes leads to the
use of polluted river water for irrigation and for washing vegetables [7,22]. The indirect consumption
of such polluted river water contaminated with different enteric viruses, protozoa, and bacteria may
have adverse effects on human health. The polluted river water not only pollutes its surroundings,
but it also contaminates any nearby groundwater. 4 Discussion
4. Discussion Chemical analysis has provided evidence for the
interconnectivity between groundwater and surface water, a link that allows for the exchange of
chemicals between each water source [23]. The same interconnectivity of waterborne pathogens may
thus occur, which increases the risk of waterborne diseases in the Kathmandu Valley. There is evidence that the physical, chemical, and biological deterioration of water of the Bagmati
River shows an alarming situation of river environment, which affects the surrounding environment. The lowest abundance ratio of Arcobacter at Sundarijal indicates that the upstream region has been
less affected by anthropogenic pollution when compared to the midstream and downstream regions. This result is supported by a previous study that found lower concentrations of protozoa and human
enteric viruses at Sundarijal than at Thapathali and Chovar [9]. In addition to the microbiological
water quality, solid waste levels and the chemical quality of river water in the downstream region
become worse as the river travels through urban areas [24,25]. The relationships of Arcobacter with fecal indicator bacteria (Escherichia coli), human-fecal markers
(BK and JC polyomaviruses, and human Bacteroidales), and plant viruses (tobacco mosaic virus and
pepper mild mottle virus) were determined using data from Tandukar et al. (2018) [9]. Index viruses
were also included in this analysis because they have been proposed as an indicator of the prevalence
of human enteric viruses in irrigation water sources in the Kathmandu Valley [7]. The Pearson’s
correlation coefficient (r) values in Table 2 show the significant correlation between Arcobacter and
E. coli, BK polyomaviruses, pepper mild mottle virus, and human Bacteroidales, but there was no
significant correlation between Arcobacter and JC polyomaviruses and tobacco mosaic virus. The
lack of correlation with the second group of viruses may be due to the difference in the properties
between viruses and bacteria. The presence of Arcobacter, along with other fecal indicator bacteria,
human-fecal markers, index viruses, and human enteric viruses in the river water samples, should
not be neglected. Thus, the river water’s microbial quality needs to be studied more, and strict rules
and regulations should be imposed in order to improve waste disposal and management in facilities
impacting the river. 7 of 9 Water 2019, 11, 1416 Table 2. Relationships of fecal indicator bacteria, human-fecal markers, and index viruses with
Arcobacter. Bacteria and Viruses Tested #
Indicators
r Value with Arcobacter
Fecal indicator bacteria
E. 4 Discussion
4. Discussion coli
0.86 *
Human-fecal markers
BK polyomaviruses
0.72 *
JC polyomaviruses
0.54
Human Bacteroidales
0.93 *
Index viruses
Tobacco mosaic virus
0.36
Pepper mild mottle virus
0.60 *
# Data from Tandukar et al. (2018) [9]; * Statistically significant (p < 0.05). 5. Conclusions In summary, of the 111 potential pathogenic bacteria that were identified by NGS, 18 (16%) had
abundance ratios of >1%. Arcobacter, Acinetobacter, and Prevotella were frequently detected at the three
sites of the Bagmati River. The bacterial communities in upstream, midstream, and downstream of the
Bagmati River were identified with a wide range of bacteria. Using qPCR, Arcobacter was successfully
detected in 14 (78%) of 18 river water samples, at concentrations of 6.7–10.7 log10 copies/100 mL. Arcobacter was detected in all of the samples that were collected from the midstream and downstream
sites of the Bagmati River. The prevalence of Arcobacter, along with other presumptive bacterial
pathogens in river water samples, shows poor water quality, which suggests a need to prevent further
fecal contamination of the river water. Author Contributions: R.G.S. processed the samples, analyzed the results, and prepared a draft of the manuscript. S.T. and D.B. conceived the design of the study and processed the samples, S.P.S. processed the samples, Y.T. checked the analyzed results and corrected the draft of the manuscript, J.B.S. conceived the design of the study. E.H. conceived the design of the study, checked the analyzed results, and corrected the draft of the manuscript. Funding: This study was supported by Kurita Water and Environment Foundation, the Science and Technology
Research Partnership for Sustainable Development (SATREPS) program of Japan International Cooperation
Agency (JICA) and Japan Science and Technology Agency (JST), entitled “Hydro-microbiological Approach for
Water Security in Kathmandu Valley, Nepal”, and the Japan Society for the Promotion of Science (JSPS) through
Fund for the Promotion of Joint International Research (Fostering Joint International Research (B) (grant number
JP18KK0297)). Acknowledgments: The authors thank Bijay Man Shakya (University of Yamanashi, Japan) for his help in
map preparation. Conflicts of Interest: The authors declare no conflict of interest. 5.
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https://openalex.org/W3177327652 | https://pure.uva.nl/ws/files/87590253/ijerph_18_06966_v2.pdf | English | null | Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic | International journal of environmental research and public health/International journal of environmental research and public health | 2,021 | cc-by | 13,851 | UvA-DARE (Digital Academic Repository)
Factors influencing adjustment to remote work: Employees’ initial responses to
the covid-19 pandemic
van Zoonen, W.; Sivunen, A.; Blomqvist, K.; Olsson, T.; Ropponen, A.; Henttonen, K.;
Vartiainen, M.
DOI
10.3390/ijerph18136966
Publication date
2021
Document Version
Final published version
Published in
International Journal of Environmental Research and Public Health
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CC BY
Link to publication
Citation for published version (APA):
van Zoonen, W., Sivunen, A., Blomqvist, K., Olsson, T., Ropponen, A., Henttonen, K., &
Vartiainen, M. (2021). Factors influencing adjustment to remote work: Employees’ initial
responses to the covid-19 pandemic. International Journal of Environmental Research and
Public Health, 18(13), Article 6966. https://doi.org/10.3390/ijerph18136966 UvA-DARE (Digital Academic Repository) Factors influencing adjustment to remote work: Employees’ initial responses to
the covid-19 pandemic Citation for published version (APA):
van Zoonen, W., Sivunen, A., Blomqvist, K., Olsson, T., Ropponen, A., Henttonen, K., &
Vartiainen, M. (2021). Factors influencing adjustment to remote work: Employees’ initial
responses to the covid-19 pandemic. International Journal of Environmental Research and
Public Health, 18(13), Article 6966. https://doi.org/10.3390/ijerph18136966 General rights General rights
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7
Department of Industrial Engineering and Management, Aalto University, Maarintie 8, 00076 Aalto, Finland;
matti.vartiainen@aalto.fi *
Correspondence: w.vanzoonen@uva.nl Citation: van Zoonen, W.; Sivunen,
A.; Blomqvist, K.; Olsson, T.;
Ropponen, A.; Henttonen, K.;
Vartiainen, M. Factors Influencing
Adjustment to Remote Work:
Employees’ Initial Responses to the
COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph
18136966 Citation: van Zoonen, W.; Sivunen,
A.; Blomqvist, K.; Olsson, T.;
Ropponen, A.; Henttonen, K.;
Vartiainen, M. Factors Influencing
Adjustment to Remote Work:
Employees’ Initial Responses to the
COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph
18136966 Abstract: The COVID-19 crisis has disrupted when, where, and how employees work. Drawing
on a sample of 5452 Finnish employees, this study explores the factors associated with employees’
abrupt adjustment to remote work. Specifically, this study examines structural factors (i.e., work
independence and the clarity of job criteria), relational factors (i.e., interpersonal trust and social
isolation), contextual factors of work (i.e., change in work location and perceived disruption), and
communication dynamics (i.e., organizational communication quality and communication technology
use (CTU)) as mechanisms underlying adjustment to remote work. The findings demonstrate that
structural and contextual factors are important predictors of adjustment and that these relationships
are moderated by communication quality and CTU. Contrary to previous research, trust in peers
and supervisors does not support adjustment to remote work. We discuss the implications of these
findings for practice during and beyond times of crisis. Keywords: work adjustment; remote work; structural factors; relational factors; contextual factors;
COVID-19 pandemic Publisher’s Note: MDPI stays neutral
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will be contacted as soon as possible. Download date:24 Oct 2024 International Journal of
Environmental Research
and Public Health International Journal of
Environmental Research
and Public Health Article
Factors Influencing Adjustment to Remote Work: Employees’
Initial Responses to the COVID-19 Pandemic Ward van Zoonen 1,*
, Anu Sivunen 2
, Kirsimarja Blomqvist 3, Thomas Olsson 4
, Annina Ropponen 5
,
Kaisa Henttonen 6 and Matti Vartiainen 7 1
Amsterdam School of Communication Research, University of Amsterdam, Nieuwe Achtergracht 166,
1018 WV Amsterdam, The Netherlands 2
Department of Language and Communication Studies, University of Jyväskylä, Seminaarinkatu 15,
40014 Jyväskylä, Finland; anu.e.sivunen@jyu.fi 2
Department of Language and Communication Studies, University of Jyväskylä, Seminaarinkatu 15,
40014 Jyväskylä, Finland; anu.e.sivunen@jyu.fi y
y
jy
3
School of Business and Management, LUT University, Yliopistonkatu 34, 53850 Lappeenranta, Finland;
kirsimarja.blomqvist@lut.fi 4
Faculty of Information Technology and Communication Sciences, Tampere University, Kalevantie 4,
33100 Tampere, Finland; Thomas.olsson@tuni.fi p
5
Finnish Institute of Occupational Health, 40, 00032 Helsinki, Finland; annina.ropponen@ttl.fi
6 6
UEF Business School, Kuopio Campus, University of Eastern Finland, 1627, 70211 Joensuu, Finland;
kaisa.henttonen@uef.fi
Citation: van Zoonen, W.; Sivunen,
A.; Blomqvist, K.; Olsson, T.;
Ropponen, A.; Henttonen, K.;
Vartiainen, M. Factors Influencing
Adjustment to Remote Work:
Employees’ Initial Responses to the
COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph
18136966
Academic Editors: Jose
M. León-Pérez, Mindy K. Shoss,
Aristides I. Ferreira and
Gabriele Giorgi
Received: 29 May 2021
Accepted: 25 June 2021
Published: 29 June 2021 1. Introduction Even the most conservative estimates anticipate that at least 45 million jobs in the
EU-27 labor market (approximately 23% of the total EU-27 employment) are directly at risk
from the coronavirus disease 2019 (COVID-19) disruptions [1]. The outbreak of COVID-19
has had a drastic impact on work at a global scale [2]. Changes in when, where, and how
work is completed are profound, evidenced, for instance, by widespread remote work
directives [3–5]. The extent to which employees can adjust to remote work is crucial for
individual outcomes (e.g., mental health, well-being, job satisfaction) and organizational
outcomes (e.g., organizational performance). Hence, this study explores factors related to
employees’ adjustment to remote work practices during the first phases of the COVID-19
pandemic. In achieving the aim of this study, we contribute to emerging research on the
impact of the COVID-19 pandemic on work [3,5–8]. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). In line with Raghuram et al. [9], we view adjustment to remote work as an overall
state of adaptation to environmental demands and conditions. Several critical indicators of Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph18136966 https://www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2021, 18, 6966 2 of 19 adjustment to remote work have been identified, including employees’ satisfaction with
remote work conditions, perceived job performance as a consequence of remote work, and
the ability to balance work and non-work demands [9,10]. In contrast to previous investiga-
tions of adjustment [9], the COVID-19 crisis required organizations and their employees to
abruptly change their work environments and ways of working. As such, there is a need to
understand what factors are related to employees’ adjustment to remote work during this
crisis [6]. Based on the theory of work adjustment [11,12] and previous work on individual
adjustment in a work context [10,13] and adaptation to virtual work [9], we identify and
examine a framework of environmental factors that may affect individual adjustment to
remote work during the COVID-19 pandemic. 1. Introduction Specifically, based on cross-sectional survey
data, we provide empirical insights into the extent to which employees’ adjustment to
remote work is associated with structural factors (i.e., work independence and clarity of
job criteria), relational factors (i.e., social isolation and interpersonal trust), and contextual
factors (i.e., perceived disruption and change in work location). Furthermore, we investi-
gate moderating factors (i.e., organizational communication quality and communication
technology use (CTU)) that potentially influence the relationships underlying employees’
adjustment to remote work. Organizational communication quality has been found to
be pivotal when dealing with uncertainty and crises, including organizational responses
to the COVID-19 pandemic [14]. At the same time, technological advances have been
heralded for their ability to facilitate work across spatial distances and both synchronous
and asynchronous collaboration [15–18]. Hence, we investigate the role of organizational
communication quality and CTU in qualifying the impact of structural, relational, and
contextual factors on adjustment to remote work. j
Remote work settings involve temporal and spatial dispersion and depend on CTU
to allow employees to interact across these boundaries [19–23]. Remote work is defined
as “work done by an individual while at a different location than the person(s) directly
supervising and/or paying for it” [24] (p. 2). In the context of the COVID-19 pandemic,
this location was typically employees’ homes. Although previous studies have indicated
that working from home might help employees collaborate across time zones, concentrate
better than in the primary work location, and accomplish work tasks [25], it is unclear what
factors impact employees’ ability to adjust to new demands of their work environment
when they are mandated to work from home. We use remote work to refer to the current
situation in which employees are mandated to work from home during the pandemic (i.e.,
the Finnish government introduced the Emergency Powers Act on 16 March, 2020, and
advised all workplaces in Finland to utilize remote work if possible). 2. Literature Review and Hypotheses This study takes a work adjustment perspective to examine how employees have ad-
justed to an abrupt transition to remote work. Adjustment to new work contexts typically
involves adaptation to new environmental stimuli or demands. It has been suggested [9]
that adjustment to virtual work refers to employees’ ability to adapt to virtual work modes
as they transition from traditional office environments to remote work. Specifically, adjust-
ment refers to an overall state of adaptation because a transition to remote work highlights
the inherent tradeoffs involved in adjustment [9]. Several aspects are considered critical
indicators of employees’ successful adaptation to a virtual work including satisfaction,
commitment, productivity, and the ability to balance work and nonwork demands. Success-
ful adaptation often requires a trade-off between these aspects. To examine the underlying
factors that impact employees’ adjustment to remote work, we identified several structural,
relational, and contextual factors that may impact employees’ adaptation (see Figure 1). These factors align with those proposed by Raghuram and colleagues [9], but we extend
this framework by including crisis-specific concepts such as perceived disruptions and
social isolation. Our conceptual model (see Figure 1) has its theoretical roots in the theory
of work adjustment [11,12,26] and in the interactional model of individual adjustment [13]. It identifies several categories of factors relevant to individual adjustment, including in- Int. J. Environ. Res. Public Health 2021, 18, 6966 3 of 19 dividual, job, and organizational factors. Recently, Carillo and colleagues [6] adopted a
similar approach to identify the individual, job, and organizational factors underlying
telework adjustment in a crisis context. We further extend this work by exploring the role
of several moderating factors, including organizational communication quality and CTU. Figure 1. Hypothesized model. 2 1 S
l Figure 1. Hypothesized model. 2.1. Structural Factors Structural factors are the fundamental preconditions and organizational expectations
related to a job description that may facilitate or forestall the possibilities to work remotely. Key aspects include work independence and clarity of job criteria [9]. When work can be
conducted independently and the criteria for a specific job are clear, employees may be
more confident in their ability to complete work remotely, facilitating better adjustment. 2.1.1. Work Independence Work independence refers to the ability of remote employees to complete tasks without
having to engage in continual interaction with their coworkers [27]. Work independence can
be facilitated by supporting asynchronous work, for example, allowing access to common
databases through technology and ensuring that colleagues can connect with others if
needed [9]. Remote employees, who must rely continually on their coworkers, thereby mak-
ing them reciprocally or sequentially interdependent with others, are likely to experience
time pressures, loss of control, and a decline in personal productivity [28,29]. However,
independence may facilitate adjustment to remote work [9] because it allows workers to
exercise more control over their behavior, for instance, when drawing boundaries between
work and nonwork [30] or when enacting discipline to organize their work and apply
their skills in an isolated work environment [9]. Hence, employees with greater degrees
of independence are found to experience greater adjustment to a remote work context [9]. This is in line with research suggesting that individuals have an innate need for autonomy
and self-determination [31,32]. Thus, we propose the following: Hypothesis 1 (H1). Work independence is positively associated with employees’ adjustment to
remote work. 2.1.2. Clarity of Job Criteria The clarity of job criteria means that performance assessment at work is perceived
as objective, quantifiable, and transparent [9]. Clear and explicit criteria are especially
beneficial to guide the performance of remote employees and develop accurate expecta- Int. J. Environ. Res. Public Health 2021, 18, 6966 4 of 19 tions among them [9,30]. This is because remote employees, compared with non-remote
employees, have fewer opportunities to seek or receive informal performance feedback or
clarifications from their supervisors and coworkers. Unclear evaluation criteria may lead
to insecurity and uncertainty concerning work-related expectations. However, when clear
and explicit evaluation criteria are in place, remote employees may be even more capable
of managing themselves, which may lead to enhanced performance and satisfaction [9,30]. Additionally, clear evaluation criteria can help build mutual expectations and perceptions
of procedural fairness and establish perceptions of equity among remote employees who
cannot use physical behaviors to compare work outcomes [29,33]. When evaluation criteria
are clearly understood, remote employees are also more likely to work on initiatives that
are valued by their organization [34]. Hence, we propose the following: Hypothesis 2 (H2). Clarity of job criteria is positively associated with employees’ adjustment to
remote work. 2.2.1. Interpersonal Trust Because remote work inherently involves physical and psychological distances, fac-
tors that create a stronger sense of relationships between coworkers may prevent physical
distance from becoming psychological distance [9] and are expected to have a positive
influence on employees’ ability to adjust to remote work [36]. Feelings of trust, for instance,
may give remote employees greater confidence in their role within the work group or
organization and facilitate further adjustment [37]. Interpersonal trust can be defined
as the willingness to accept vulnerability and a positive expectation of others’ trustwor-
thiness [38]. It has been shown to have a positive effect on workplace cooperation [39],
knowledge sharing [40], and organizational commitment [41]. Trusting relations between
employees [42] and employees’ trust in supervisors [43] enhance organizational change
and can therefore affect how employees adjust to remote work. Trust also lowers the need
for both employees and their supervisors to monitor and verify each other’s work in the
virtual context [44] and is crucial to the effectiveness of virtual workers [45]. Thus, we
hypothesize the following: Hypothesis 3 (H3). Interpersonal trust is positively associated with employees’ adjustment to
remote work. 2.2. Relational Factors Relational factors refer to the social relationships and forms of collaboration within
an organization. In the context of remote work, they relate to, for example, support and
interpersonal trust [9] among employees working remotely and their supervisors and
coworkers. Hence, we examine how trust can help to overcome barriers to adjusting to
remote work [9]. In addition, issues of social isolation at work are especially profound dur-
ing the COVID-19 pandemic; hence, we investigate how these issues may deter adjustment
to remote work [35]. 2.2.2. Social Isolation Social isolation is related to physical and psychological distance between coworkers. Isolation can be defined as the perception of a lack of availability of support and recognition,
missed opportunities for informal interactions with coworkers, and not being part of the
group [35]. In other words, isolation is a state of mind or a belief that one is out of touch
with others in the workplace; as such, the desire to feel socially connected is thwarted [46]. In a remote work setting, perceptions of social isolation may be exacerbated, even though
it is proposed that isolation is created mainly due to the lack of availability and not just
spatial distance [35]. Perceived isolation has been identified as a potential obstacle for
effectiveness among remote employees [47] and may reduce job satisfaction [46]. Hence,
we hypothesize the following: 5 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 Hypothesis 4 (H4). Social isolation is negatively associated with employees’ adjustment to remote
work. Hypothesis 4 (H4). Social isolation is negatively associated with employees’ adjustment to remote
work. 2.3.2. Disruption of Work Routines Unlearning refers to the “breakdown of routines, habits, and cognitive frameworks” [49]
(p. 509). We use the term disruption to refer to an unlearning process in which routines,
habits, norms, and procedures are changing [50] as a result of the COVID-19 pandemic. The adjustment required by employees depends on the level of disruption experienced by
employees: greater disruption requires greater adjustment. Prior research demonstrates
that environmental turbulence causes organizations and their subunits to face performance
gaps, work stress, toxic work environments, and blame shifting as well as anxiety and
fears [50]. Hence, we hypothesize the following: Hypothesis 6 (H6). Disruption of work routines is negatively associated with employees’ adjust-
ment to remote work. 2.3. Contextual Factors We extend previous models [9] of adjustment by explicitly considering the COVID-19
context within which adjustments are required. Specifically, we suggest that the severity of
the change in work location—here, the discrepancy between earlier remote work experi-
ence and current remote work frequency—and the extent of broader disruptions of work
routines triggered by the COVID-19 crisis impact on employees’ adjustment to the “new
normal” [5,48]. 2.3.1. Change in Work Location The sudden requirement to work from home has led most employees to increase the
frequency with which they work from home. For some, these changes are more substantial
because they either did not engage in remote work practices or did so to a very limited
extent prior to the COVID-19 outbreak. In contrast, for employees who are more familiar
with these work practices either because they frequently work remotely or are used to
working with dispersed colleagues, these new work realities may require less adjustment. Limited connections and access in remote locations seem to be the main challenges of virtual
working spaces despite recent technological advances. We examine the role of changes in
work location as the discrepancy between current remote work practices and remote work
practices before the COVID-19 crisis. Transitioning to a remote work location may require
adjustment to the working environment, including physical, technological, and social
conditions of work [16]. The intuitive hypothesis here is that larger differences indicate
more substantial changes in where work is conducted, which in turn could complicate
adjustment. Hypothesis 5 (H5). Changes in work location are negatively associated with employees’ adjustment
to remote work. 2.4. Moderating Factors In addition to structural, relational, and contextual factors, remote work is structured
and shaped by communication technologies that enable employees to interact across
temporal and spatial boundaries. The quality of organizational communication and the
frequency of CTU in times of changing work environments and dispersed work may
prove to be of particular importance for employees to adjust to new work conditions. Organizational communication quality is defined here as the informativeness, accuracy,
and timeliness of communication about organizational changes during the pandemic [51]. 6 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 2.4.1. Organizational Communication Quality and Relational and Contextual Factors g
y
Communication has been found to mitigate the relationship between geographical
distribution and conflict [52]. Although not directly related to adjustment, these findings
imply that communication might have a positive impact on conflict identification and
conflict handling, and as such may optimize remote work effectiveness and satisfaction,
which are key indicators of adjustment. In addition, high-quality organizational com-
munication can be viewed as a sign of organizational support that may help employees
refocus on collective goals [53] to meet their performance expectations. In the absence of
a traditional office environment, the role of organizational communication may be even
more profound because it may substitute in part for a lack of face-to-face interaction while
facilitating the information purposes of social support networks that are normally present
in organizations [54]. Finally, communication tends to clarify role expectations and enhance
performance by reducing uncertainty [51]. Therefore, we ask the following question: RQ1: Does organizational communication quality moderate the impact of structural, relational,
and contextual factors underlying adjustment? 2.4.2. Communication Technology Use and Relational and Contextual Factors Communication technologies are the enabling force behind most remote work set-
tings, allowing workers to maintain necessary levels of connectivity to share information
and coordinate work across various boundaries [55,56]. In addition, the effective use of
communication technology is an important facilitator of trust in virtual teams [17,57,58]. Indeed, many organizations can be argued to have adopted some degree of virtual prac-
tices under the studied conditions, and collaboration strongly depends on the effective
use of communication technology. ter Hoeven and van Zoonen [59] demonstrated that
control over CTU reduces the negative consequences of spatial distance in remote work
arrangements for helping behavior. 2.4. Moderating Factors Because CTU may amplify the positive association of
relational factors (e.g., interpersonal trust) with adjustment while mitigating the negative
impact of other relational factors (e.g., social isolation), we pose the following research
question: RQ2: Does CTU moderate the impact of relational and contextual factors underlying adjustment? 3. Materials and Methods This cross-sectional study targeted employees who had been asked to work remotely
in Finland since the lockdown began in mid-March 2020. The survey started on the 26th
of March 2020 and was open for responses until the 13th of April 2020. Open survey
invitations were published online, and we solicited the help of several large labor unions
and ministries to distribute the survey link to their members. The survey included about
100 items in total, including background questions and attention checks. The survey
was administered through the XM platform Qualtrics and programmed such that all
statements needed to be answered for the survey to be completed and responses to be
considered for analysis. Explicit informed consent was obtained from all participants prior
to the survey. Data were exported to IBM statistical software packages SPSS and AMOS
for further analysis. There were no missing values as we used forced response options,
respondents who failed the attention checks or dropped out were automatically excluded. Embedded data (e.g., IP addresses) and identifying information (i.e., email addresses) were
assessed to guard against duplicate responses, but were not used in the analysis stage. This
convenience sampling procedure resulted in a total response of 5452 Finnish employees. Employees in our sample indicated low probabilities of job loss in the near future, with
84.4% indicating that this was (highly) improbable (M = 2.07 SD = 1.43; on a 7-point scale). The average age of the respondents was 45.3 years old (SD = 10.7). Most respondents were
female (N = 3747; 69%), and 1593 were male (29%). Most respondents were employed
by the state or public utility (N = 3267; 60%), while 1318 respondents worked for private
enterprises (24%), and others worked in nongovernmental (2%) or semigovernmental (8%) Int. J. Environ. Res. Public Health 2021, 18, 6966 7 of 19 organizations. The respondents mostly worked in organizations with 50 to 249 employees
(22%), 250 to 999 employees (29%), or more than 2000 employees (25%). The majority of
respondents worked remotely 4 or more days per week (90.8%), 6.5% worked remotely 2
or 3 days, and 2.6% worked remotely 1 day per week or less. Furthermore, respondents
indicated they worked 38.6 h per week on average (SD = 6.6), and the average reported
overtime was 2.3 h per week (SD = 5.9). 3.1.3. Relational Factors Interpersonal trust was measured using four items based on [61] adopted from [9]. In
line with earlier research [9], our measurement strategy focused on an overall measure
of trust rather than assessing the many specific determinants of trust. Two items relate
how much the individual trusts his/her supervisor and colleagues, and two items measure
the extent to which the respondent perceives that his/her supervisor and colleagues trust
the individual. Social isolation was measured using three items derived from [35]. Social
isolation measures the extent to which employees feel isolated and separated from others
in the workplace. 3.1. Measures All statements were measured using seven-point response scales ranging from strongly
disagree to strongly agree unless indicated otherwise. All survey items were derived from
earlier studies and reviewed by the research team, but we did not conduct a pilot study. Table 1 lists all measurement items, including descriptive statistics and factor loadings. 3.1.2. Structural Factors Independence was measured using four items adopted from [60]. Similar to Raghuram
et al. [9], respondents were asked to indicate the degree to which their performance was
dependent on working with others. Clarity of job criteria was measured using four items
adopted from [61]. The items deal with handling problems on the job, figuring out what
should be done to accomplish one’s work, and being sure of how the job needs to be
done. Items are based on role conflict and role ambiguity scales proposed by House and
colleagues [62]. 3. Materials and Methods Approximately 14% of the respondents worked in
a managerial position, their average organizational tenure was 10.9 years (SD = 10.1), most
respondents were part of single (N = 1029; 19%) or two-person (N = 2152; 40%) households,
and 40% had at least 1 child under the age of 18 in their household. 3.1.1. Dependent Variable Adjustment to remote work was measured with a five-item scale assessing satisfaction
with remote work, perceived performance as the consequence of remote work, and ability
to balance work and non-work demands. The measure was adopted from Raghuram
et al. [9], who used it in the context of virtual work. Adjustment refers to an overall state of
adaptation because a transition to remote work highlights the inherent tradeoffs involved
in adjustment [9]. For instance, research by [9] indicated that expending greater efforts to
increase (or maintain) productivity may come at the expense of greater work/nonwork
balance. Hence, an overall measure of adjustment may most accurately assess employees’
relative level of adaptation to environmental demands. 3.1.5. Moderators Organizational communication quality was measured using six items from Bordia et al. [64]. These items have previously been applied in the context of uncertainty during organi-
zational change. Quality of communication was measured using items such as “the
communication my organization provided adequately answered my questions about the
changes.” g
Communication technology use was measured by asking respondents to indicate the
frequency with which they used various technologies to communicate with their colleagues. The communication technologies we inquired about were email, telephone, instant messag-
ing (e.g., WhatsApp), online meetings (e.g., through Zoom or MS Teams), collaborative
tools (e.g., Google Drive or Office365), enterprise social media (e.g., Yammer), and public
social media (e.g., Facebook). Responses ranged from 1 (never) to 7 (hourly). The items
were computed to indicate an overall score for the frequency of CTU, with higher scores
indicating more frequent communication with colleagues through these technologies. Table 1. Measurement items and descriptive statistics. Table 1. Measurement items and descriptive statistics. Measurement Items
Mean
(SD)
R2
St. Factor
Loading
Unst. 3.1.5. Moderators Factor
Loading
Se
Adjustment to remote work [9]
All in all, I am satisfied with remote work
5.66 (1.43)
0.61
0.781
1.000
Remote work allows me to perform my job better than I ever could when I worked in the office
4.39 (1.62)
0.76
0.871
1.261
0.02
If I were given the choice to return to a traditional office environment (i.e., no longer work
remotely), I would be very unlikely to do so
3.98 (2.02)
0.43
0.657
1.184
0.02
Since I started working remotely, I have been able to balance my job and personal life
4.87 (1.75)
0.44
0.663
1.036
0.02
Since I started working remotely, my productivity (e.g., sales orders, output, support) has increased
4.39 (1.66)
0.70
0.835
1.076
0.02
Structural Factors
Independence [59]
I have to obtain information and advice from colleagues to complete my work (R) c
4.15 (1.66)
0.69
0.832
1.000
I depend on colleagues for the completion of my work (R)
3.85 (1.75)
0.73
0.855
1.082
0.02
I rarely have to check in with other people to do my work
4.72 (1.61)
0.35
0.587
0.685
0.02
I have to work closely with other people to do my job properly (R)
4.06 (1.82)
0.43
0.659
0.869
0.02
Clarity of job criteria [60]
I frequently don’t know how to handle problems that occur in my job (R)
2.28 (1.30)
0.51
0.713
1.000
I often find that I cannot figure out what should be done to accomplish my work (R)
1.96 (1.15)
0.76
0.869
1.073
0.02
I am frequently confused about what I have to do on my job (R)
1.86 (1.15)
0.80
0.894
1.100
0.02
I am frequently unsure about how to do my work (R)
1.94 (1.19)
0.77
0.875
1.115
0.02
Relational Factors
Interpersonal trust [9]
I trust my supervisors
5.64 (1.35)
0.60
0.773
1.000
My supervisors trust me
5.84 (1.03)
0.48
0.694
0.690
0.02
I trust my peers
6.00 (0.86)
0.34
0.587
0.485
0.02
My peers trust me
5.96 (0.82)
0.29
0.541
0.422
0.02
Social isolation [35]
I am separated from my coworkers
5.29 (1.67)
0.61
0.712
1.000
I often feel I am no longer close to anyone
3.33 (1.71)
0.35
0.592
0.849
0.03
I am isolated from others at work
4.35 (1.82)
0.71
0.841
1.281
0.03
Contextual Factors
Remote work location a
How often did you normally (before the COVID-19 pandemic) work remotely (e.g., from home)? 3.1.4. Contextual Factors Change of work location was measured by calculating the difference between remote
work before the pandemic and current remote work frequency. Respondents were asked
about the frequency with which they normally (before the pandemic) worked remotely,
ranging from 1 (never) to 7 (6 or 7 days per week). Subsequently, we asked respondents to
indicate the frequency with which they worked remotely since the moment their organiza-
tion took measures related to the COVID-19 crisis. By subtracting the scores, we calculated Int. J. Environ. Res. Public Health 2021, 18, 6966 8 of 19 a difference score such that a higher value indicates a larger discrepancy in remote work
practices compared with normal circumstances. Perceived disruption was measured by adopting eight items from [50,63]. The items
address changes in work routines. Since routines are reflected in operating procedures
during the performance of work, changes in plans, deadlines, and information-sharing
mechanisms are indicative of an overall disruption of work. We asked employees to
indicate the extent to which several activities, including project plans and deadlines, have
changed since the organization took measures related to the COVID-19 crisis. Independence [59] Interpersonal trust [9]
I trust my supervisors
My supervisors trust me
I trust my peers
My peers trust me
Social isolation [35]
I am separated from my coworkers
I often feel I am no longer close to anyone
I am isolated from others at work 3.1.5. Moderators 2.77 (1.40)
-
-
-
-
How often have you worked at home during the COVID-19 pandemic? 5.70 (1.05)
-
-
-
- Table 1. Measurement items and descriptive statistics. Organizational communication quality [63] Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score
indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates
that items were reverse coded. Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score
indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates
that items were reverse coded. Remote work location a Disruptions [50]
During the COVID-19 crisis, the following aspects of my work changed:
Work procedures
4.37 (1.74)
0.39
0.624
1.000
Project plans
3.67 (1.51)
0.41
0.643
0.895
0.02
Technologies used to complete work tasks
3.80 (1.85)
0.42
0.649
1.108
0.03
Decision-making processes
3.35 (1.56)
0.44
0.666
0.957
0.02
My work tasks
2.97 (1.66)
0.51
0.715
1.092
0.03
The coordination of my work
3.56 (1.66)
0.54
0.737
1.130
0.03
The deadlines of work projects
3.41 (1.74)
0.38
0.619
0.994
0.03 Remote work location a 9 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 Table 1. Cont. Measurement Items
Mean
(SD)
R2
St. Factor
Loading
Unst. Factor
Loading
Se
Disruptions [50]
During the COVID-19 crisis, the following aspects of my work changed:
Work procedures
4.37 (1.74)
0.39
0.624
1.000
Project plans
3.67 (1.51)
0.41
0.643
0.895
0.02
Technologies used to complete work tasks
3.80 (1.85)
0.42
0.649
1.108
0.03
Decision-making processes
3.35 (1.56)
0.44
0.666
0.957
0.02
My work tasks
2.97 (1.66)
0.51
0.715
1.092
0.03
The coordination of my work
3.56 (1.66)
0.54
0.737
1.130
0.03
The deadlines of work projects
3.41 (1.74)
0.38
0.619
0.994
0.03
Moderators
Organizational communication quality [63]
The communication my organization provided has been useful
5.65 (1.11)
0.71
0.840
1.000
The communication my organization provided has adequately answered my questions about the
changes
5.50 (1.28)
0.73
0.854
1.167
0.02
The communication my organization provided has been positive
5.25 (1.22)
0.55
0.743
0.975
0.02
The communication by my organization has been appropriate
5.63 (1.11)
0.79
0.890
1.056
0.01
The communication my organization provided has been timely
5.25 (1.36)
0.69
0.829
1.206
0.02
The communication my organization provided has been accurate
5.87 (1.02)
0.58
0.760
0.826
0.01
Communication technology use b
Over the past two weeks, how often did you communicate about your work with
colleagues using
Phone calls
3.08 (1.37)
-
-
-
-
E-mails
4.79 (0.94)
-
-
-
-
Online meetings (e.g., Skype, MS Teams, Zoom)
4.27 (1.05)
-
-
-
-
Text or instant messaging (e.g., WhatsApp, Messenger)
3.06 (1.64)
-
-
-
-
Collaboration tools (e.g., Office 365, Google Drive)
2.81 (1.75)
-
-
-
-
Enterprise social media (e.g., Yammer, Happeo)
1.91 (1.45)
-
-
-
-
Public social media (e.g., Facebook, Twitter)
1.58 (1.15)
-
-
-
-
Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score
indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates
that items were reverse coded. Table 1. Cont. 4.1. Measurement Model A confirmatory factor analysis (in AMOS) was used to examine the hypothesized
factor structure and investigate the validity of our measurement model. Subsequently, we
examined common method variance using a common latent factor approach. The model demonstrated good model fit: χ2 (469) = 4432.49; CFI = 0.96; TLI = 0.95;
SRMR = 0.04; PClose 1.000; and RMSEA = 0.039 (CI: 0.038, 0.040). Following recom-
mendations and threshold values reported by Hair et al. [65], the model demonstrated
convergent and discriminant validity of the measures in our model (see Table 1). The
average variance extracted (AVE) ranged between 0.43 and 0.71. Discriminant validity
was examined through the maximum shared variance (MSV), which ranged between 0.07
and 0.37 for the constructs in our model and is smaller than the AVE values. Additionally,
the square root of the AVE was greater than the inter-construct correlations. Inspection of
the model parameters indicated the absence of cross-loadings, overall suggesting good
discriminant validity. Reliability was examined through the composite reliabilities (CR)
and the maximum reliability (H), which ranged between 0.75 and 0.93 and between 0.77
and 0.93, respectively. Second, we examined common method variance using a common latent factor ap-
proach. Squared regression estimates indicated that common method variance was 3.6%,
indicating that common method variance is not a substantial concern in our data. Curve
estimations for all relationships in our model indicated that these relationships were suf-
ficiently linear. Finally, the correlation between interpersonal trust and communication
quality was relatively high (0.61; see Table 2). Hence, we inspected collinearity statistics
(i.e., the variance inflation factor, VIF) for all independent variables and discovered no Int. J. Environ. Res. Public Health 2021, 18, 6966 10 of 19 10 of 19 problems with multicollinearity. In sum, these results justify further inspection of the
structural model. Table 2. Correlation Matrix of variables with validity statistics. Variable
M (SD)
CR
AVE
MSV
MaxR(H)
1
2
3
4
5
6
7
8
9
1. Independence
4.20 (1.40)
0.83
0.55
0.07
0.86
0.74
2. Clarity of job criteria
5.99 (1.05)
0.91
0.71
0.10
0.92
−0.27
0.84
3. Interpersonal trust
5.86 (0.82)
0.75
0.43
0.37
0.77
0.06
0.32
0.66
4. Social isolation
4.32 (1.41)
0.76
0.52
0.09
0.80
0.03
−0.25
−0.10
0.72
5. Disruption
3.59 (1.21)
0.85
0.44
0.08
0.85
0.13
−0.28
−0.12
0.15
0.67
6. Change a
3.92 (1.53)
−
−
−
−
0.14
−0.11
0.01
0.15
0.18
–
7. 4.1. Measurement Model Communication quality
5.53 (1.01)
0.93
0.67
0.37
0.93
0.05
0.22
0.61
−0.13
−0.11
−0.01 0.82
8. Technology use b
3.07 (0.75)
−
−
−
−
0.27
0.10
0.09
0.13
0.12
0.07
0.11
−
9. Adjustment
4.66 (1.34)
0.88
0.59
0.10
0.90
−0.25
0.32
0.06
−0.30
−0.26
−0.32 0.15
0.06
0.77
Notes: CR = composite reliability; AVE = average variance extracted; MSV = maximum shared variance; MaxR(H) = maximum reliability. Square root of the AVE is reported on the diagonal. a Change was calculated as a difference score between two observed variables and
therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and
therefore not included in the CFA. Technology use is treated as the index score, where higher scores mean higher general technology use. All correlations equal to or above 0.03 are significant at p < 0.05. Table 2. Correlation Matrix of variables with validity statistics. Notes: CR = composite reliability; AVE = average variance extracted; MSV = maximum shared variance; MaxR(H) = maximum reliability. Square root of the AVE is reported on the diagonal. a Change was calculated as a difference score between two observed variables and
therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and
therefore not included in the CFA. Technology use is treated as the index score, where higher scores mean higher general technology use. All correlations equal to or above 0.03 are significant at p < 0.05. 4.2. Controls We considered several potentially confounding factors in our analysis. Specifically, we
controlled for gender, age, working hours per week, managerial position, organizational
tenure, and job security. Gender significantly predicted adjustment (B = 0.091, p = 0.009),
suggesting that female respondents were better able to adjust to remote work. Gender did
not affect any of the hypothesized relationships in the model. Age did not affect adjustment
to remote work (B = 0.000, p = 0.766). Similarly, the number of work hours per week did
not significantly affect adjustment to remote work (B = −0.001, p = 0.691). However, the
results indicated that managerial positions had a significant and negative relationship with
adjustment (B = −0.176, p < 0.001), suggesting that individuals in managerial positions
seem to have more difficulties adjusting to remote work. Finally, organizational tenure
(B = −0.001, p = 0.202) and job security (B = 0.012, p = 0.274) did not affect adjustment to
remote work or any of the relationships in our model. In sum, all hypothesized relationships
remained unaffected when these variables were included. Hence, these variables were
excluded from the final model for reasons of parsimony. 4.3. Hypotheses Testing The hypothesized model was examined using path modeling in AMOS by estimating
regression coefficients between the structural, relational, and contextual factors on adjust-
ment to work. Table 3 provides the standardized and unstandardized regression results for
the full model. Structural factors. Hypothesis 1 assumes that work independence is positively related
to adjustment to remote work. The results demonstrate a significant positive relationship
(B = 0.168 (0.143; 0.192), p = 0.001). Hence, hypothesis 1 is supported. In addition, hypoth-
esis 2 reflects the assumption that clarity of job criteria makes it easier for employees to
adapt to remote work. The findings demonstrate a significant positive relationship between
the clarity of job criteria and adjustment to remote work (B = 0.174 (0.136; 0.211), p = 0.001). Hence, hypothesis 2 is also supported. Overall, these results provide strong support that
the structural factors of an employee’s job have an important influence on the employee’s
adjustment to remote work. Relational factors. Hypothesis 3 posits that interpersonal trust is positively related to
employees’ adjustment to remote work. The results demonstrate a significant negative
relationship between trust and adjustment (B = −0.069 (−0.117; −0.021), p = 0.006). Hence,
contrary to our expectations, trust between coworkers and supervisors does not increase
adjustment to remote work but rather decreases it. A possible explanation could be that
employees who exhibit lower levels of trust in their peers and supervisors rather work
(alone) remotely, as this gives them more autonomy from people they do not trust and, Int. J. Environ. Res. Public Health 2021, 18, 6966 11 of 19 11 of 19 therefore, they are less frequently confronted with such relationships. However, as the
relationship is in the opposite direction than the one we hypothesized, we do not find
support for hypothesis 3. Hypothesis 4 suggests that social isolation is negatively related
to adjustment to remote work. The results demonstrate a significant negative relationship
between perceived social isolation and adjustment to remote work (B = −0.178 (−0.202;
−0.152), p = 0.001), providing support for Hypothesis 4. Contextual factors. Hypothesis 5 reflects the rationale that the relative change in work
locations influences employees’ adjustment to remote work. The results show that a change
in work location is negatively related to adjustment to remote work (B = −0.209 (−0.234;
−0.186), p = 0.001). 4.3. Hypotheses Testing This result suggests that a larger change in work location (e.g., a change
in remote work from half a day per week to five days per week versus a change in remote
work from two days per week normally to five days per week currently) reduces employees’
adjustment to remote work. Hence, hypothesis 5 is supported. This implies that employees
who were already used to working remotely before the pandemic adjusted better to the
new situation. Hypothesis 6 suggests that perceived disruption is negatively related to
adjustment to remote work. The findings demonstrate a significant negative relationship
(B = −0.122 (−0.153; −0.093), p = 0.001), providing support for hypothesis 6. The more
work practices changed during the pandemic, the less employees were able to adjust. Table 3. Parameter estimates of path model. Table 3. Parameter estimates of path model. Table 3. Parameter estimates of path model. Bootstrapping
BC 95% CI
B
SE
Beta
Lower
Upper
p
Hypotheses
H1
Independence →Adjustment
0.168
0.012
0.175
0.143
0.192
0.001
H2
Clarity of job criteria →Adjustment
0.174
0.017
0.136
0.136
0.211
0.001
H3
Interpersonal trust →Adjustment
−0.069
0.023
−0.042
−0.117
−0.021
0.006
H4
Social isolation →Adjustment
−0.178
0.012
−0.188
−0.202
−0.152
0.001
H5
Remote work transition →Adjustment
−0.209
0.011
−0.239
−0.234
−0.186
0.001
H6
Perceived disruption →Adjustment
−0.122
0.014
−0.110
−0.153
−0.093
0.001
RQ1: Communication quality × Relational and contextual factors
RQ1
Communication quality × Trust →Adjustment
0.002
0.015
0.002
−0.039
0.041
0.995
Communication quality × Isolation →Adjustment
0.019
0.010
0.023
−0.007
0.043
0.149
Communication quality × Change in location →Adjustment
−0.045
0.010
−0.057
−0.070
−0.021
0.001
Communication quality × Disruption →Adjustment
0.007
0.130
0.007
−0.025
0.036
0.722
Communication quality × Independence →Adjustment
0.016
0.011
0.014
−0.012
0.039
0.263
Communication quality × Clarity of job criteria →adjustment
−0.009
0.015
−0.010
−0.044
0.024
0.620
RQ2: Communication technology use × Relational and contextual factors
RQ2
Technology use × Trust →Adjustment
−0.107
0.024
−0.053
−0.168
−0.046
0.002
Technology use × Isolation →Adjustment
0.009
0.015
0.007
−0.007
0.043
0.149
Technology use × Change in location →Adjustment
−0.031
0.014
−0.028
−0.065
−0.001
0.045
Technology use × Disruption →Adjustment
0.050
0.017
0.035
0.013
0.085
0.006
Notes: Bootstrapping is a technique from which the sampling distribution of statistic is estimated by taking repeated samples from the
dataset. Bootstrapping was used to obtain model estimates. BC95% CI indicate the bias-corrected 95% confidence interval of the beta
coefficient. 4.4. Moderations Before discussing the interactions, it should be noted that both moderators, organiza-
tional communication quality (B = 0.114 [0.075; 0.152], p = 0.001) and the frequency of CTU
(B = 0.103 [0.059; 0.152], p = 0.001), are significantly and positively related to adjustment. Note that all variables that comprise product terms were mean centered prior to testing
the interactions. For all interactions, we inspected the values of the interactions effect at
different values of the moderator using the Johnson–Neyman technique. When the interac-
tion reported was not significant at all values of the moderator, we reported the value of Int. J. Environ. Res. Public Health 2021, 18, 6966 12 of 19 12 of 19 the moderator at which the interaction becomes significant. To facilitate interpretation, the
mean-centered values are also reported as actual (raw) values. the moderator at which the interaction becomes significant. To facilitate interpretation, the
mean-centered values are also reported as actual (raw) values. p
Organizational communication quality. There was no significant interaction effect be-
tween organizational communication quality and trust (B = 0.002 (−0.039; 0.041), p = 0.995),
social isolation (B = 0.019 (−0.007; 0.043), p = 0.149), and disruption (B = 0.007 (−0.025;
0.036), p = 0.722) on employees’ adjustment to remote work. There was a significant in-
teraction between organizational communication quality and change in work location
(B = −0.045 (−0.070; −0.021), p = 0.001) on adjustment to remote work. This result sug-
gests that at low levels of organizational communication quality starting at −4.11 (i.e.,
1.42 in raw values), perceived change in work location negatively impacts adjustment to
remote work. Organizational communication quality has a limited impact in mitigating
this negative relationship. Finally, we did not find significant interactions between orga-
nizational communication quality and clarity of job criteria on adjustment (B = −0.010
(−0.044; 0.024), p = 0.620), nor did we find an interaction between communication quality
and job independence on adjustment (B = 0.014 (−0.012; 0.039), p = 0.263). j
p
j
p
Communication technology use. There were no significant interactions between social
isolation and CTU (B = 0.009 (−0.007; 0.043), p = 0.149). CTU was found to moderate the
negative relationship between trust and adjustment to remote work (B = −0.107 (−0.168;
−0.046), p = 0.002). The result indicates that trust negatively affects adjustment to work
when the mean-centered value of CTU is below 0.562 (i.e., 3.63 in raw values). 4.4. Moderations This suggests
that when CTU is low, trust stifles adjustment to remote work, but when CTU is high
(above 0.562, approximately 22% of the responses), there is no significant negative effect of
trust on adjustment to remote work. Arguably, frequent CTU is important when trust is low,
to mitigate a decline in employees’ commitment, satisfaction, and productivity. However,
CTU is also important for adjustment when trust is high as a lack of communication may
be more detrimental to adjustment in high-trusting environments. For instance, trust may
be an indicator of high-quality relationships, missing out on such relationships in remote
work settings may be detrimental to several aspects of adjustment, increasing the frequency
of CTU to communicate and collaborate with trusted peers and supervisors might reduce
the negative impact on employees’ adjustment. g
p
p
y
j
In addition, CTU was found to moderate the negative relationship between change
in work location and adjustment (B = −0.031 (−0.065; −0.001), p = 0.045). The findings
suggest that change is negatively related to adjustment at all levels of CTU. However,
smaller levels of change and a higher frequency of CTU yield the highest levels of adjust-
ment. At one standard deviation below the mean (−1.92) of change, adjustment is higher
(5.33) when CTU is one standard deviation above the mean (0.786) rather than below the
mean (−0.786), in which case adjustment is 5.07. Finally, CTU moderates the relationship
between disruption and adjustment to remote work (B = 0.050 (0.013; 0.085), p = 0.006). The confidence interval of the slope indicates that disruption has a negative impact on
adjustment to remote work at all levels of CTU. However, it should be noted that higher
frequencies of CTU allow employees to adjust better to remote work when disruption is
high than when the frequency of CTU in these situations is low. 5.1. Theoretical Implications The findings have several theoretical implications. First, based on the theory of
work adjustment [12] and the interactional model of individual adjustment [13], this
study identified several crisis-specific environmental factors [6] in addition to “traditional”
environmental factors proposed by [9] that may underlie employees’ adjustment to remote
work. For instance, we demonstrated that isolation is a relevant predictor that could be
conceptualized as a relational factor underlying adjustment. In addition, we conceptualized
contextual factors that include crisis-specific indicators such as changes in work location
and perceived disruptions that impact adjustment. Finally, this study further considered
how communication quality and CTU may mitigate some of the challenges in adapting
to remote work. Ultimately, the study contributes to the literature on adjustment by
identifying how employees’ ability to adjust to abrupt transitions to remote work has
been affected by various relevant factors of the work environment. Specifically, this
study contributes to person–environment theories and the theory of work adjustment by
identifying how the work environment may enable or constrain employees’ ability to adapt. In other words, the work environment has reinforcement capabilities that can satisfy a
person’s needs (in this case, adjustment) [12]. p
j
Second, work independence and clarity of job criteria were positively and significantly
related to work adjustment. This suggests that employees who know what is expected from
them and can complete their tasks without others adjust better to working remotely. Hence,
with regard to the structural factors underlying remote work, we were able to replicate
the findings presented by [9] in the context of virtual work and add that these factors
operate in similar ways across organizational settings during a global health pandemic
characterized by abrupt lockdowns and en masse remote work directives. Furthermore,
the findings align with [66], who find that telecommuters with higher autonomy report
greater job satisfaction relative to those with less autonomy. Our findings are in line with
previous literature linking performance management and goal-setting theory in co-located
work settings. It has been established that specific goals can enhance motivation and
performance by leading people to focus their attention on specific objectives [67], facilitate
their attempts to achieve these objectives [68], persist in the face of setbacks [69], and invent
new strategies to better deal with complex challenges related to goal attainment [70]. 5. Discussion The findings of this cross-sectional study during the early phase of the COVID-19
outbreak in 2020 in Finland indicate that structural factors (i.e., high work independence
and clarity of job criteria) make it easier for employees to adjust to remote work settings. In turn, relational factors (i.e., interpersonal trust and isolation) are negatively related to
adjustment. Contrary to our expectations and to the earlier findings by [9], interpersonal
trust was negatively associated with adjustment to remote work. Arguably, trust serves
as a proxy for important interpersonal functions, such as socialization and support; when
such cues are missing, employees may feel less satisfied and effective and may therefore
experience lower levels of adjustment to remote work. Our findings also show that feelings
of social isolation decrease adjustment to remote work, providing further evidence that Int. J. Environ. Res. Public Health 2021, 18, 6966 13 of 19 13 of 19 the social dynamics of work present a key barrier in adjustment during the COVID-19
pandemic. Furthermore, the results indicate that greater discrepancy between the amount
of current and “normal” remote work and greater disruption in work practices (i.e., contex-
tual factors) both decrease adjustment. These results imply that beyond smaller changes in
work location, greater experience with remote work seems to enhance adjustment to remote
work. Finally, the findings demonstrate a relatively small positive impact of organizational
communication quality and CTU in adapting to increased remote work. Organizational
communication quality does not mitigate the negative impacts of relational factors on
adjustment (i.e., interpersonal trust and feelings of isolation) or facilitate the relationship
between disruption of work practices and adjustment. However, more frequent use of
various communication technologies with colleagues seems to mitigate the negative re-
lationship between trust and adjustment, probably by reviving social relations. More
research is needed to study the potential buffering effects of communication technology
use and remote work adjustment. 5.1. Theoretical Implications More broadly, the finding that work independence and clarity of job criteria are
positively related to adjustment also signals a potentially important tension in remote work
designs. While some level of independence and clarity at the individual level is desirable
for job satisfaction, effectiveness, and performance in remote settings, modern work tasks
require some level of interdependency, and employees may desire feedback, socialization
and relatedness with peers. For example, in self-determination theory, relatedness is
considered a basic human need that consists of interacting with, being connected to,
and experiencing caring for others [31]. Recent studies on remote work [69] and global Int. J. Environ. Res. Public Health 2021, 18, 6966 14 of 19 14 of 19 work [54] demonstrate the importance of considering both the job characteristics (e.g.,
complexity and problem solving) and the social characteristics (e.g., social support and
interdependence) of work. Research [54,55] indicates that as workers are afforded more
autonomy and work becomes more unpredictable and volatile, employees need to adapt
to contend with the demands of their work environment, including relational demands. This means that employees are active agents crafting their own jobs rather than passive
recipients of work characteristics. This perspective aligns well with the findings of this
study, which refer to agentic processes—here, independence and clarity, which empower
employees to meet the demands of remote work and to adjust. p
y
j
Third, with regard to the relational factors, our findings do not support the hypothesis
of a positive relationship between interpersonal trust and adjustment to remote work. The
negative relationship between trust and remote work adjustment is a counterintuitive
finding that contradicts most of the past research on the relationship between trust and
remote work [9,71]. The findings indicate that higher levels of interpersonal trust decrease
individual’s adjustment to remote work. Alternatively, the reverse is also true as employees
who report low levels of trust seem to adjust better to remote work. This result can be
understood from an “out of sight out of mind” perspective, suggesting that some employees
may benefit from being separated from colleagues or supervisors they do not trust, or
even distrust. Indeed, in the context of this pandemic, scholars have chronicled that the
transition to remote work may have benefits for employees as they might be less exposed to
toxic workplace relationships, or relieved from bullying colleagues [5]. Our findings align
with such insights. 5.1. Theoretical Implications In addition, trust among colleagues and in supervisors could be an
indication of a valued interpersonal relationship. Having to miss such a relationship may
reduce one’s satisfaction with their job and make it more difficult to maintain productivity
levels or overall job performance—all indicators of adjustment. Hence, employees who
report high levels of trust in coworkers and supervisors and who feel trusted by them may
be less satisfied with remote work, feel less effective, and feel less adjusted. Employees
may even want to return to the office as soon as possible to reconnect with their colleagues
because the gratification of social needs is arguably satisfied through recurring physical
interactions with colleagues. Furthermore, trust built in the physical context may not have
transferred to the technology-mediated interactions of remote work environments yet, and
if the respondents see limited opportunities to do so, this could lead to a less gratifying
remote work experience. Finally, the notion that greater disruption requires greater adaptation certainly rings
true for most individuals. The findings suggest that employees who experience greater
disruption appear to face more difficulties adjusting to the work setting. Hence, it seems
that disruption may indeed require adaptation, but the negative relationship suggests that
employees have difficulty making the required adjustments, arguably because adaptation
in these cases requires employees to learn new skills and competencies to deal with
environmental demands. Hence, the findings demonstrate that employees’ adjustment to
abrupt remote work transitions is complicated by the perceived “strength” of the disruption. Overall, the findings suggest that factors underlying agentic processes (i.e., independence
and clarity of job criteria) facilitate adaptation and the reappraisal of event outcomes, while
relational factors—trust and isolation—operate as barriers to adjustment. This phenomenon
calls for further research into the managerial and sociopsychological processes that help to
understand the relationship between disruptive events and organizational outcomes. 5.2. Practical and Managerial Implication This study investigated the antecedents of adjustment to remote work. Some factors
are directly within the scope of organizational control (e.g., structural factors), while others
may be more difficult to influence directly (e.g., contextual factors). However, the results
provide important and actionable implications for organizations. First, our results indicate
that employees who report higher levels of independence and clarity of job instructions
are better able to adjust to remote work. In these circumstances, organizations could Int. J. Environ. Res. Public Health 2021, 18, 6966 15 of 19 15 of 19 provide clearer objectives and goals (decreasing ambiguity) and minimize interdependen-
cies between organizational members by designing and allocating autonomous jobs and
tasks where possible. In doing so, organizations facilitate agentic processes of individual
employees, improving their adjustment to these settings. In addition, organizations need
to ensure that there are adequate resources for employees to conduct work independently
while maintaining interdependencies at the collective level. For instance, our findings
show that CTU in particular, as well as organizational communication quality, may bolster
adjustment to remote work. j
Managing relational factors deserves slightly more thought because higher levels
of trust reduce adjustment, but isolation also reduces adjustment. Social isolation can
be reduced in various ways, such as through synchronous video meetings and informal
communication. For example, virtual coffee breaks may help employees feel connected
to their coworkers and may lead to less isolation in the workplace. In addition, these
initiatives might be important in the context of trust. We found a negative relationship
with adjustment; however, we argue that trust in this case signals the absence of important
interpersonal cues in the physical workplace. Hence, facilitating interpersonal mechanisms
of socialization and support might mitigate the negative impact of trust on adjustment. Furthermore, to facilitate greater adjustment in times where resources could be particularly
scarce and feelings of isolation particularly high, scholars have suggested that teleconsulta-
tions and informal online support groups could help people stay connected [72–74]. In addition, the findings demonstrate that greater change in work location and greater
perceived disruption hamper adjustment to remote work. This is important because it sig-
nals that organizations and managers should be attentive, especially to employees whose
work processes require the greatest adaptation. Our findings show that employees with
more experience in remote work adapt to new situations better because they have already
learned some practices and competencies needed in remote work. 5.2. Practical and Managerial Implication This implies the impor-
tance of training. Organizational support for work–home issues significantly improves
well-being [75] and may aid adjustment. For instance, organizations may support their
employees through lower workloads or other job demands, giving them greater opportuni-
ties to adjust. Additionally, for employees working on vital processes, organizations could
have different approaches based on the extent to which the work routines of individuals or
groups are disrupted. For instance, these workers could be given priority to use workplace
facilities. 5.3. Limitations and Future Research Several limitations need to be acknowledged. First, this study relies on cross-sectional
survey data obtained through a convenience sampling method. This method presents
two limitations. First, the data do not permit any causal inferences and do not permit us
to track how changes in, for instance, perceived disruptions and continued adjustment
to the work environment develop over time. Second, the sampling method resulted in a
relatively homogeneous group of employees, limiting the generalizability of the findings. The nonrandom sampling technique as well as the sample and population information
do not provide sufficient auxiliary information to correct survey responses using weight
adjustments. The sample consisted predominantly of Finnish civil servants (60%), many
of whom engaged in what could best be described as knowledge work. In addition,
we surveyed respondents who had the available means to participate in the study (e.g.,
stable Internet connection and time). Furthermore, the relatively stable work context of
these employees and the Finnish socioeconomic system may be fertile ground for the
adjustment of employees, which may not be the case in other types of occupations [5],
other socioeconomic systems, or countries that were (at least at the time of the study)
more strongly affected by the pandemic (e.g., France, Italy, and Spain) [6]. Future research
is needed to demonstrate the generalizability of our findings across a broader range of
occupations, countries, and socioeconomic systems. Int. J. Environ. Res. Public Health 2021, 18, 6966 16 of 19 Second, some of the effect sizes are relatively small, which raises questions about the
predictive validity of the model. To substantiate these findings, future research is needed to
confirm these results over time with various occupational groups in different socioeconomic
systems. In addition, although the measures were adopted from previous studies, not all
measures have been validated and we do not have pre-pandemic benchmark indices for
our population, limiting our ability to draw a conclusion about the relative changes. In
addition, responses were collected within the first month of the outbreak. Although this
timeframe is considered appropriate to investigate adjustment processes, these processes
are also likely to continue as the pandemic evolved. In addition, people now have had more
time to adjust and find ways to meet challenges and demands associated with teleworking. Hence, it would be worthwhile to follow up on this study as the relative newness of the
pandemic and associated teleworking has decreased. 5.3. Limitations and Future Research Finally, our findings suggest that
employees seem to adjust well to remote work. This aligns with studies that conclude that
the general attitude toward working from home seems positive [76]. However, this study
was conducted in the early stages of the pandemic; therefore, limited assumptions can
be made about the long-term implications. In addition, future research may probe more
deeply into different aspects that are central to adjustment to remote work, such as those
related to work–life dynamics. For instance, now is the opportune time to study whether
childless and single employees face increased expectations and work responsibilities, and
how these demands may interfere with non-work demands [3]. 6. Conclusions The findings presented in this study provide important insights into the factors that
are consequential to employees’ adjustment to remote work. These findings contribute to
our understanding of how the COVID-19 pandemic has impacted work. This is impor-
tant because the current crisis is far from over [74,77], future pandemics are increasingly
likely [74], and other disruptive events, such as economic downturn, natural disasters,
activism, and war, may require continuous adjustment from employees and organizations. Our findings contribute to an understanding of how employees adjust to (abrupt) changes
in their work environment by identifying and demonstrating the interplay between various
environmental and contextual factors. Author Contributions: Conceptualization, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; methodology,
W.v.Z.; software, W.v.Z.; validation W.v.Z.; formal analysis, W.v.Z.; investigation, W.v.Z.; resources,
A.S. and K.B.; data curation, W.v.Z.; writing—original draft preparation, W.v.Z.; writing—review and
editing, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; supervision, K.B.; project administration, A.S. and K.B. All authors have read and agreed to the published version of the manuscript. Author Contributions: Conceptualization, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; methodology,
W.v.Z.; software, W.v.Z.; validation W.v.Z.; formal analysis, W.v.Z.; investigation, W.v.Z.; resources,
A.S. and K.B.; data curation, W.v.Z.; writing—original draft preparation, W.v.Z.; writing—review and
editing, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; supervision, K.B.; project administration, A.S. and K.B. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Funding: This research received no external funding. Institutional Review Board Statement: Ethical review and approval were waived for this study,
as the study did not involve any of the following: underage subjects, exposure to strong stimuli,
potential for long-term mental distress, or intervention with the physical integrity of the participants. Informed Consent Statement: Informed consent was obtained from all participants involved prior
to the study. Data Availability Statement: The data presented in this study are not publicly available. Survey
respondents were assured raw data would remain confidential and would not be shared. Data Availability Statement: The data presented in this study are not publicly available. Survey
respondents were assured raw data would remain confidential and would not be shared. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. )
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https://openalex.org/W2783520694 | https://www.cambridge.org/core/services/aop-cambridge-core/content/view/949402C56ECEC4CBCBC2A519BEE8BD76/S0955603600085822a.pdf/div-class-title-black-marks-for-black-daisies-div.pdf | English | null | Black marks for Black Daisies | Psychiatric bulletin of the Royal College of Psychiatrists/Psychiatric bulletin | 1,993 | cc-by | 1,377 | Psychiatry and the media
Black marks for Black Daisies Brice Pitt reviews
'Black Daisies for the Bride' by Tony Harrison;
directed by Peter Symes; Screenplay, BBC2 Brice Pitt reviews
'Black Daisies for the Bride' by Tony Harrison;
directed by Peter Symes; Screenplay, BBC2 ::•'
Scene from 'Black Daisies for the Bride'
(Copyright BBC) I've had difficulty in writing this review. I initially
caught the last half of Tony Harrison's 'docudrama'
about Alzheimer's disease shown at the outset of
Alzheimer Awareness Week in July and hated it. My
heart sank at the Brechtian device of putting the
dialogue to the tune of a hymn (in this case the carol
'In the Bleak Midwinter'), and I found the approach
to the three 'star' patients chosen for the film from
those in Whernside ward. High Royds Hospital,
sentimental and patronising. Scene from 'Black Daisies for the Bride'
(Copyright BBC) p
g
Yet Harrison isa highly respected poet and drama
tist. His translation
of Le Misanthrope delighted
National
Theatre audiences in 1973, his Phaedra
Britannica in 1975 was a notable achievement, and
his translation
of The Oresteia, directed by Peter
Hall, in 1981was one of the NT's greatest triumphs. A more recent poem is The Mother of the Muses
(who is, of course, Memory) in 1987, the product of
his involvement in his father-in-law's
Alzheimer's
disease. This, then, is a return to a subject which
clearly concerns him deeply. Neurological disorders
are increasingly fascinating to other than doctors-
hence the adaptation to the cinema of'Awakenings',
to opera of 'The Man who Mistook his wife for
his Hat' and the impressive film about finding a
treatment
for
adrenoleucodystrophy,
'Lorenzo's
Oil'. N
th t I'
f
d
lf t
t h th
h l agreed to do so and were paid. What about the
patients? Do they now hold Equity cards? Was Leeds
Community and Mental Health Services Teaching
NHS
Trust
happy
to give its consent
to their
exposure? I f
d th
'd
'
t
f th pI found the 'docu' part of the programme more
successful than the drama. Whernside isan authentic
dementia ward and one wouldn't
doubt that the
patients
need
to
be there. The
screams,
yells
and squawks, the tussle between two old ladies,
Kathleen's
relentless perambulations,
the slurped
yoghurt now on the floor are utterly real; only the shit
is missing. "Thinking what they all have been
Makes Alzheimer's horrible and obscene". Well, yes. But is that all? Is it enough to be made
aware of just how dreadful an affliction it is? https://doi.org/10.1192/pb.17.11.672 Published online by Cambridge University Press Psychiatrie Bulletin (1993), 17,672-673 Psychiatrie Bulletin (1993), 17,672-673 (or My Girlfriend
is a Rover Metro) RICHARDC. BARNES,Registrar in Psychiatry, Rathbone Hospital, Mill Lane, Liverpool
L13 4AW; and STEPHENEARNSHAW,Registrar in Psychiatry, Winwick Hospital,
WarringtonWA28RR The main source of topical information
in most parts
of the world is through
the mass media - principally
newspapers
and
television. Television
news
and
current
affairs have a duty to remain
impartial,
as
they
provide
a service
for the whole
population. Newspapers,
on
the
other
hand,
have
a greater
journalistic
and
editorial
freedom
as they
target
subgroups. British
newspapers
are currently
being
scrutinised
as to how they report
both factual
and
speculative
information
of a general
kind. At the
same
time
there
seems to be an increase
in their
interest in psychological
matters. However,
work on
newspaper
reporting
of psychiatric
disorders
(Day &
Page,
1986; Matas
et al, 1986) has shown
that the
mentally ill are usually portrayed
in a rather negative
light with few positive images. about
mental
illness, and these totalled
7 (13%)
in
The Mirror and 15 (33%) in The Independent. Of the
broadsheet
articles,
13 were written
by journalists
and two by medically trained writers. They covered a
wide range of illnesses, and six of the articles reported
directly
on published
work
in psychiatric
journals
as part of a regular
review of medical
literature. In
contrast
to this, the tabloid
newspaper,
with only
seven articles,
had no reports
on scientific research,
and
over
half of the articles
were written
by the
newspaper's
resident medical journalist,
a practising
general practitioner. g
p
Reports
of
individual
cases
of
mental
illness
formed
the second
group,
and
yielded
39 (71%)
tabloid
and 20 (43%) broadsheet
items. Despite
the
large numbers
of cases reported
on, only seven were
reported
in both newspapers. This meant a total of 52
cases, 31 of which related to criminal acts or suicide. The study The tabloid
newspaper
contained
a much greater
proportion
of reports
of suicides,
12 (31%)
com
pared with two (10%), and these typically in unusual
or otherwise
noteworthy
circumstances
('Love-rift
tycoon's
suicide
horror',
'Santa's
suicide
plunge',
'Suicide of pilot who nearly hit a hotel'). In total, nine
cases
of people
with
identifiable
psychotic
illness
were reported,
and
in all these cases
the circum
stances involved
violent crime or murder. Of those
cases concerning
non-psychotic
illness,
all the re
ports (11 in total)
linked the illness to unusual
and
generally
humorous
presentations
('Bizarre
bagpipe
phobia
baffles doctors',
'Student
stuns shrinks,
"My
girlfriend
is a
Rover
Metro"
',
'Little
boy
eats
nothing
but Spam'). Nine further articles mentioned
doctors
working
in the psychiatric
field, all but two We have recently
examined
two different
formats
of newspaper;
'broadsheet'
(The Independent)
and
'tabloid'
(The Mirror),
collecting
all reports
related
to mental illness over the three months
from October
to December
1992. The Mirror
has average
daily
sales of around
3.5 million, while The Independent's,
circulation
averages around
368.000. Black marks for Black Daisies doll". Cringe-making? Possibly-until
Maria
gives
him her wonderful
'A' and Kathleen
first sways and
then claps to the rhythm! Music,
for the moment,
makes a link between these lost souls and the world
they have almost left. In a thoughtful
epilogue
on The
Late
Show',
Michael
Ignatieff,
who has a grim family history of
the disease,
accuses
the poet of offering
too much
hope! He is referring to the one sequence which I shall
treasure. Enter guitarist
Richard
Muttonchops(i/f),
who serenades
the ladies with "Oh,
you beautiful Psychiatry and the media
Black marks for Black Daisies On the other hand the arty direction-
shots in a convex mirror, confetti, petals, leaves
and snowflakes in the blizzard which symbolises
Alzheimer's,
veils and bridal gloves discarded
in
woodland - sometimes borders on kitsch. The link
ing of the ward's coded entrance to the patients' loss
of an access code to their memories, and the remark
that Death has the only exit code from Whernside, is
somewhat pretentious. But I liked the echoing howl
which turns out to be the electric trolley making its
way through the corridors of the old mental hospital. Now that I ve forced myself to watch the whole
film I see that it is better than my first impression, but
qualms remain. The 'black daisies' are the motif of a
mosaic floor at High Royds. and Harrison links this
to the song 'Daisy, Daisy' and shows the younger
selves of his protagonists as brides. The still beautiful Maria, an opera singer, who can
now sing only one note, a thrilling 'A', is seen as
Lucia di Lammermoor. Kathleen, 'angler, climber,
gardener, cook, accordionist and pianist', who now
just cleans and cleans, is shown as a bride singing of
motorbike mountaineering
with her fiance Harold. One or other of two Muriels - one was a 'therapist',
the other says little more than 'I love you' - is also a
bride. Another person of few words is Matthew, who
just says 'Go away'. Actresses play the younger trio
(and a rather challenging therapist) and presumably What is Harrison trying to say? In one of his (fairly
excruciating) couplets his angry therapist remarks: "Thinking what they all have been
Makes Alzheimer's horrible and obscene". Well, yes. But is that all? Is it enough to be made
aware of just how dreadful an affliction it is? 672 https://doi.org/10.1192/pb.17.11.672 Published online by Cambridge University Press 2 Published online by Cambridge University Press 673 Black marks for Black Daisies Findings
Th The
survey
yielded
a total
of 55 reports
in "The
Mirror'
and
46 in 'The
Independent',
and
these
reports
were divided
up into four groups. The first
group
included
those
reports
giving
information 2 Published online by Cambridge University Press |
W4392168650.txt | https://essd.copernicus.org/preprints/essd-2023-331/essd-2023-331.pdf | en | Reply on RC3 | null | 2,024 | cc-by | 38,155 | ERROR: type should be string, got "https://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nThe Total Carbon Column Observing Network’s GGG2020 Data\nVersion\nJoshua L. Laughner1 , Geoffrey C. Toon1 , Joseph Mendonca2 , Christof Petri3 , Sébastien Roche4,5 ,\nDebra Wunch6 , Jean-Francois Blavier1 , David W.T. Griffith7 , Pauli Heikkinen8 , Ralph F. Keeling9 ,\nMatthäus Kiel1 , Rigel Kivi8 , Coleen M. Roehl10 , Britton B. Stephens11 , Bianca C. Baier13 ,\nHuilin Chen14 , Yonghoon Choi15,16 , Nicholas M. Deutscher7 , Joshua P. DiGangi15 , Jochen Gross17 ,\nBenedikt Herkommer17 , Pascal Jeseck18 , Thomas Laemmel19,* , Xin Lan12,13 , Erin McGee6 ,\nKathryn McKain13 , John Miller13 , Isamu Morino20 , Justus Notholt3 , Hirofumi Ohyama20 , David\nF. Pollard21 , Markus Rettinger22 , Haris Riris23 , Constantina Rousogenous24 , Mahesh Kumar Sha25 ,\nKei Shiomi26 , Kimberly Strong6 , Ralf Sussmann22 , Yao Té18 , Voltaire A. Velazco7,27 , Steven C. Wofsy4 ,\nMinqiang Zhou25,** , and Paul O. Wennberg10,28\n1\n\nJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA\nClimate Research Division, Environment and Climate Change Canada, Toronto, ON, Canada\n3\nInstitute of Environmental Physics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany\n4\nJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA\n5\nCenter for Astrophysics, Harvard & Smithsonian, Cambridge, MA, USA\n6\nDepartment of Physics, University of Toronto, Toronto, Canada\n7\nCentre for Atmospheric Chemistry, School of Earth, Atmospheric and Life Sciences, University of Wollongong,\nWollongong, New South Wales, Australia\n8\nSpace and Earth Observation Centre, Finnish Meteorological Institute, Sodankylä, Finland\n9\nScripps Institute of Oceanography, La Jolla, California, USA\n10\nDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA\n11\nEarth Observing Laboratory, National Center for Atmospheric Research (NCAR), Boulder, CO, USA\n12\nCooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, USA\n13\nNOAA Global Monitoring Laboratory, Boulder, USA\n14\nCenter for Isotope Research, University of Groningen, Groningen, the Netherlands\n15\nNASA Langley Research Center, Hampton, VA 23681\n16\nAnalytical Mechanics Associated, Hampton, VA 23666\n17\nKarlsruhe Institute of Technology (KIT), Institute of Meteorology and Climate Research (IMK-ASF), Karlsruhe, Germany\n18\nLaboratoire d’Études du Rayonnement et de la Matière en Astrophysique et Atmosphères (LERMA-IPSL), Sorbonne\nUniversité, CNRS, Observatoire de Paris, PSL Université, 75005 Paris, France\n19\nUniversité Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l’Environnement (LSCE/IPSL),\nGif-sur-Yvette, France\n20\nNational Institute for Environmental Studies (NIES), Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan\n21\nNational Institute of Water and Atmospheric Research Ltd (NIWA), Lauder, New Zealand\n22\nKarlsruhe Institute of Technology (KIT), IMK-IFU, Garmisch-Partenkirchen, Germany\n23\nNASA Earth Science Technology Office (ESTO), B22, 242, 8800 Greenbelt Rd., Greenbelt, MD. 20771\n24\nClimate and Atmosphere Research Centre (CARE-C), The Cyprus Institute, Nicosia, Cyprus\n25\nRoyal Belgian Institute for Space Aeronomy, Brussels, Belgium\n26\nEarth Observation Research Center (EORC), Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan\n27\nDeutscher Wetterdienst, Meteorological Observatory Hohenpeissenberg, 82383 Hohenpeissenberg, Germany\n28\nDivision of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA\n2\n\n1\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n*\n\nNow at: University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences and Oeschger Center for\nClimate Change Research, Bern, Switzerland\n**\nNow at: Institute of Atmospheric Physics, Chinese Academy of Sciences, China\nCorrespondence: Joshua Laughner (josh.laughner@jpl.nasa.gov)\nAbstract. The Total Carbon Column Observing Network (TCCON) measures column-average mole fractions of several greenhouse gases (GHGs) beginning in 2004 from over 30 current or past measurement sites around the world, using solar absorption\nspectroscopy in the near infrared region. TCCON GHG data have been used extensively for multiple purposes, including in\nstudies of the carbon cycle and anthropogenic emissions as well as to validate and improve observations made from space5\n\nbased sensors. Here, we describe an update to the retrieval algorithm used to process the TCCON near IR solar spectra and\nthe associated data product. This version, called GGG2020, was initially released in April 2022. It includes updates and improvements to all steps of the retrieval, including but not limited to: converting the original interferograms into spectra, the\nspectroscopic information used in the column retrieval, post hoc airmass dependence correction, and scaling to align with the\ncalibration scales of in situ GHG measurements.\nAll TCCON data are available through tccondata.org and hosted on CaltechDATA (data.caltech.edu). Each TCCON site has\n\n10\n\na unique DOI for its data record. An archive of all sites’ data is also available with the DOI 10.14291/TCCON.GGG2020\n(Total Carbon Column Observing Network (TCCON) Team, 2022). The hosted files are updated approximately monthly, and\nTCCON sites are required to deliver data to the archive no later than one year after acquisition. Full details of data locations\nare provided in the data availability section.\n\n15\n\n1\n\nIntroduction\n\nThe Total Carbon Column Observing Network (TCCON) is a network of nearly 30 ground-based, solar-viewing, Fourier\ntransform infrared (FTIR) spectrometers that report observations of column average mole fractions of CO2 , CH4 , N2 O, CO,\nHF, H2 O, and HDO in the atmosphere. The first two TCCON stations were established in 2004, with additional stations\njoining over the following years. As of July 2023, 30 sites exist. In that time, TCCON data have been used to estimate or\n20\n\nevaluate carbon fluxes (e.g. Keppel-Aleks et al., 2012; Peiro et al., 2022), for satellite validation (e.g. Wunch et al., 2017; Chen\net al., 2022; Lorente et al., 2022), for model verification (e.g. Byrne et al., 2023), and for other purposes.\nTCCON instruments measure solar spectra in the near-infrared (NIR) wavelengths; these spectra are converted into the final\ncolumn average mole fractions (henceforth denoted as “Xgas ”, e.g. “XCO2 ”) using the retrieval software GGG.1 Major versions\nof GGG are identified by the year of development. The previous version used to generate public TCCON data was GGG2014\n\n25\n\nand is described in Wunch et al. (2015). GGG2020 is the first major update applied to TCCON public data since GGG2014.\nGGG retrieves trace gas column amounts by iteratively scaling an a priori vertical trace gas profile until the best fit between\na spectrum simulated from those trace gas profiles by the built-in forward model and the observed spectrum is found. A single\ngas may be fit in more than one spectral window; for example, GGG2020 retrieves the standard TCCON CO2 product from\n1 GGG\n\nis the proper name of the software, and is not an acronym.\n\n2\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\ntwo separate windows (6220 to 6260 cm−1 and 6297 to 6382 cm−1 ). Each window is run separately and produces its own\n30\n\nposterior scaled trace gas profile, which can be integrated to generate a column density. Retrieving each window separately,\nrather than concatenating the spectral information, makes it simpler to handle non-contiguous windows that need different state\nvector elements. It also allows biases that differ between these windows to be expressed separately in the resulting output data\nand, if necessary, corrected separately. The output values (column densities and profile scaling factors) from different windows\nwith similar averaging kernels for the same target gas are combined in a weighted average during post processing.\n\n35\n\nThe post processing step includes the above window-to-window averaging alongside an empirical airmass-dependent correction, a scaling correction to tie TCCON data to the relevant calibration scales, and the conversion from column densities\nto column-average mole fractions. Airmass-dependent errors can arise from, for example, errors in the relative intensities of\nstrong and weak absorption lines for a target gas. At large solar zenith angles (SZAs), the longer light paths through the atmosphere will cause strong absorption lines to completely absorb incoming light within their core wavelengths; such lines may be\n\n40\n\nreferred to as “blacked out”. Blacked out lines cannot contribute information to the retrieval, so the retrieval must get a greater\nfraction of its information from weaker lines in the spectral window or the wings of saturated lines. If there is a different bias\nin the forward model between the strong and weak lines, it will manifest as an error in the retrieved column amounts that varies\nwith SZA and is symmetric about solar noon. Once the magnitude of this error is derived (§7.1), a post-processing correction\ncan be applied to remove it.\n\n45\n\nThe scaling factor used to tie to calibration scales is necessary because the spectroscopic parameters needed by the forward\nmodel are not in general known to the ∼ 0.25% or better accuracy needed for greenhouse gas data. However, since all TCCON\n\nsites use the same retrieval (and thus the same forward model), we use a single mean scaling factor to remove the mean bias\ncaused by errors in the spectroscopic parameters. This does implicitly assume that imperfect instrument line shape (ILS) or\n\nimperfect representation of the instrument in the forward model are either (a) consistent across sites and thus accounted for by\n50\n\nthe scaling factor or (b) random and average to zero. The scaling factors for the various gases are derived from comparisons\nbetween TCCON data and in situ vertical profiles measured by aircraft- or balloon- borne instruments (§7.3).\nFinally, the conversion from column densities to column-average dry mole fractions is done by dividing the target gas column\n(Vgas ) by the O2 column (VO2 ), then multiplying by the mean O2 mole fraction (fO2 ) in the atmosphere:\nXgas =\n\n55\n\nVgas\n· fO2\nVO2\n\n(1)\n\nGGG2020 assumes that fO2 = 0.2095 for all retrievals except those listed in §7.3.2. The advantages of normalizing to the O2\ncolumn are:\n1. It normalizes for path length. Observations at surface elevations will have smaller column densities compared to those\nfrom lower altitudes, due to the shorter vertical extent. Normalizing to the O2 column removes this effect.\n2. Because O2 and the primary TCCON gases are measured on the same detector, many biases related to the detector and\n\n60\n\npointing will be cancelled out (Wunch et al., 2011, Appendices A and B).\n\n3\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nGGG is comprised of several sub-programs, which handle these various elements of the retrieval. Each of these has been\nupgraded for GGG2020:\n– i2s: converts interferograms to spectra. Updates include identifying detector nonlinearity and better phase correction\n(§5).\n– gsetup: prepares the input files needed to run gfit (a priori meteorology and trace gas profiles, atmospheric path infor-\n\n65\n\nmation, etc.) in the required formats. Updates include the source of a priori meteorology and trace gas profiles and the\nretrieval grid (§4).\n– gfit: retrieves column densities from the spectra output by i2s. Updates include the forward model spectroscopy (§3) and\ncontinuum fitting (§6).\n– Post processing: a suite of programs that collates the output from gfit and applies any required post hoc corrections.\n\n70\n\nUpdates include the airmass correction (§7.1), window to window averaging (§7.2), and scaling to tie to in situ calibration\nscales (§7.3).\nGGG2020 data is available through tccondata.org. A repository containing the full set of publicly available data is available\nthrough CaltechDATA (Total Carbon Column Observing Network (TCCON) Team, 2022). Each TCCON site’s data record\n75\n\nhas its own unique DOI. On occasions that a site needs to reprocess and redeliver data already released to the public, the\nrevised dataset will receive a new DOI with the revision number incremented. TCCON sites are permitted to withhold data\nfrom the public archive for up to one year from acquisition. This public archive is updated approximately once per month\nwith newly delivered or released data. The TCCON data product is documented extensively through the TCCON Wiki (https:\n//tccon-wiki.caltech.edu/). Users are asked to familiarize themselves with the data use policy and license, which are available\n\n80\n\nat https://tccon-wiki.caltech.edu/Main/DataUsePolicy.\n2\n\nNew Xgas products\n\nGGG2020 introduced XCO2 mole fractions retrieved in two new windows: a strong band between 4809.74 and 4896.0 cm−1\nand a weak band between 6041.8 and 6105.2 cm−1 . We refer to these as “lCO2 ” and “wCO2 ”, respectively. These are reported\nas separate CO2 products (XlCO2 and XwCO2 ) and are not averaged together with the standard TCCON XCO2 product. Figure\n85\n\n1 shows the column averaging kernels (AKs) and CO2 absorption lines in these two windows. The lCO2 AKs increase towards\nthe surface, while, at small slant Xgas amounts (i.e. small solar zenith angle) the wCO2 AKs are greater in the stratosphere\nthan in the lower troposphere. This is because, as seen in Fig. 1b and d the CO2 absorption lines in the lCO2 band are mostly\nsaturated at the line center, while the wCO2 lines are not. In theory, when used together with the standard TCCON XCO2\nproduct (which has an AK profile that is more constant with altitude than the wCO2 or lCO2 products, see Fig. 25), this\n\n90\n\nprovides the potential to separate changes in CO2 at the surface, from those in the free troposphere or stratosphere (Parker\net al., 2023).\n4\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable 1. List of TCCON sites and their associated data citations as of 20 Dec 2022. Some sites (Lauder, JPL) have had different FTIR\ninstruments operating over different periods, and so are listed multiple times.\nSite ID\n\nSite Name\n\nLocation\n\nData Citation\n\nae\n\nascension01\n\nAscension Island, Saint Helena\n\nFeist et al. (2017)\n\nan\n\nanmeyondo01\n\nAnmyeondo, South Korea\n\nGoo et al. (2017)\n\nbi\n\nbialystok01\n\nBialystok, Poland\n\nPetri et al. (2017)\n\nbr\n\nbremen01\n\nBremen, Germany\n\nNotholt et al. (2022)\n\nbu\n\nburgos01\n\nBurgos, Philippines\n\nMorino et al. (2022c)\n\nci\n\npasadena01\n\nPasadena, California, USA\n\nWennberg et al. (2022c)\n\ndb\n\ndarwin01\n\nDarwin, Australia\n\nDeutscher et al. (2023a)\n\ndf\n\nedwards01\n\nAFRC, Edwards, CA, USA\n\nIraci et al. (2022b)\n\net\n\neasttroutlake01\n\nEast Trout Lake, Canada\n\nWunch et al. (2022)\n\neu\n\neureka01\n\nEureka, Canada\n\nStrong et al. (2022)\n\nfc\n\nfourcorners01\n\nFour Corners, NM, USA\n\nDubey et al. (2022b)\n\ngm\n\ngarmisch01\n\nGarmisch, Germany\n\nSussmann and Rettinger (2017a)\n\nhf\n\nhefei01\n\nHefei, China\n\nLiu et al. (2022)\n\nhw\n\nharwell01\n\nHarwell, UK\n\nWeidmann et al. (2023)\n\nif\n\nindianapolis01\n\nIndianapolis, Indiana, USA\n\nIraci et al. (2022a)\n\niz\n\nizana01\n\nIzana, Tenerife, Spain\n\nBlumenstock et al. (2017)\n\njc\n\njpl01\n\nJPL, Pasadena, California, USA\n\nWennberg et al. (2022e)\n\njf\n\njpl02\n\nJPL, Pasadena, California, USA\n\nWennberg et al. (2022a)\n\njs\n\nsaga01\n\nSaga, Japan\n\nShiomi et al. (2022)\n\nka\n\nkarlsruhe01\n\nKarlsruhe, Germany\n\nHase et al. (2022)\n\nlh\n\nlauder01\n\nLauder, New Zealand\n\nSherlock et al. (2022a)\n\nll\n\nlauder02\n\nLauder, New Zealand\n\nSherlock et al. (2022b)\n\nlr\n\nlauder03\n\nLauder, New Zealand\n\nPollard et al. (2022)\n\nma\n\nmanaus01\n\nManaus, Brazil\n\nDubey et al. (2022a)\n\nni\n\nnicosia01\n\nNicosia, Cyprus\n\nPetri et al. (2023)\n\nny\n\nnyalesund01\n\nNy-Ålesund, Svalbard, Norway\n\nBuschmann et al. (2022)\n\noc\n\nlamont01\n\nLamont, Oklahoma, USA\n\nWennberg et al. (2022d)\n\nor\n\norleans01\n\nOrleans, France\n\nWarneke et al. (2022)\n\npa\n\nparkfalls01\n\nPark Falls, Wisconsin, USA\n\nWennberg et al. (2022b)\n\npr\n\nparis01\n\nSorbonne Université, Paris, FR\n\nTe et al. (2022)\n\nra\n\nreunion01\n\nReunion Island, France\n\nMaziere et al. (2022)\n\nrj\n\nrikubetsu01\n\nRikubetsu, Hokkaido, Japan\n\nMorino et al. (2022a)\n\nso\n\nsodankyla01\n\nSodankylä, Finland\n\nKivi et al. (2022)\n\ntk\n\ntsukuba02\n\nTsukuba, Ibaraki, Japan, 125HR\n\nMorino et al. (2022b)\n\nwg\n\nwollongong01\n\nWollongong, Australia\n\nDeutscher et al. (2023b)\n\nxh\n\nxianghe01\n\nXianghe, China\n\nZhou et al. (2022)\n\nzs\n\nzugspitze01\n\nZugspitze, Germany\n\nSussmann and Rettinger (2017b)\n\nBeginning with GGG2020, experimental mid-IR data products will be available from select TCCON sites equipped with an\nInSb (indium antimonide) detector that enables measurements in the 1800 to 4000 cm−1 frequency range. Gases measured in\nthis range include, but are not limited to, O3 , N2 O, CO, CH4 , NO, NO2 , carbonyl sulfide, formaldehyde, and ethane. These\n95\n\nproducts offer the potential to extend the applications of TCCON data to new areas of research. However, it is important to\n\n5\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n104\n\n0\n\n(b)\n\nSlant XlCO2\n\nPressure (hPa)\n\n200\n400\n\n103\n\n600\n800\n\n(c)\n\n0\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXlCO2 column AK (unitless)\n\n104\n\nSlant XwCO2\n\nPressure (hPa)\n\n200\n400\n\n103\n\n600\n800\n1000\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25\nXwCO2 column AK (unitless)\n\n0.8\n0.6\n0.4\n0.2\n0.0\n\n102\n\n(d)\nIntensity (arbitrary units)\n\n1000\n\n1.0\n\nIntensity (arbitrary units)\n\n(a)\n\n102\n\n4820\n\n1.00\n\n4840\n4860\nFrequency (cm 1)\n\n4880\n\n4900\n\n0.95\n0.90\n0.85\n0.80\n6040\n\n6050\n\n6060\n\n6070 6080\nFrequency (cm 1)\n\n6090\n\n6100\n\nFigure 1. Column averaging kernels (panels a, c) and calculated CO2 absorption lines (panels b, d) in the lCO2 (panels a, b) and wCO2\n(panels c, d) windows, respectively. The absorption lines in panels (b) and (d) are for a TCCON spectrum measured at solar zenith angle =\n39.684◦ in Jul 2004 at Park Falls, WI, USA. In panels (a) and (c), the different colors indicate AKs for different slant Xgas amounts. “Slant\nXgas ” is a measure of total absorber column along the light path. See §9.1 for details.\n\nnote that these data do not have any postprocessing corrections for airmass dependence (§7.1) or scaling to in situ data (§7.3)\napplied.\n3\n\nUpdated spectroscopy\n\n3.1\n100\n\nTelluric & Solar line lists\n\nThe telluric linelist (atm.161, Toon, 2022c) is a \"greatest hits\" compilation based heavily on HITRAN predecessor lists, but\nwith ad hoc empirical corrections performed to some lines, bands, and gases. The linelist is updated when improved linelists\nbecome available, as determined by 1) improved fits to laboratory and atmospheric spectra, 2) better consistency of retrieved\ngas amounts from different windows and bands, and 3) reduced airmass-dependence of the retrieved gas amounts. Since the\nGGG2016 version of the linelist, there have been many improvements to the H2 O and HDO spectroscopy throughout the main\n\n105\n\nTCCON region (4000 to 8000 cm−1 ).\nThe solar linelist (Toon, 2022b) is completely empirical, based on high-resolution solar spectra measured by various instruments from the ground, balloon, and space. In the 4000 to 8000 cm−1 spectral region covered by TCCON, the linelist is based\nprimarily on ground-based Kitt Peak and TCCON spectra, with additional balloon-borne MKIV spectra from 40 km altitude\nup to 5600 cm−1 . To deduce which absorption features are solar, rather than telluric, we fit out the telluric spectrum as best we\n\n110\n\ncan. Remaining dips in the residuals are solar, unless they grow with airmass, in which case they are missing tellurics. Since\nGGG2016 the improvements have been modest, adding new weak lines (< 0.1% depth) in the TCCON windows.\n\n6\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n3.2\n\nNon-Voigt lineshapes for O2 , CO2 , and CH4\n\nAbsorption coefficients calculations were improved in GGG2020. In previous versions of GGG absorption coefficients were\ncalculated using a Voigt spectral line shape. Numerous spectroscopic studies have shown that the Voigt line shape is insufficient\n115\n\nfor use with CO2 and other molecules, so a more sophisticated line shape is required to achieve the necessary retrieval accuracy.\nSo quadratic speed-dependent Voigt (qSDV) with line mixing (LM) code from Tran et al. (2013) was implemented into forward\nmodel of GGG (Toon, 2022a).\nIt was shown in Mendonca et al. (2016) that using the qSDV with first order LM and adopting the spectroscopic parameters\nfrom Devi et al. (2007b) for the CO2 lines in CO2 window centered at 6220 cm−1 and Devi et al. (2007a) for the window cen-\n\n120\n\ntered at 6339 cm−1 resulted in an up to 40% improvement to both spectral fit RMS and a reduction in the airmass dependence\nof the retrieved XCO2 . For the strong CO2 band lines, in the window centered at 4850 cm−1 , the spectroscopic parameters\nfrom Benner et al. (2016) are used with the qSDV and first order LM to calculate absorption coefficients. This resulted in\nimproving the quality of XCO2 retrievals from this spectral region. New spectroscopic studies aimed at improving CO2 absorption coefficient calculations are ongoing. Recent studies like Hashemi et al. (2020) that provide spectroscopic parameters\n\n125\n\nfor CO2 can be tested with TCCON spectra to see if the retrievals can be improved.\nTCCON CH4 is retrieved from three windows that are composed of the P, Q, and R branches of the 2ν3 CH4 band. To\nimprove the forward model of GGG the spectroscopic parameters from Devi et al. (2015, 2016) are used to calculate the\nabsorption coefficients with the qSDV with full line mixing. Unlike CO2 that uses first order line mixing requiring one extra\nparameter to be added to the linelist per spectral line, CH4 requires full line mixing. This requires spectroscopic parameters\n\n130\n\nfrom all coupled lines (i.e. a relaxation matrix) be used to calculate the effective spectral line parameters for each spectral line.\nIn previous versions of GGG absorption coefficients could only be calculated by reading in spectroscopic parameters line by\nline making it awkward to take into account full line mixing. GGG2020 has been updated to read in spectroscopic parameters\nand the relaxation matrix (supplied with Devi et al. (2015, 2016)) at the same time for spectral lines that require full line mixing.\nMore details on how this is done are provided in Mendonca et al. (2017). The improved absorption coefficient calculations for\n\n135\n\nCH4 lines for the 2ν3 CH4 band has improved the quality of the spectral fits and airmass dependence of the retrieved XCH4 .\nThe addition of full line mixing can be extended to other molecules to improve retrievals.\nTo improve the retrievals of O2 columns, which are required to calculate Xgas , spectroscopic parameters for the O2 singlet\ndelta band were retrieved by fitting cavity ring down spectra as detailed in Mendonca et al. (2019). The spectroscopic parameters derived from the cavity ring down spectra were tested on TCCON spectra where they were shown to slightly improve the\n\n140\n\nquality of the spectral fit as well as greatly decrease the airmass dependence of the retrieved O2 column. The study by Mendonca et al. (2019) is the first to show the need for a spectral line shape that takes into account speed-dependence. Since then,\nnewer spectroscopic studies such as Tran et al. (2020) and Fleurbaey et al. (2021) have shown the need to take into account\nDicke narrowing and line mixing in order to fit new cavity ring down spectra in the O2 singlet delta band. The spectroscopic\nparameters of Mendonca et al. (2019), Tran et al. (2020), and Fleurbaey et al. (2021) were used to fit TCCON O2 spectra in\n\n7\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n145\n\nTran et al. (2021). The study showed that the newer spectroscopic parameters slightly improved the quality of the spectral fit\nbut they should also be assessed on how they impact the airmass dependence of retrieved O2 columns.\n3.3\n\nEmpirical optimization of O2 line widths\n\nDuring pre-release testing, we found that a diagnostic quantity we call Xluft had a noticeable temperature dependence (Fig.\n2a). Xluft is a ratio of two ways of calculating the column of dry air (one from surface pressure and the a priori H2 O profile,\n150\n\nand one from the column of O2 retrieved in the singlet delta band—or put another way, it is the column-average mole fraction\nof dry air), and thus should not have a temperature dependence. Since dry mole fractions of O2 in the atmosphere are highly\nconstant over space and time, this implied that either temperature-dependence or the water broadening of the O2 line widths in\nthe forward model was incorrect, as the concentration of water in the atmosphere is generally correlated with temperature.\nTo disentangle the effect of temperature and water, we first examined data from the Darwin, Australia TCCON station.\n\n155\n\nDarwin is located in the tropics, and so experiences greater water columns and a narrower range of temperatures than other\nTCCON sites (Fig. 3a,b). We chose approximately 14 months of data from Darwin when the instrument was performing well,\nand processed that year three times, with water broadening set to 1.0, 1.4, and 1.8 times that of the air broadening half width.\nTo identify the optimal strength for water broadening, we examined the slope of Xluft vs. water column in 10° SZA bins\nfor each of these tests. Binning the data by SZA helps to separate the water dependence from airmass dependence. Figure 3c\n\n160\n\nshows that a water broadening of 1.4 times that of air minimized the dependence of Xluft on water.\nWith the water broadening optimized, we turned to the temperature dependence of the O2 line widths. Reducing the dependence of Xluft on temperature was the primary goal; however, we had to account for the interplay between the temperature and\npressure dependence. In particular, our concern was that changing the temperature dependence of the O2 line widths would\nintroduce or increase an SZA dependence by changing the average line widths.\n\n165\n\nOur solution was to simultaneously adjust both the temperature and pressure dependence of the O2 line widths. To find the\noptimal combination of these coefficients, we minimized a cost function of three quantities. For each quantity, we tested how\nthe results changed using a different collection of TCCON sites:\n1. The average magnitude of the Xluft vs. temperature at 700 hPa (T700) slope across various combinations of 1–3 of the\nEast Trout Lake, Lamont, and Park Falls sites.\n\n170\n\n2. The variance of the Xluft vs. SZA slopes across the Darwin, East Trout Lake, Lamont, and Park Falls sites.\n3. The variance of the magnitude of Xluft across the same sites as #2.\nOur rationale was that the temperature dependence of Xluft was the most important error to eliminate, thus minimizing its\nmagnitude took priority. T700 is taken from the a priori meteorology data and was chosen as a useful metric of synoptic-scale\nchange (Keppel-Aleks et al., 2011). We then minimized the variance in slopes of Xluft vs. SZA across different TCCON sites\n\n175\n\nbecause GGG already has a well-tested program to remove spurious SZA dependencies in the output Xgas products, so long as\nthose dependencies are the same across sites. While minimizing the magnitude of the SZA dependence itself would have been\n8\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(a) 1.005\n\ny = 1.03 + -0.00013x\n\n102\n\n0.995\n\nCounts\n\nXluft (unitless)\n\n1.000\n\n101\n0.990\n0.985\n0.980\n\n100\n\n(b) 1.015\n\ny = 1.01 + -3.31e-05x\n\n102\n\n1.005\n\nCounts\n\nXluft (unitless)\n\n1.010\n\n101\n1.000\n0.995\n0.990\n\n260\n\n270\nT700 (K)\n\n280\n\n290\n\n100\n\nFigure 2. Correlation between Xluft and temperature at 700 hPa (a) before and (b) after optimizing the O2 line broadening in terms of\nits water, pressure, and temperature dependencies. Note that (a) is not from the previous TCCON data version (GGG2014), it is from a\npreliminary beta test of GGG2020. In both panels, the colored background is a 2D histogram, the gray diamonds mark the mean Xluft in 5\nK bins, and the black line is a linear fit to the gray diamonds. The data shown here is from the Lamont TCCON site between 2 Sep 2017 to\n30 Sep 2018. Note that the y-axis limits shift between the panels; this is because the mean magnitude of Xluft changed with the increase of\nO2 line intensities (see text) between the tests plotted in the two panels. The slope is visually comparable between the panels, since the span\nof Xluft is the same (0.025) in both panels.\n\n9\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n# spectra per bin\n\n(a)\n\nDarwin, Australia\nLamont, OK, USA\n\n15000\n10000\n5000\n0\n\n255\n\n260\n\n265\n\n6000\n5000\n4000\n3000\n2000\n1000\n0\n\n280\n\n285\n\n290\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\n1e23\nH2O column (molec. cm 2)\nH2O +0%\n1e 26\n\n(c)\n\nSlope of Xluft vs. H2O column\n( 1/[molec. cm 2] )\n\n270 275\nT700 (K)\n\nT700\n\nH2O +40%\n\nH2O +80%\n\n[281.0 K, 285.0 K]\n\n0.5\n\n8000\n\n0.0\n\n6000\n\n# spectra\n\n# spectra per bin\n\n(b)\n\n0.5\n\n4000\n\n1.0\n\n2000\n\n1.5\n0\n\n10\n\n20\n\n30\n\n40 50\nSZA\n\n60\n\n70\n\n80\n\n0\n\nFigure 3. (a) Histogram of temperatures at 700 hPa at the Darwin (located at 12.5° S) and Lamont (at 36.6° N) TCCON sites. (b) Histogram\nof water column amounts at the same sites. (c) Slopes of Xluft vs. water column in 10° SZA bins at Darwin with water broadening of O2 set\nas equal to, 40% greater, and 80% greater than air. The grey bars give the number of spectra in each bin. The Lamont data in (a) and (b) is\nfrom the period 2 Sep 2017 to 30 Sep 2018, and the Darwin data in all bins is from 21 Jul 2015 to 30 Sep 2016.\n\n10\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nNot optimal\n\nOptimal\n\nTest parameter / original value\n\n1.50\n1.25\n1.00\n0.75\n0.50\n0.25\n0.00\n0.25\n\ns.\npe v\n\n0\n\nT70\n\nSlo\n\nA)\n. SZ\ns\nv\npe\n2 (Slo\n\nuft)\n\n2 ( Xl\n\nGGG2020\n\n(c)\n\nO2 T-dependent pres. broadening half-width\n\n(b)\nO2 air broadening half-width (cm 1/atm)\n\n(a)\n\nGGG2014\n0.055\n0.050\n0.045\n0.040\n0.035\n0.030\n0.025\n\n7800 7900 8000\nFrequency (cm 1)\n\n0.825\n0.800\n0.775\n0.750\n0.725\n0.700\n0.675\n7800 7900 8000\nFrequency (cm 1)\n\nFigure 4. Result of the O2 spectroscopy optimization. (a) The values of each criterion for each test using different values of pressure and\ntemperature broadening coefficients. The values are normalized to their values in the baseline test (before optimizing the O2 spectroscopy).\nThe points within each parameter are spread horizontally for clarity. (b) The air broadening half widths used in GGG2020 (after optimization)\ncompared with GGG2014. The mean GGG2020/GGG2014 ratio is 1.0025, so the points are barely different on this scale. (c) As (b), but for\nthe temperature broadening coefficient. The mean GGG2020/GGG2014 ratio is 0.9323.\n\npreferable, we were not certain there would be enough flexibility in the Xluft -O2 spectroscopy relationship to simultaneously\nminimize the temperature and SZA dependencies. Similarly, we minimized the variance in Xluft itself because the average\nmagnitude of Xluft depends on the strengths of the O2 lines, rather than the pressure and temperature effects on line width\n180\n\nadjusted in this initial experiment.\nTo carry out this optimization, we ran approximately one year of data from four TCCON sites (Darwin, Australia; East Trout\nLake, Canada; Lamont, OK, USA; Park Falls, WI, USA) multiple times. In each test, we scaled the temperature dependence,\npressure dependence, or both of all lines in the O2 band. We could then interpolate between these test runs to estimate the three\ncost function quantities for any pressure/temperature broadening coefficients, and from that find the combination of coefficients\n\n185\n\nthat minimized the overall cost function. Note that we did not use Darwin data to calculate the Xluft versus T700 slopes for the\ncost function, as the small range of temperatures that Darwin experiences (Fig. 3a) make it difficult to get reliable fits versus\ntemperature.\nThe results of the optimization are shown in Fig. 4. Figure 4a shows how the three criterion described above (slope of Xluft\nvs. T700, variance in slope of Xluft vs. SZA, variance in Xluft ) varied across the tests performed with different pressure and\n\n190\n\ntemperature broadening coefficients. The values are normalized to their respective pre-optimization values. We found that the\nbest combination of coefficients reduced the slope of Xluft vs. T700 by 82%, the variance in Xluft vs. SZA slopes across\nTCCON sites by 89%, and the variance in Xluft itself by 49%. The optimized air broadening half widths and temperature\ndependence coefficients for GGG2020 are shown in Fig. 4, panels b and c respectively, with GGG2014 values for comparison.\n\n11\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nThe air broadening half widths were increased by 0.25% and the temperature dependence coefficients were decreased by\n195\n\n6.77%. The effect on the Xluft vs. T700 relationship is shown in Fig. 2b, where the slope is reduced by a factor of 4 compared\nto its pre-optimization value.\nFinally, the O2 line intensities were increased by ∼ 1% to bring Xluft closer to 1. This effect is apparent in Fig. 2, where the\n\npost-optimization Xluft in panel b is near 1, but the pre-optimization values are between 0.990 and 0.995.\n4\n200\n\nImproved a priori profiles\n\n4.1\n\nModified retrieval grid\n\nIn GGG the retrieval is done on a fixed altitude grid. In GGG2014 the altitude grid had a constant spacing of 1 km with 71\nlevels between 0-70 km above sea level. In GGG2020 the grid was updated to 51 levels between 0-70 km above sea level with\nspacing increasing away from the surface following the expression:\n\nzi = i · (0.4 + 0.02 · i)\n205\n\n(2)\n\nwhere zi is the altitude of the ith level in kilometers. As the altitude grids are fixed to sea level, this does mean that some\nsites have some levels below the terrain which are not included in the integration.\n4.2\n\nMeteorological updates\n\nIn GGG2014 the a priori H2 O, pressure, density, and temperature profiles were derived from NCEP 6-hourly reanalyses. In\nGGG2020, these profiles are now derived from GEOS 5 FP-IT 3-hourly product in addition to potential temperature, potential\n210\n\nvorticity, O3 , and CO profiles. The potential vorticity profiles are used to derive equivalent latitude profiles based on the\nequation in Allen and Nakamura (2003). Equivalent latitude is used in deriving the stratospheric part of the a priori trace gas\nconcentration profiles (Laughner et al., 2023). GGG2020 will transition to the GEOS IT product when it replaces GEOS FP-IT;\nan analysis to quantify the impact of that change on TCCON Xgas products is planned.\n4.3\n\n215\n\nTrace gas profile updates\n\nGGG2020 includes a substantial redesign of the algorithm that generates the CO2 , CH4 , N2 O, HF, CO, and O3 a priori\nprofiles. Generating these profiles is now handled by ginput, a separate program from gsetup. The ginput algorithm is described\nin detail in Laughner et al. (2023). Briefly, the CO2 , CH4 , and N2 O profiles are tied to the long term records from the NOAA\nobservatories in Mauna Loa, Hawaii and American Samoa (Lan et al., 2022b, a, c), in order to ensure the growth rates of these\ngases are correctly accounted for. Individual profiles are produced based on the mean transport time between the profile location\n\n220\n\nand the Mauna Loa/American Samoa observatories and (in the stratosphere) chemical loss. HF profiles are derived from CH4\nprofiles using the HF-CH4 relationships previously identified by Washenfelder et al. (2003) and Saad et al. (2014, 2016). CO\n12\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nprofiles are drawn from the GEOS FP-IT chemical product2 (Lucchesi, 2015) with adjustments in the stratosphere to better\nmatch observations. (See Laughner et al. (2023) for details on these adjustments.)\nOne additional change compared to GGG2014 is that the a priori profiles are now given in wet, rather than dry, mole fraction.\n225\n\nThis is necessary as GGG calculates absorber number densities as the prior mole fractions times the number density of air,\nwhich is assumed to include water. The a priori profiles provided in the published data files are also in wet mole fraction. Thus,\nwhenever comparing GGG2020 a priori profiles in the published netCDF files with other sources, care must be taken to ensure\nthat the comparisons convert both profiles to the same (wet or dry) mole fractions.\n5 Improved interferogram-to-spectrum conversion\n\n230\n\nThere have been substantial code changes and streamlining of common code in i2s, the interferogram-to-spectrum conversion\nsubroutine. The main substantive improvements to the code are in the handling of detector nonlinearity, the phase correction,\nand other changes.\n5.1\n\nDetector nonlinearity\n\nThe largest signals in an interferogram generated by a Fourier transform spectrometer are found near zero-path difference\n235\n\n(ZPD), where light from all wavelengths is in phase. The signal levels drop significantly away from ZPD. If the detector\nmeasuring the interferogram has a nonlinear response, the variations in the signal near ZPD will be more distorted than in\nthe rest of the interferogram. This causes a discrepancy between the low-resolution spectral envelope and the high resolution\nspectral lines. Nonlinear detector responses can be strongly pronounced or subtle, and several improvements to i2s have been\nmade to address these situations.\n\n240\n\nWe have implemented a check early in i2s processing to remove interferograms affected by detector or signal chain saturation, an extreme form of detector nonlinearity. If the signal intensity is too large, the ZPD signal will reach the maximum\nvalue permitted by the detector electronics, and no additional light can be detected. We call this “detector saturation” and this\ncauses irreversible detector nonlinearity in which spectral information is permanently lost. To resolve the problem, detectors\nused for TCCON measurements have reduced pre-amplifier gain settings. Additionally, we must limit the number of photons\n\n245\n\nincident on the detector through reducing the field stop or aperture stop diameter or by placing an optical filter in the beam.\nMeasured interferograms that are saturated cannot be recovered, and therefore should be discarded before producing their\nspectra. Because this effect depends on sunlight intensity, saturation could occur near noon but not later or earlier in the day,\nit can be seasonally dependent, or dependent on the amount of water vapor in the atmosphere. In GGG2020, we have implemented a detector saturation check to discard any saturated interferograms based on the maximum and minimum values of the\n\n250\n\ninterferogram signal.\nWe now compute and store a detector nonlinearity diagnostic variable (“DIP”) as part of the regular TCCON data processing.\nKeppel-Aleks et al. (2007) described the solar intensity variation correction applied to the TCCON interferograms that has been\n2 We\n\nexpect to transition to the GEOS IT product when it supersedes GEOS FP-IT. However, that had not yet occurred at time of writing.\n\n13\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\npart of the TCCON processing software since 2007. In this correction, a low-pass filtered interferogram is used to re-weight\nthe original interferogram, largely removing the impacts of solar intensity fluctuations during a measurement. As part of this\n255\n\nwork, Keppel-Aleks et al. realized that detector nonlinearity becomes observable in the low-pass filtered interferogram as a\n“dip” at zero path difference (see Fig. 6b in Keppel-Aleks et al., 2007). The magnitude of this dip is a diagnostic of the severity\nof detector nonlinearity, and is now computed, stored, and reported as part of the routine TCCON processing.\nA subtle detector nonlinearity in the Sodankylä TCCON data persisted from early in their record until the problem was\nfound in 2017. The problem in the early data was resolved by applying the nonlinearity correction developed by Hase (2000)\n\n260\n\ndirectly to the interferogram before transforming it into a spectrum. This correction process and its results are described in\ndetail in Appendices A and B of Sha et al. (2020). In that paper, the authors show that the nonlinearity caused a bias in XCO2\nof about 0.5 ppm in the 2017 Sodankylä data. After 2017, the problem was resolved by optically limiting the light entering\nthe interferometer. This correction process is being applied to GGG2020 data at other sites for periods when significant nonlinearity is identified. We are in the process of incorporating the correction process as a standardized part of the interferogram-\n\n265\n\nto-spectrum processing to make this process easier to complete in the future.\nA second class of nonlinearity results in supralinear detector response, rather than sublinear response as was seen at Sodankylä. The correction procedure described in the last paragraph is not effective at correcting the supralinear behavior as it\nhas a different physical cause than the sublinear behavior. Based on tests performed at the Garmisch TCCON site, our current\nhypothesis is that this behavior results from overfilling the detector element with the light beam (Corredera et al., 2003), and\n\n270\n\nthe magnitude of the effect varies from detector to detector. Another possible cause of supralinearity in detectors can come\nfrom absorptive layers on the InGaAs active region itself (Fox, 1993), but we do not yet have evidence that this is occurring in\nour instruments.\n5.2\n\nPhase correction\n\nSampled interferograms are always asymmetrical, either because the sampling grid does not include the ZPD position, or\n275\n\nbecause the under-lying continuous igram is already asymmetrical even before it is sampled. This asymmetry causes the\nresulting, post-FFT, complex spectrum to have substantial imaginary terms. A phase correction is necessary to resample the\ninterferogram such that is it sampled symmetrically about ZPD, resulting in a computed spectrum that has the signals of interest\n\n280\n\nin the real component and only the noise is divided between both the real and imaginary component.\n√\nIf we used a power spectrum ( <2 + =2 ), avoiding phase correction, it would compute a spectrum that is entirely real, but\n\nwould retain all of the noise in the real and imaginary component of the spectrum. Therefore the final noise level in a power\n√\nspectrum would be a factor of 2 greater than in a phase-corrected and Fourier transformed spectrum. Additionally, in a power\nspectrum, saturated (zero intensity) regions would no longer be centered at zero, as any noise present is rectified and so made\nall positive. For these reasons, we compute a phase correction.\nWe use the phase correction method described by Forman et al. (1966), with a spectral domain convolution as described by\n\n285\n\nMertz (1965, 1967). The phase correction is performed using a low resolution double-sided interferogram, apodized with a cos2\nfunction, to compute the angle between the real and imaginary components of the spectrum. This angle is a smoothly varying\n14\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nfunction of wavenumber, and is called the phase curve. Its counterpart in interferogram space is called the phase correction\noperator. In regions of the spectrum with sufficient signal, the phase curve well defined, but where the spectrum is blacked out\nby water vapor, another strong absorber, or an optical component, it can become undefined. Therefore, to compute the phase\n290\n\ncorrection operator, we need to set a signal threshold so that we can compute a well-behaved phase curve across the spectral\nregion of interest. We interpolate the phase curve linearly across the blacked-out regions of the spectrum where the phase curve\nis below the signal threshold. The phase curve is interpolated to 0 at 0 cm−1 and at the Nyquist frequency (15798 cm−1 ).\nIn GGG2014, several TCCON stations showed retrievals of Xgas with systematic differences between spectra generated\nfrom interferograms collected while the scanning mirror moves away from zero path difference (“forward” scans) and while\n\n295\n\nmoving toward zero path difference (“reverse” scans). These differences are typically less than 0.5 ppm in XCO2 , but with\nlarger differences observed at the Ny Ålesund, Eureka, Paris, and Zugspitze TCCON stations. This forward-reverse bias was\ntracked down to the phase correction operator, and, more specifically, the minimum signal level threshold for which the phase\noperator is calculated. We have lowered the phase curve threshold from 0.02 (2%, in GGG2014) to 0.001 (0.1%, in GGG2020)\nof the peak spectral signal which improves the consistency between forward and reverse scans. This does not completely\n\n300\n\nresolve the problem, and we hope to develop a future version with a phase correction scheme that is independent of the signal\nlevel.\n5.3\n\nOther i2s changes\n\nWe now make better use of the entire interferogram collected by the spectrometer in i2s. In typical linear single-passed Fourier\ntransform spectrometers, we collect most of our interferometric data between zero path difference (ZPD) and the maximum\n305\n\noptical path difference (MOPD) positions of the scanning mirror. However, in order to perform a phase correction, a small\namount of data must be collected on the other side of ZPD, which we call the “short arm” of the interferometer. The “long\narm” is the section from ZPD to MOPD. In previous versions of GGG, the short arm data were discarded after the phase\ncorrection was completed. We now use the short arm data along with the long arm data to compute the spectrum. This is a\nmore efficient use of the data collected.\n\n310\n\n6\n\nContinuum fitting\n\nTCCON spectra are a combination of narrow features due to solar and telluric absorptions superimposed on the much broader\nspectral responses of the instrument and the solar Planck function (the continuum). To accurately fit the telluric features\nof interest, all other components of the spectrum must be accurately modelled simultaneously. Since TCCON spectra are\nnot radiometrically calibrated, the continuum can vary from instrument to instrument or even from day to day (if optical\n315\n\ncomponents are inserted or replaced) and therefore a general approach was needed to model the continuum. Prior to GGG2014,\nthe continuum was fitted with only two terms (mean and slope) over the <100 cm−1 wide windows used to retrieve atmospheric\ngases. To make use of wider spectral windows, it became necessary to include additional complexity in the model of the\ncontinuum, to account for optical components within the instrument (e.g., detectors, optical filters, beamsplitter, etc.) that\n15\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\ninduce curvature in the spectral response (e.g., Kiel et al., 2016b). In GGG2014, we implemented the ability to fit higher order\n320\n\npolynomials to the continuum level using discrete Legendre polynomials for test purposes, although this capability was not\nuniformly used in the GGG2014 TCCON data processing (Wunch et al., 2015). Higher order polynomials are now used widely\nin the GGG2020 spectral windows to better account for continuum shape changes between instruments and over time. The\ncontinuum curvature fitting option is not intended to fit out spectroscopic deficiencies; they will be airmass-dependent and\nso should be fixed separately. The default polynominal order in GGG2020 for each window has been chosen to capture the\n\n325\n\ncontinuum shapes of all sites in GGG2020 and reduce the spectral residuals without over-fitting the spectrum.\n6.1\n\nChannel Fringe Fitting\n\nParallel optical surfaces delay a small fraction of the transmitted beam, which subsequently interferes with the main, un-delayed\nbeam, resulting in a small periodic modulation of the spectral transmittance. This modulation has an amplitude of R2 where R\n330\n\nis the reflectivity of each surface, and a period of (2 · n · d · cos θ)−1 cm−1 , where n in the refractive index of the optic, d is its\n\nthickness (in cm) and θ is the angle to the normal.\n\nFor decades, GFIT has the capability to fit a channel fringe to determine its amplitude (as a fraction of the continuum), its\nperiod, and its phase, and then remove it from the measured spectrum during the spectral fitting. This capability was not used\nby TCCON until GGG2020, when spectral fits from some sites were noticed to exhibit the tell-tale periodicities in the residuals.\nLeft untreated, channel fringes can seriously bias the retrieved gas amounts, by an amount that can vary from instrument to\n335\n\ninstrument and even over time for a single instrument, e.g., if its temperature changes.\nAn important code change for GGG2020 was to prevent channel fringes from being mistaken for higher-order continuum\nterms. This was much less of a problem for GGG2014 when we only ever fitted a straight line to represent the continuum. But\nnow, if a particular wavelike feature in the continuum could be fitted by a higher order polynomial or by a channel fringe, this\ntends to slow down convergence as the continuum fitting and channel fringe fitting vie with each other. To prevent this, a lower\n\n340\n\nlimit was imposed on the channel fringe period that was fittable in a given window, such that it always was narrower than the\nperiodicities in the continuum fitting polynomial. So if we are fitting an N -term polynomial to the spectrum (called the number\nof continuum basis functions, or NCBF ), in a window of width w cm−1 , then the period of the fitted channel fringes must be\nless than w/(NCBF − 1).\n7\n\n345\n\nPost-retrieval data processing\n\nGGG incorporates several post-retrieval steps to (1) collate and average data (§7.2) from the individual retrieval windows into\nthe final Xgas products and (2) correct post hoc for known errors in the forward model. There are two corrections. The first is\nan airmass-dependent correction (§7.1), which aims to eliminate spurious dependence of Xgas quantities on SZA. The second\nis an in situ-based, or airmass-independent correction (§7.3), which aims to eliminate the mean bias in Xgas values arising\nfrom incorrect spectroscopic line strengths.\n\n350\n\nIn the following sections, the post processing steps are presented in the order in which they are applied in GGG2020.\n16\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n7.1\n\nUpdated airmass dependence correction\n\nIn the limit of no horizontal variation in trace gas dry air mole fraction, Xgas quantities are independent of atmospheric path\nlength, as the change in column density due to path length is multiplicative and so will cancel out between the target gas in\nthe numerator and O2 in the denominator. However, a spurious dependence of Xgas on airmass can arise from errors in the\n355\n\nspectroscopic forward model.\nGGG2020, like GGG2014, applies a post hoc correction to the Xgas values to remove airmass dependences. We calculate a\ncorrection for each Xgas value as\n\nfc =\n\n\u0012\n\nθ+g\n90 + g\n\n\u0013p\n\n−\n\n\u0012\n\n45 + g\n90 + g\n\n\u0013p\n\n(3)\n\nand use this to correct the Xgas value as\n\n360\n\nXgas,corr =\n\nXgas,raw\n1 + αfc\n\n(4)\n\nIn Eq. (4), α is a coefficient for each gas (in GGG2014) or each window (in GGG2020). In Eq. (3), θ is the solar zenith angle\n(SZA) in degrees and g and p are coefficients chosen to best represent the SZA-dependent behavior. This form was chosen to\nnormalize to a 90° window centered on (45 + g)◦ . While the basic approach is the same in GGG2020 as it was in GGG2014,\nwe made two changes to the implementation:\n365\n\n1. In GGG2014, column densities from different spectral windows used to retrieve a target gas were averaged first, then\na single airmass correction applied to each gas. In GGG2020, each spectral window is airmass corrected first, then the\nresulting Xgas values are averaged.\n2. In GGG2014, g = 13 and p = 3 for all gases. In GGG2020, different values of g and p were selected for each window.\nThe rationale for the first change is clear from Fig. 5. The standard TCCON CO2 and CH4 products are derived from two\n\n370\n\nand three spectral windows, respectively. Although the overall SZA dependence has a similar shape for all windows of a given\ngas, there are clear differences in low and high SZA behavior. Thus, we decided to apply an SZA dependent correction to\nindividual windows, rather than the average Xgas value.\nThe rationale for the second change is that we do not know a priori the best form to represent the airmass dependence in\nany given window. For GGG2020, we used data from the Darwin TCCON site for all of 2015 to choose the values of g and\n\n375\n\np for each window. We used Darwin because, as a tropical site, it sees a wide range of SZAs (useful for examining SZA\ndependence) and water columns (useful to check for water effects on the derived airmass dependence). We used 2015 data\nbecause the instrument at Darwin was well aligned during that year.\n\n17\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nXCO2 - daily medians (ppm)\n\n(a)\n\n0.5\n0.0\n0.5\n1.0\nCO2 6220\nCO2 6339\n\n1.5\n\nXCH4 - daily medians (ppb)\n\n(b)\n2\n0\n2\nCH4 5938\nCH4 6002\nCH4 6076\n\n4\n6\n10\n\n20\n\n30\n\n40 50 60\nSZA (degrees)\n\n70\n\n80\n\nFigure 5. Variation of (a) the two CO2 and (b) three CH4 windows used by TCCON with SZA without the airmass correction applied.\nIn both panels, the y-axis is column average dry mole fraction of CO2 or CH4 derived from a single spectral window, with the central\nwavenumber given in the legend. The y values have the daily median values subtracted (to remove day-to-day variability), and each point\nrepresents the median of all such values in a 5° SZA bin.\n\nTo understand how g and p were determined, we must first explain how the airmass dependent correction factor (ADCF, i.e.\nα in Eq. 4) is calculated for a given g and p. The ADCF is calculated by fitting the following function to each day’s data:\n\n380\n\nf (t, θ|c1 , c2 , c3 ) = c1 + c2 · (2π(t − tnoon )) + c3 fc\n\n(5)\n\nwhere t and tnoon are the measurement time and solar noon time (in day of year), fc is the polynomial defined in Eq. (3), and\nc1 , c2 , and c3 are the fitted coefficients. The coefficients and their errors are calculated with a weighted least squares fit using\nthe individual windows’ Xgas uncertainties as the weights. The ADCF for a given window is the error-weighted mean of all\ndays’ c3 values.\n385\n\nTo find the optimal g and p values, we derived ADCFs for five subsets of the 2015 Darwin data (data with SZA > 20°, 30°,\n40°, 50°, and 60°, all with H2 O column < 1.1 × 1023 molec. cm−2 ) for values of g between −45 and +45 and p between 1\nand 6. We then find the combination of g and p that gives the smallest standard deviation across all five subsets and choose that\n18\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n0.005\n0.010\n0.015\n0.020\n\n20\n\n25\n\n30\n\n35 40 45\nSZA min (deg)\n\n50\n\n55\n\n40\n20\n10\ng\n\n0.009474\n0.008421\n0.007368\n0.006316\n0.005263\n0.004211\n0.003158\n0.002105\n0.001053\n0.000000\n\n0\n10\n20\n30\n40\n1\n\n2\n\n3\n\np\n\n4\n\n5\n\n6\n\n1\n\n0.005\n0.010\n0.015\n0.020\n\n60\n\n20\n\n25\n\n30\n\n35 40 45\nSZA min (deg)\n\n50\n\n55\n\n40\n\nxco2_6220 ADCF std. dev.\n\n30\n\nCO2 from window centered on 6339 cm\n\n0.000\nxco2_6339 ADCF\n\nxco2_6220 ADCF\n\n1\n\n30\n\n60\n0.009474\n0.008421\n0.007368\n0.006316\n0.005263\n0.004211\n0.003158\n0.002105\n0.001053\n0.000000\n\nxco2_6339 ADCF std. dev.\n\nCO2 from window centered on 6220 cm\n\n0.000\n\n20\n10\n0\n10\n20\n30\n40\n1\n\n2\n\n3\n\np\n\n4\n\n5\n\n6\n\nFigure 6. Example of how g and p in Eq. (3) were chosen for the two TCCON CO2 windows. The left two panels are for the CO2 window\ncentered at 6220 cm−1 and the right two for the window at 6339 cm−1 . The line plots at the top show how the value of the ADCF (α in\nEq. (4)) changes as we increase the lower limit in SZA for the data fit to. Each gray line represents one combination of g and p, with the\nblack line representing the combination with the smallest standard deviation in the ADCF. The contour plots show the standard deviation\nof the ADCF across different minimum SZAs for each combination of g and p. The white star represents the combination with the smallest\nstandard deviation; it corresponds to the test show with the black line in the line plots.\n\nas the optimal combination. This approach assumes that the values of g and p (and thus the form of fc ) which best capture the\nairmass dependence of a particular window will have the smallest change in ADCF as smaller subsets of data are fit.\n390\n\nThis procedure is illustrated for the two TCCON CO2 windows in Fig. 6. In the top panels, the gray lines show the variation\nin ADCF with the minimum SZA in the subset of data fit to; each line represents one combination of g and p. It is clear that the\nvariation in ADCF is much greater for some combinations of g and p than others. The contour plots in Fig. 6 show the standard\ndeviation of ADCF for each g and p combination. In both windows, there is a clear minimum valley. The white stars in the\ncontour plots and thicker black lines in the upper panels show the g and p combination with the smallest standard deviation.\n\n395\n\nThe final step in selecting ADCFs for GGG2020 was to account for spurious temperature dependence in the Xgas values. As\nwe saw with O2 in §3.3, incorrect temperature dependence in the line widths introduces a temperature dependence in retrieved\nXgas , which could alias into the airmass dependence. To check this, we derived ADCFs from data from 18 TCCON sites, using\ntwo month long subsets of data to sample different temperatures. Figure 8 shows how the CH4 ADCFs vary with potential\ntemperature averaged between 500 and 700 hPa (θmid ) as an example. (Figure 7 shows how θmid and T700 relate to assist\n\n400\n\ncomparisons with Fig. 2.) Here, we see that the 6002 cm−1 and 6076 cm−1 windows’ ADCFs have no or little temperature\ndependence (Fig. 8b,c), but the 5938 cm−1 window has a clear temperature dependence. To compute the final ADCFs for\neach window, we used the value of the fit to this data at θmid = 310 K. 310 K was chosen as it is approximately the midpoint\ntemperature for the TCCON network, as can be seen in Fig. 8.\n\n19\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n320\n\n101\n\n280\n\n#\n\nmid\n\n(K)\n\n300\n\n260\n240\n\n240\n\n260\n\n280\n300\nT700 (K)\n\n320\n\n100\n\nFigure 7. A heatmap of the relationship between θmid and T700, taken from the Park Falls TCCON data. The red dashed line denotes the\n1:1 line.\n\nADCF\n\n(a) 0.015\n\nADCF\n\n1\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (0.0711 +/- 0.00729) + (-0.000261 +/- 2.35e-05)x\n0.020\n290\n295\n300\n305\n310\n315\n\n(b) 0.015\n\nCH4 from window centered on 6002 cm\n\n320\n1\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (-0.0085 +/- 0.00788) + (7.99e-06 +/- 2.53e-05)x\n0.020\n290\n295\n300\n305\n310\n315\n\n(c) 0.015\n\nADCF\n\nCH4 from window centered on 5938 cm\n\nCH4 from window centered on 6076 cm\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (0.0356 +/- 0.00698) + (-0.000134 +/- 2.24e-05)x\n0.020\n290\n295\n300\n305\n310\n315\nmid (K)\n\n320\n1\n\nBialystok\nBurgos\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nJPL 01\nSaga\nKarlsruhe\nLauder 03\nLamont\nOrleans\nPark Falls\nReunion Island\nRikubetsu\nTsukuba 02\nWollongong\n\n320\n\nFigure 8. ADCFs derived from two month periods from 18 sites throughout the TCCON network versus mean potential temperature between\n500 hPa and 700 hPa over the same two month period. Each panel is one of the TCCON CH4 windows. The text inset in each panel gives\nthe intercept and slope of the robust fit through the data shown by the black dashed line.\n\n20\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nADCF\n\n0.2\n\nCO from window centered on 4233 cm\n\n1\n\n(b)\n\n0.1\n\n0.1\n\n0.0\n\n0.0\n\n0.1\n0.2\n0.3\n\n0.1\n\n0.3\n\n320\n\nwCO2 from window centered on 6073 cm\n\n1\n\n0.000\n\n0.000\n0.005\n\n0.010\n0.015\n\ny = (0.133 +/- 0.0715) + (-0.000486 +/- 0.000229)x\n290\n295\n300\n305\n310\n315\n320\n\nwCO2 from window centered on 6500 cm\n\n(d) 0.005\n\n0.005\n\n0.020\n\n1\n\n0.2\ny = (-0.448 +/- 0.139) + (0.00132 +/- 0.000446)x\n290\n295\n300\n305\n310\n315\n\nADCF\n\nADCF\n\n(c) 0.005\n\nCO from window centered on 4290 cm\n\n0.2\n\nADCF\n\n(a)\n\n1\n\nBialystok\nBurgos\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nJPL 01\nSaga\nLauder 03\nLamont\nOrleans\nPark Falls\nReunion Island\nRikubetsu\nTsukuba 02\nWollongong\n\n0.010\n0.015\n\ny = (0.000425 +/- 0.00238) + (-8.95e-06 +/- 7.64e-06)x\n290\n295\n300\n305\n310\n315\n320\n\n0.020\n\ny = (0.0225 +/- 0.00412) + (-0.000104 +/- 1.33e-05)x\n290\n295\n300\n305\n310\n315\n320\nmid (K)\n\nFigure 9. Similar to Fig. 8, except for two CO windows (a, b) and two weak CO2 windows (c, d).\n\nThe magnitude of this temperature dependence varies from gas to gas: the primary TCCON CO2 windows have almost\n405\n\nno slope, while the N2 O windows have slopes of ADCF vs. θmid similar to or larger than the CH4 5938 window. We plan to\ninvestigate these temperature dependence behaviors more thoroughly in the next major GGG version and identify spectroscopic\nimprovements that will reduce or eliminate this behavior using a similar approach to that described for O2 in §3.3.\n7.1.1\n\nFitting windows excluded in GGG2020\n\nBased on the ADCF analysis, several spectral windows were excluded from the TCCON GGG2020 product. Figure 9 shows\n410\n\nthe ADCF versus θmid plots for two CO windows and two weak CO2 windows. The CO window centered on 4233 cm−1\n(Fig. 9a) has slightly stronger temperature dependence and clearly larger scatter than the 4290 cm−1 CO window (Fig. 9b). We\nsuspect this is due to water interference; the 4233 cm−1 CO window has more water lines in it than the 4290 cm−1 window.\nWe examined the spectral residuals in both CO windows to try to identify and correct the water interference, but were not able\nto reduce it to satisfactory levels. Thus, in GGG2020, the XCO product relies on only the 4290 cm−1 window.\n\n415\n\nSimilarly, the new XwCO2 product was planned to use two windows, one centered on 6073 cm−1 and another on 6500 cm−1 .\nHowever, as shown in Fig. 9c and 9d, the 6500 cm−1 window’s ADCF have more scatter and stronger temperature dependence\nthan the 6073 cm−1 window. As the 6500 cm−1 also has more water interference than the 6073 cm−1 window, we elected to\nuse only the 6073 cm−1 window.\nLastly, we also removed a number of HCl windows. TCCON used 16 windows to measure HCl in GGG2014, but like the CO\n\n420\n\nand wCO2 windows, many of these have water absorption lines in them. We can diagnose unaccounted for water interference\nby computing the ADCFs for each HCl window from Darwin 2015 data, split by the amount of water in the column. The\nresult is shown in Fig. 10. Most of the GGG2014 windows have a clear difference in ADCF with small or large water column\namounts. Based on this, we chose to only retain the 5625, 5687, 5702, 5735, and 5739 cm−1 windows. Most of the windows\nremoved clearly have a water interference. The 5754 and 5763 cm−1 windows are special cases. The 5754 cm−1 window was\n\n21\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n0.06\n\nH2O < 1.1 × 1023 molec. cm\nH2O 1.1 × 1023 molec. cm\n\nADCF\n\n0.04\n\n2\n2\n\n0.02\n0.00\n0.02\n5577 5597 5625 5683 5687 5702 5706 5719 5735 5739 5749 5754 5763 5767 5779 5790\nWindow central wavenumber\n\nFigure 10. ADCF calculated for each HCl window from 2015 Darwin data, divided by the total column amount of water.\n425\n\nrejected because its airmass dependence is slightly more negative than the retained windows. The 5763 cm−1 window was\nrejected because it exhibits a clear temperature dependence in the window-to-window scale factors (§7.2).\n7.2\n\nUpdated window-to-window averaging\n\nMany gases retrieved by GGG are retrieved in more than one spectral window. GGG retrieves the column amount in each\nwindow separately, then averages together the columns with similar averaging kernels to produce a mean value. Specifically,\nP\n2\nj sj yij /\u000fij\n430 y i = P 2 2\n(6)\nj sj /\u000fij\nwhere subscript j represents the spectral window. That is, the average value for the ith measurement (y i ) is an error weighted\n\naverage of the individual windows’ column amounts (yij , with errors \u000fij ) with a mean bias in each window removed by the\nper-window scale factor, sj . The errors \u000fij are the posterior errors in the Xgas amounts as calculated from the retrieval error.\nIn GGG2014, the sj values were determined online, using an iterative process that minimizes the differences between yij\n435\n\nand the corresponding sj y i values. While this calculates sj values that best fit the data being averaged, it means that how the\nwindows are combined depends on how much data is averaged at once—processing a month could give different results than\nprocessing a year of data, for example. Thus, while GGG2020 retains the capability to compute the sj values on-the-fly, the sj\nvalues are prescribed for standard TCCON processing.\nTo determine the standard TCCON sj values, we used a very similar approach to how we derived the ADCFs in §7.1.\n\n440\n\nSpecifically, we calculated the sj values for two month subsets of data from the same 18 TCCON sites as in §7.1 and fit these\nvalues versus θmid . As with the ADCFs, we used the values of the fit at θmid = 310 K as the final choices of sj .\n7.3\n\nUpdated in situ bias correction\n\nAs in GGG2014, the GGG2020 XCO2 , XCH4 , XN2 O , and XH2 O products are tied to standard scales by in situ aircraft, balloon,\nand/or radiosonde measurements to remove any mean multiplicative bias introduced by error in absorption line intensity.\n445\n\nUnlike GGG2014, XCO in GGG2020 is not tied to in situ measurements, due to previous work that found the difference\n22\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nbetween TCCON XCO and both NDACC (Kiel et al., 2016a) and MOPITT (Hedelius et al., 2019) XCO was approximately the\nmagnitude of the in situ correction. However, we do evaluate XCO against a subset of in situ data from AirCore only below.\nComparison of TCCON data against in situ data follows the following steps:\n1. Identify in situ vertical profiles in available data and convert to a standardized file format\n450\n\n2. Extend the profiles’ tops to 70 km altitude using the standard GGG2020 priors and to the surface by extrapolation or use\nof surface data\n3. Match profiles to available TCCON spectra\n4. Run custom retrievals using the match profiles as the a priori trace gas profile\n5. Compare integrated in situ Xgas values against matched TCCON data, accounting for TCCON vertical sensitivity\n\n455\n\nPoints 1–4 are described in detail in Appendix C. Briefly, we use profiles from:\n– the GlobalviewPLUS 5.0 CO2 (Cooperative Global Atmospheric Data Integration Project, 2019) and GlobalviewPlus\n2.0 CH4 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020) products,\n– AirCore balloon measurements (Tans, 2009; Karion et al., 2010) flown by NOAA (v20201223, Baier et al., 2021) at\nmultiple TCCON sites and by FMI/LSCE/RUG at the Sodankylä, Finland (Kivi and Heikkinen, 2016) and Nicosia,\nCyprus (Rousogenous, in prep) TCCON sites,\n\n460\n\n– the Infrastructure for Measurement of the European Carbon Cycle (IMECC) campaign,\n– Profiles over the Manaus, Brazil TCCON site (Dubey et al., 2016),\n– ARM radiosondes over the Darwin, Australia (Deutscher et al., 2010) and Lamont, OK, USA TCCON sites\nCH4 profiles have an additional correction to the stratospheric levels obtained from the GGG2020 priors, see §C3 for details.\n465\n\nWe have addressed the recent change of CO2 data from the X2007 to X2019 WMO scales, which will be covered in §7.3.2.\nDue to the relative sparsity of N2 O profiles, GGG2020 TCCON N2 O products were evaluated against surface N2 O data and a\ndifferent approach, which will be covered in §7.3.3.\n7.3.1\n\nCO2 , CH4 , CO, and H2 O in situ comparisons\n\nThe first step in comparing TCCON XCO2 , XCH4 , XCO , or XH2 O to their respective in situ profiles is to match each in situ\n470\n\nprofile to temporally proximate, good quality TCCON retrievals. For this step, we define custom quality filters. A TCCON\nretrieval is considered to be good quality in this context if:\n– Fractional variation in solar intensity (FVSI) is ≤ 0.05. This filters out observations impacted by intermittent clouds.\n23\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– Solar zenith angle (SZA) is ≤ 80◦ . This avoids observations at large airmasses, where spectroscopic errors can be more\npronounced.\n\n475\n\n– The unscaled Xgas value is > 0 mol mol−1 . A negative retrieved value is unphysical, and the distribution of retrieved\nvalues should not be large enough to make negative values a reasonable part of it.\n– The Xgas error is < 2\u000fmedian , where \u000fmedian is the median error for that Xgas across all the spectra used for the given\ngas. This limits for observations where the observed spectra was fit reasonably well.\n– The median Xluft for a comparison is between 0.996 and 1.002. Xluft and this rational are explained near the end of this\nsubsection.\n\n480\n\nFor each in situ profile, we require 30 TCCON observations passing these quality checks within a certain window of time\naround the corresponding profile’s lowest altitude measurement. Our initial window is ±1 hour. If 30 points meeting these\ncriteria are not present within ±1 hour, we increase both the time window and the allowed Xgas error, trying the combinations\n\n(±1 hr, < 2\u000fmedian ), (±2 hr, < 3\u000fmedian ), and (±3 hr, < 4\u000fmedian ). We use the smallest of these time/error window that yields\n485\n\n30 passing TCCON observations, but if a profile does not have 30 passing TCCON observations in the (±3 hr, < 4\u000fmedian )\nrange, it is removed from the comparison.\nThe remaining in situ profiles are integrated following Wunch et al. (2010), where the integrated in situ Xgas value, zinsitu\nis calculated as:\n\nzinsitu = I(γxa , p, xH2 O ) + I(δx, p, xH2 O )\n490\n\n(7)\n\nwhere\n– p is the vector of pressure at each profile level\n– xH2 O is the vector of water dry mole fractions at each profile level\n– γxa is the TCCON posterior profile (i.e. the prior times the retrieved VMR scale factor γ)\n– δx is the difference between the in situ and TCCON posterior profiles, modified by the TCCON averaging kernel:\nδxi = ai (xinsitu,i − γxa,i )\n\n495\n\nI represents the pressure-weighted integration function:\n· dpi · Di\ni dpi Di\n\u0012\n\u0013\nMH2 O\nDi = gi · Mair · 1 + xH2 O,i ·\nMair\n\nI(x, p, xH2 O ) =\n\nwhere\n\nP\n\nxi\niP\n\n(8)\n(9)\n\n24\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n500\n\n– dpi represents the pressure thickness of layer i\n– gi represents the acceleration from gravity at layer i,\n– Mair and MH2 O represent the mean molecular masses of dry air and water, respectively.\nThe integrated in situ Xgas values are compared against the median of the TCCON Xgas values from the matched observations. The TCCON Xgas values used here have the airmass correction (§7.1) and window-to-window averaging (§7.2) applied.\n\n505\n\nBecause we expect the bias in the TCCON data to arise from incorrect absorption line strengths or broadening coefficients, it\nshould be a multiplicative bias. Therefore, we calculate an uncertainty-weighted mean of the TCCON/in situ Xgas values to\nderive the bias correction. We consider five sources of uncertainty.\n1. Measurement error in the in situ data.\n2. Uncertainty from the unmeasured portion of the free troposphere. (Will be zero if the in situ vertical profile extends\n\n510\n\nthrough the tropopause.)\n3. Uncertainty from the unmeasured portion of the stratosphere.\n4. Random error in the TCCON observations.\n5. Bias in the TCCON observations from instrument misalignment or similar hardware concerns.\nThe calculation of each term and how they are combined is detailed in Appendix C6.\n\n515\n\nThe results of the TCCON-in situ comparison are shown in Fig. 11. In this plot, the y-axes are the ratio of TCCON to in\nsitu Xgas amounts and the x-axes show Xluft , a diagnostic quantity defined as the ratio of the column of dry air derived from\nsurface pressure to the column of dry air derived from the O2 retrieval. We will return to the significant of Xluft shortly. The\nuse of TCCON to in situ ratios to derive the in situ correction is equivalent to the best fit lines forced through the origin used\nin Wunch et al. (2010), as the best fit line through the origin is essentially the mean TCCON to in situ ratio. The use of ratios\n\n520\n\ndirectly in Fig. 11 allows us to more clearly identify outliers and evaluate the correlation of the TCCON vs. in situ bias with\nother variables, such as Xluft here.\nThe ratios from Fig. 11 indicate that the mean biases are within approximately 1% of unity in all cases, with water being the\nfurthest from unity at 0.9883 (−1.17%). The differences among the CO2 products are interesting; the standard CO2 product\nis biased about 1% high before correction (which is in line with expected uncertainties for the CO2 lines), while the other two\n\n525\n\nCO2 products are much closer to unity (0.08% for wCO2 and 0.14% for lCO2 ). This suggests that the absorption coefficients\nin these latter two windows are more accurate than in the standard TCCON windows (which are centered on 6220 and 6339\ncm−1 ). However, as the wCO2 and lCO2 are more sensitive to the upper and near-surface atmosphere, respectively, it may be\nthat this reflects other factors, such as the accuracy of the a priori temperatures at those levels.\nThe CO comparison (Fig. 11e) suggests that, without scaling, the GGG2020 XCO has no significant bias with respect to\n\n530\n\nAirCore CO measurements. Figure 11e shows significant variation in the TCCON/in situ CO agreement, with individual points\n25\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(b)\n\n(c)\n1.015\n\n1.015\n\n1.010\n\n1.010\n\n1.010\n\n1.005\n1.000\n0.995\n\nr = 1.01010\n2 r = 0.00050\n\n1.005\n1.000\n0.995\n0.990\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(d)\n\n0.995\n0.990\n\nTCCON XCO / in situ XCO\n\n1.010\n1.005\n1.000\n0.995\n0.990\n\nr = 1.00310\n2 r = 0.00140\n\n0.980\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(f)\n\n1.8\n1.6\n\n1.2\n1.0\n0.8\n0.6\n\nr = 1.00140\n2 r = 0.00070\n\nr = 1.00850\n2 r = 0.05260\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\nATom\nAirCore\nCOBRA\nGSFC\nHIPPO\nHarvard\nIMECC\nLARC\nNOAA Manaus\nORCAS\nRadiosonde\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n1.4\n\n1.015\nTCCON XCH4 / in situ XCH4\n\n1.000\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(e)\n\n1.020\n\n0.985\n\nr = 1.00080\n2 r = 0.00050\n\n1.005\n\nTCCON XH2O / in situ XH2O\n\n0.990\n\nTCCON XlCO2 / in situ XlCO2\n\n1.015\nTCCON XwCO2 / in situ XwCO2\n\nTCCON XCO2 / in situ XCO2\n\n(a)\n\n1.4\n1.2\n1.0\n0.8\n0.6\n0.4\n\nr = 0.98830\n2 r = 0.01570\n\n0.2\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\nAnmyeondo\nArmstrong\nBialystok\nBremen\nDarwin\nLamont\nLauder 01\nLauder 02\nManaus\nNicosia\nPark Falls\nPasadena\nRikubetsu\nSodankyla\n\nFigure 11. Plots of the TCCON/in situ Xgas ratios for (a) CO2 , (b) wCO2 , (c) lCO2 , (d) CH4 , (e) CO, and (f) H2 O. In all plots, the y-axis\nis the ratio of TCCON/in situ Xgas and the x-axis is the median Xluft value for the TCCON observations in a comparison (see text for\nexplanation of Xluft ). The marker style of each comparison indicates the source of the in situ data and the color indicates which TCCON site\nthe comparison occurred at. The text inset in the lower-right corner of each plot gives the uncertainty-weighted mean TCCON/in situ ratio\nand its 2σ uncertainty. The dashed black lines mark the mean ratio. Panels a, b, and c are set to use the same y-limits; some of the error bars\nin (b) go outside the y-limits.\n\nalso having large uncertainty. This resulting 2σ uncertainty in the mean ratio is significantly larger than for the other gases, at\n0.0526. Thus, the mean TCCON/in situ CO ratio is well within its 2σ uncertainty of 1. We do acknowledge that limiting the\nCO comparisons to AirCore profiles alone may contribute to a larger uncertainty than if aircraft campaigns were included, due\nto the use of a CO-spiked fill gas in AirCores (see §2.1 of Martínez-Alonso et al., 2022). However, comparing TCCON XCO\n535\n\nto AirCore profiles was significantly more straightforward than including aircraft profiles, since the already-matched AirCore\nprofiles for CO2 and CH4 intrinsically include CO as well. Given the other reasons discussed above for not applying an in\nsitu-derived scaling to GGG2020 XCO and the process needed to match aircraft data with TCCON (see Appendix C1.1), we\nchose to accept the additional uncertainty from using AirCore profiles only. Future versions of the TCCON data product will\nreevaluate the inclusion of aircraft profiles alongside AirCore ones.\n\n540\n\nFigure 11 also provides insight into how instrumental errors affect different TCCON products. Under ideal circumstances,\nXluft (the quantity on the x-axis) should be 1; in practice, the nominal value for the TCCON network is 0.999, due to small\nresidual biases in the O2 spectroscopy. Deviations of Xluft from the nominal value indicate either (a) variable errors in spectroscopy, such as temperature or pressure broadening, or (b) instrument issues, such as a misalignment in the beam path. From\nFig. 11a, we can see that the TCCON/in situ ratio tends to be less when Xluft < 0.999 and greater when Xluft > 0.999. The\n\n26\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n545\n\nslope for Fig. 11a is 0.363. This translates to a bias in CO2 of about 0.15%, or approximately 0.5 ppm, when Xluft is 0.004 units\naway from the nominal value of 0.999 (0.15% = 0.0015 = 0.363 × 0.004). To keep this bias well below the expected 0.25%\naccuracy, we limit the comparison used here to those where Xluft is between 0.996 and 1.002 and have instituted additional\n\nquality checks of TCCON data that filter out observations when Xluft is outside the range of 0.995 to 1.003 for an extended\nperiod of time. Additionally, Xluft is now reported in the public data set alongside other Xgas retrievals.\n550\n\nWe note that the standard CO2 and the near surface-sensitive lCO2 products show the clearest dependence on Xluft . The\nreason for this is not clear at this time, though it implies a stronger dependence of these products on instrument line shape\n(ILS) compared to the other four products discussed in this section. Future versions of GGG are planned to account for errors\nin the ILS, which we hope will mitigate this bias and improve the accuracy of CO2 data when Xluft is outside the 0.995 to\n1.003 range.\n\n555\n\nThe correlation of XCO2 and XlCO2 with Xluft implies that we could develop an Xluft -based bias correction for those CO2\nproducts. Such a correction is planned for a minor update to the GGG data product. Our aim is to quantify the underlying\nphysical drivers of the XCO2 bias and use the correlation of those factors with Xluft to derive the bias correction. This would\nallow us to use the comparison to in situ data shown here as an independent verification of the bias corrections efficacy.\n7.3.2\n\n560\n\nAddressing the CO2 scale change from X2007 to X2019 and changing O2 mole fraction\n\nThe update from the previous WMO CO2 X2007 calibration scale to the new X2019 calibration scale (Hall et al., 2021)\noccurred late enough in the process of releasing GGG2020 that we were not able to incorporate it into the initial release. Given\nthe clear need expressed by the community to have TCCON data tied to the same scale as in situ data, we have since derived\nnew in situ correction factors to tie all three TCCON XCO2 products to the X2019 scale. Doing so required obtaining in situ\ndata that had been adjusted to the new scale, which we did in one of three ways:\n\n565\n\n1. The preferred approach was for the data originator to fully recalibrate their data to the new scale using the updated standards provided by the NOAA Global Monitoring Laboratory. NOAA AirCore and some NOAA ObsPack data followed\nthis approach.\n2. The second approach was for the data originator or an intermediate provider to adjust the CO2 data using the linear\ncorrection described in §9.1 of Hall et al. (2021). The remaining NOAA ObsPack data not covered by approach #1\n\n570\n\nfollowed this approach.\n3. The third approach was for us to perform the same linear correction as #2 ourselves. All other data used this approach.\nAlso recall that the profiles must be extended to 70 km altitude using the TCCON standard priors to ensure that the same\nvertical extent is captured in the in situ and TCCON column averages. As discussed in Laughner et al. (2023), the standard\npriors are derived from NOAA data at the Mauna Loa and American Samoa observatories, and so are also intrinsically tied to\n\n575\n\nWMO calibration scales. To ensure consistency throughout the in situ profiles, we used the latest available monthly average\n\n27\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nCO2 flask data on the X2019 scale as input to the priors when generating the profile extensions. Once this was complete, we\nredid the analysis described in §7.3 with the in situ profiles adjusted to the X2019 scale to generate updated correction factors.\nThe overall effect of the scale change for each of the three TCCON CO2 products is shown in Fig. 12 compared to the “raw,”\nun-bias corrected XCO2 value on the x-axis. The magnitude is about +0.15 ppm for typical current XCO2 values of 400 ppm.\n580\n\nIn the TCCON data products, there are three CO2 variables with the suffix _x2019 which are adjusted to the new X2019\nscale.\nAnother source of bias that is of similar magnitude to the effect of the scale change is the assumed O2 mole fraction. As\nshown in Eq. (1), the column-average mole fractions reported by TCCON are computed by dividing the column density of the\ntarget gas by the O2 column density, and scaling by the mean O2 mole fraction in the atmosphere. We have assumed that this\n\n585\n\nmole fraction is fixed for the initial GGG2020 data products; however, it is in fact changing over time due to various processes,\npredominantly fossil fuel combustion and the land biosphere (Keeling et al., 1998; Keeling and Manning, 2014).\nBecause the effect of ignoring the change in the global average O2 mole fraction is of similar magnitude to the X2007 to\nX2019 scale change, we decided to account for the change in O2 mole fraction over time in the CO2 products updated to the\nX2019 scale. We did not retroactively apply this correction to the X2007 XCO2 or the other Xgas products, as doing so would\n\n590\n\nchange the Xgas values and require a new data version. This correction will be applied to all Xgas values in the next GGG data\nversion.\nOur approach to account for changing O2 mole fraction takes advantage of the anticorrelation between atmospheric O2 and\nCO2 to derive the O2 mole fraction from CO2 measured by TCCON. (For our application, this assumption is sufficiently\naccurate; however, we note that this is not generally true for other applications of O2 /N2 ratio data.) Specifically, the value for\n\n595\n\nfO2 in Eq. (1) is calculated as (see Appendix E1 for the full derivation):\n\nfO2 = (α − α · fO2 ,ref − fO2 ,ref ) ·\n\nXCO2 − XCO2 ,ref\n+ fO2 ,ref\n1 − XCO2 − α · XCO2\n\n(10)\n\nwhere:\n– α = ∂NO2 /∂NCO2 = −1/0.4575, i.e. the change in the number of moles of O2 in the atmosphere for a given change in\n600\n\nthe number of moles of CO2 in the atmosphere. The choice of −1/0.4575 comes from the agreement with the measured\nchange in fO2 as shown in Fig. 13. This value is chosen to remove the effect of long term trends in the O2 mole fraction,\nand ignores synoptic-scale variations due to e.g. photosynthesis or fossil fuel emissions.\n\n– fO2 ,ref is the reference value for the mole fraction of O2 . We use 0.209341 based on the value measured by Aoki et al.\n(2019) at Hateruma Island, Japan in 2015 and adjusting by ∼ 2 ppm to approximate the global mean fO2 by using the\n\ndifference between the annual mean CO2 reported for Hateruma Island by Aoki et al. (2019) and that for the NOAA\n605\n\nglobal marine boundary layer reference. (A revised calculation accounting for possible influence of fossil fuel emissions\non Hateruma Island puts the global mean O2 mole fraction closer to 0.209347, however the 0.209341 value is what is\nused in GGG2020.)\n28\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nX2019 - X2007\nX2019+Var. O2 - X2019\nX2019+Var. O2 - X2007\n\nXCO2 (ppm)\n\n(a)\n0.0\n0.5\n1.0\n\n350\n\n400\n450\n500\n\"Raw\" XCO2 (ppm)\n\n550\n\n350\n\n400\n450\n500\n\"Raw\" XwCO2 (ppm)\n\n550\n\n350\n\n400\n450\n500\n\"Raw\" XlCO2 (ppm)\n\n550\n\nXwCO2 (ppm)\n\n(b)\n0.0\n0.5\n1.0\n\nXlCO2 (ppm)\n\n(c)\n0.0\n0.5\n1.0\n\nFigure 12. The change in TCCON (a) XCO2 , (b) XwCO2 , and (c) XlCO2 due to the WMO scale change, change in assumed O2 mole\nfraction, and the combination of both. The x-axis is the “raw” XCO2 value that has no in situ bias correction and assumes a fixed O2 mole\nfraction. The “X2019 – X2007” line shows the difference due to only the CO2 WMO scale change, the “X2019+Var O2 – X2019” shows\nthe difference due to only the change from fixed to variable O2 mole fraction, and the “X2019+Var. O2 – X2007” line shows the total change\nfrom both effects combined.\n\n29\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nReference\nBest estimate\n= 1/0.4575\n= 1/0.4000\n= 1/0.5000\n\nfO2 (mol/mol)\n\n0.209425\n0.209400\n0.209375\n0.209350\n0.209325\n\n1995 2000 2005 2010 2015 2020\nYear\nFigure 13. Comparison of fO2 values calculated using Eq. (10) for three different values of α versus a best estimate of fO2 using δ(O2 /N2\nfrom the Scripps Intitute of Oceanography (Scripps O2 Program, 2022) and NOAA global mean CO2 (Lan et al., 2023) data. The three\ncolored lines also use NOAA global mean CO2 data for the XCO2 and XCO2 ,ref values in Eq. (10). The black circle marks our reference\nvalue of fO2 = 0.209341.\n\n– XCO2 ,ref is a reference value for the column-average mole fraction of CO2 . We use 4 × 10−4 (400 ppm) to approximate\n\nthe value seen in TCCON data during 2015 (the same year as the fO2 ,ref value), though as discussed below, it is not\n\n610\n\ncrucial that the O2 and CO2 reference values be for exactly the same time.\n– XCO2 is the “raw” measured TCCON XCO2 with airmass correction and assuming fO2 = fO2 ,ref = 0.209341.\nTo validate this approach, we also compute the change in fO2 (including the effect of CO2 dilution) using δ(O2 /N2 ) data\nmeasured by the Scripps Institution of Oceanography at Alert, NWT, Canada (station code ALT); La Jolla Pier, California,\nUSA (LJO); and Cape Grim, Australia (CGO) and NOAA CO2 annual trend data (Lan et al., 2023). To approximate a global\n\n615\n\nmean δ(O2 /N2 ) value, we follow §5.15.4.2 of Keeling and Manning (2014) and combine the data from these stations as (ALT\n+ LJO)/4 + CGO/2.\nThe results of this comparison are shown in Fig. 13. The black line shows the change in fO2 computed using the Scripps\nδ(O2 /N2 ) data (see Appendix E2 for the methodology), while the other three lines represent fO2 calculated with Eq. (10)\n\n620\n\nand various values of α. We can see that Eq. (10) with α = −1/0.4575 gives quite good agreement with the change in fO2\ncomputed using the Scripps δ(O2 /N2 ) and NOAA global CO2 data.\n\nThe final step in adopting the variable O2 mole fraction was to recompute the in situ correction factor once more, using the\nvariable O2 mole fraction in the TCCON Xgas values for the comparison. Doing so ensures that any constant multiplicative\nbias introduced by incorrect or inconsistent values for the fO2,ref or XCO2 ,ref values is scaled out. This is why, in the discussion\nabove about the choice of those reference values, we note that it is not critical to have the O2 and CO2 reference value exactly\n625\n\nconsistent.\nThe orange lines in Fig. 12 show the effects of the change from a fixed O2 mole fraction to the variable one. For XCO2\nvalues around 400 ppm, the change is generally small in all three CO2 products. If CO2 mixing ratios continue to increase in\n30\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nthe future, the difference between using the incorrectly fixed and correctly varying O2 mole fraction would increase to 0.75 to\n1 ppm in magnitude.\n630\n\nThe green lines in Fig. 12 show the combined effect of the CO2 calibration scale change and the switch to a variable O2\nmole fraction. For low “raw” XCO2 values (i.e. values without the in situ bias correction and using a fixed O2 mole fraction)\nthe two effects reinforce each other, but as the raw XCO2 increases, the O2 mole fraction change starts to counteract part of the\nCO2 scale change.\nXCO2 , XwCO2 , and XlCO2 on the X2019 scale and accounting for the variable O2 mole fraction are now available in the pub-\n\n635\n\nlic data set as variables xco2_x2019, xwco2_experimental_x2019, and xlco2_experimental_x2019. Users\ncomparing to other data or model simulations/assimilations on the X2019 scale should use these variables. Anyone needing\nto compare against data still on the X2007 scale can use xco2, xwco2_experimental, and xlco2_experimental\ninstead.\n7.3.3\n\n640\n\nN2 O in situ comparisons\n\nTo derive an in situ correction for N2 O, we adopted a different approach than the other gases due to the small number of\nN2 O profiles over TCCON sites which our matching algorithm found in the NOAA CCGG Aircraft Program v1.0 ObsPack\n(Sweeney et al., 2018). Figure 14a shows the 10 profiles identified from the ObsPack, and Fig. 14b shows the TCCON/in situ\nratio vs. Xluft relationship for these profiles. We note that this scarcity of profiles was partly due to the criteria used to filter\nfor good quality profiles (Appendix C1.1). However, given how well-mixed N2 O is in the troposphere, the criteria intended to\n\n645\n\nensure a profile had enough vertical resolution to capture plumes of CO2 or CH4 could be relaxed for N2 O in future TCCON/in\nsitu comparisons to increase the number of available N2 O profiles for comparison.\nThe available profiles were further restricted by our criteria for coincidence with good quality TCCON observations. 2 of\nthese 10 profiles do not meet the coincidence criteria for inclusion in Fig. 14b, and 5 of the remaining 8 fall outside the allowed\nXluft range of 0.996 to 1.002. With the available data, it is difficult to distinguish whether there is significant correlation\n\n650\n\nbetween Xluft and TCCON XN2 O bias, and therefore whether those 5 comparisons below Xluft = 0.996 should be excluded.\nAs their exclusion would significantly alter the in situ correction for XN2 O , we tested a second approach to derive the N2 O\ncorrection.\nThis alternate approach uses NOAA surface N2 O data from the NOAA Halocarbons and other Atmospheric Trace Species\n(HATS) program (Dutton et al., 2023) combined with the GGG2020 priors to generate pseudo-in situ profiles. This takes\n\n655\n\nadvantage of the limited vertical variation in N2 O up to the tropopause seen in Fig. 14a and the good accuracy of the GGG2020\npriors in the stratosphere (Laughner et al., 2023). These pseudo-in situ profiles use the HATS N2 O data for the tropospheric\nVMRs, the GGG2020 priors for VMRs above 380 K potential temperature, and linearly interpolates in between. These pseudoin situ profiles are then integrated following Eq. (8) to produce a pseudo-in situ XN2 O and compared to TCCON in the same\nmanner as the other gases. As we are not limited by when an aircraft provided an N2 O profile over a TCCON site, we can\n\n660\n\ncompare to TCCON observations from any time. We use spectra from the same sites and days as the other gases, filtered for\nthe following criteria:\n31\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(a)\n\n(b)\nTCCON XN2O / in situ XN2O\n\nPressure (hPa)\n\n200\n400\n600\n\nEast Trout Lake\nLauder 02\nLamont\nTroposphere\nAbove tropopause\n1000\n270 280 290 300 310 320 330\nN2O DMF (ppb)\n800\n\n(c)\nTCCON XN2O / in situ XN2O\n\n1.02\n1.01\n\nEast Trout Lake\n\nLauder 02\n\n0.990\n0.985\n0.980\n0.975\nr = 0.98250\n0.970 2 r = 0.00750\n0.986\n\n0.988\n\n0.990\n\n0.992 0.994\nXluft (mol/mol)\n\n0.996\n\n0.998\n\n1.000\n\ny = (0.782 +/- 0.0023) + (0.000646 +/- 7.53e-06)x\nFit = 0.98216 at x = 310.000\n\n1.00\n0.99\n0.98\n0.97\n0.96\n0.95\n\nLamont\n\n0.995\n\nr = 0.97905\n2 r = 0.00024\n285\n\n290\n\n295\n\n300\n\n700\n\n(K)\n\n305\n\n310\n\n315\n\nAscension Island\nAnmyeondo\nBremen\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nLauder 01\n\nLauder 02\nManaus\nNicosia\nLamont\nOrleans\nPark Falls\nRikubetsu\nSodankyla\nWollongong\n\n320\n\nFigure 14. (a) The available N2 O profiles over TCCON sites from the NOAA CCGG Aircraft Program v1.0 ObsPack (Sweeney et al., 2018).\n(b) TCCON/in situ ratio vs. Xluft similar to Fig. 11, but for N2 O. (c) The TCCON/in situ XN2 O ratio derived using surface NOAA N2 O\ndata versus mid-tropospheric potential temperature. The dashed gray line is a robust fit to the data. The text in the lower right hand corner\ngives the mean TCCON/in situ ratio (denoted also by the horizontal dashed black line) and its 2σ standard deviation. The points are colored\nby TCCON site.\n\n– FVSI ≤ 0.05, as for the other gases\n– Xluft between 0.996 and 1.002, as for the other gases\n– The difference between prior HF column density and retrieved HF column density is < 2 × 1014 molec. cm−2 .\n665\n\nThe filtering on HF column helps to remove cases where the stratosphere prior N2 O used in the pseudo-in situ profiles is\nincorrect. HF is a gas found almost exclusively in the stratosphere, and in GGG2020, the HF and N2 O stratospheric priors\nare coupled. Thus, when the retrieved HF column is substantially different from the prior, that indicates that the HF prior was\nincorrect, which implies the same for the N2 O profile. HF columns tend to be between 1 and 2×1015 molec. cm−2 , so 2×1014\nmolec. cm−2 represents a 10% to 20% error in the HF prior. Given that the stratosphere component of N2 O is < 20% of the\n\n670\n\ncolumn, and assuming that the percent error in the N2 O prior is similar, this keeps the random error in the pseudo-in situ XN2 O\nto less that 2% to 4%. All together, these filtering criteria retain approximately 8600 TCCON observations from the initial set\nof ∼ 20, 000 observations used in the in situ correction analysis.\n\nThis larger sample set for N2 O allowed us to identify a correlation in XN2 O bias with atmospheric temperature. Figure 14c\n\nshows how the TCCON/in situ XN2 O ratio varies with potential temperature at 700 hPa. As in the ADCF analysis (§7.1), these\n675\n\npotential temperature values come from the GEOS FP-IT meteorology used as input to the GGG retrievals. The presence of\nthis bias suggests that there is an error in the temperature dependence of the N2 O cross sections (similar to that we identified\n32\n\n\fTCCON / in situ XN2O\n\nhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1.04 (a)\n1.02\n\nGGG2020 fit: y = 0.00066x + 0.79616\nGGG2020.1 fit: y = 0.00000x + 0.99985\n\n1.00\n0.98\n290\n\n300\n700\n\n(K)\n\n310\n\n320\n\n1.02 (b)\nGGG2020\nNotional GGG2020.1\nEast Trout Lake\nLauder 02\nLamont\nRatio = 1\n\n1.01\n1.00\n\n330\n\n285 290 295 300 305 310 315\n700 (K)\n\n(c)\n\n102\n# observations\n\nNotional GGG2020.1 XN2O (ppb)\n\n0.99\n\n320\n\n101\n\n310\n300\n300\n\n310\n320\nGGG2020 XN2O (ppb)\n\n330\n\n100\n\nFigure 15. Future correction for XN2 O . (a) Similar to Fig. 14c, except showing the ratio between TCCON and the surface-derived XN2 O\nfrom GGG2020 with the in situ correction factor of 0.9821 applied in blue, and the expected temperature-corrected XN2 O in orange, with\ntheir respective fits. (b) Similar to Fig. 14b, but like panel (a) of this figure, comparing the ratios of GGG2020 and temperature-corrected\nXN2 O to in situ. (c) A 2D histogram comparing the current and notional corrected XN2 O\n\nand removed for O2 , §3.3). In the near term, we plan to develop a post-processing correction for this temperature bias in\nN2 O for inclusion in a minor update to the TCCON GGG2020 data within 2–3 years. Long term, the underlying error in the\nspectroscopic model will be corrected so that the next major TCCON data release will have improved XN2 O data.\n680\n\nFor GGG2020, we elected to choose the XN2 O in situ correction as the value of the fit in Fig. 14c at 310 K potential\ntemperature. This is consistent with the choice of ADCF values at the same temperature (§7.1). The value of 0.9822 is very\nclose to the mean TCCON/in situ ratio using the 8 true in situ profiles in Fig. 14b. That both methods agree gives us confidence\nthat this is a reasonable value to use for the in situ correction. We are also investigating applying the slope from Fig. 14c to\nTCCON XN2 O as a temperature-based bias correction. Figure 15 demonstrates the difference this correction would make, both\n\n685\n\nin comparison to the in situ data (Fig. 15a,b) and to the column-average dry mole fractions themsleves (Fig. 15c).\n\n33\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nXgas product\n\nCorrection factor\n\nCF error\n\nCalibration scale\n\nN\n\nfO2\n\nXCO2\n\n1.0101\n\n0.0005\n\nWMO X2007\n\n67\n\nFixed\n\nXCO2 _x2019\n\n1.0090\n\n0.0005\n\nWMO X2019\n\n70\n\nVar.\n\nXwCO2\n\n1.0008\n\n0.0005\n\nWMO X2007\n\n67\n\nFixed\n\nXwCO2 _x2019\n\n0.9996\n\n0.0005\n\nWMO X2019\n\n69\n\nVar.\n\nXlCO2\n\n1.0014\n\n0.0007\n\nWMO X2007\n\n67\n\nFixed\n\nXlCO2 _x2019\n\n1.0006\n\n0.0007\n\nWMO X2019\n\n69\n\nVar.\n\nXCH4\n\n1.0031\n\n0.0014\n\nWMO X2004\n\n40\n\nFixed\n\nXN2 O\n\n0.9821\n\n0.0098\n\nNOAA 2006A\n\nN/A\n\nFixed\n\nXCO\n\n1.000\n\n0.0526\n\nN/A\n\n31\n\nFixed\n\nXH2 O\n\n0.9883\n\n0.0157\n\nARM Radiosondes\n\n94\n\nFixed\n\nTable 2. In situ correction factors and their errors for each Xgas product evaluated against in situ data. The “Calibration scale” column\nindicates which scale or source these data are tied to by the AICFs. The N column indicates how many profiles are used to calculate the\nAICF for that gas. The fO2 column indicates what O2 mole fraction was used in the column density to column-average mole fraction\nconversion: “Fixed” means fO2 = 0.2095 in Eq. (1) and “Var.” means that the variable mole fraction described in §7.3.2 was used.\n\n7.3.4\n\nIn situ bias correction summary\n\nA summary of the in situ correction factors, their errors, and what in situ calibration scales each product is tied to are given\nin Table 2. Because these correction factors are the mean TCCON/in situ ratio, dividing the airmass-corrected and windowaveraged values by these correction factors removes the mean TCCON-in situ bias.\n690\n\nIn the TCCON data, users will find two sets of XCO2 variables. Those with the _x2019 suffix (xwco2_experimental_x2019,\nxlco2_experimental_x2019, and xco2_x2019) are those tied to the WMO X2019 CO2 scale and which use the variable O2 mole fraction. Those CO2 variables without the _x2019 suffix remain tied to the WMO X2007 CO2 scale and still\nuse the fixed O2 mole fraction. All other gases (xch4, xco, etc.) also still use the fixed O2 mole fraction.\nReleasing the rescaled XCO2 as new variables, rather than creating a new TCCON data version with the existing variables\n\n695\n\nrescaled, was chosen for several reasons. First, it is logistically simpler, allowing us to provide this update more quickly.\nSecond, during this transitional period when existing CO2 data is available on both the X2007 and X2019 scales, having\nboth X2007 and X2019 XCO2 allows users to switch back and forth easily if they need to match up with other datasets on\na mix of both scales. Third, this approach provides for release of more recent TCCON data without disrupting existing users\nworkflows—users do not have to worry about existing variables changing, but can switch their analyses to use the updated\n\n700\n\nXCO2 variables if and when they wish. Incorporating the variable O2 mole fraction for all gases is planned for an upcoming\nminor revision of the TCCON data (tentatively called “GGG2020.1”). Likewise, a temperature-corrected XN2 O product will\nbe included in GGG2020.1 or the follow on GGG2020.2, depending on development time.\n\n34\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n6000\n\n90\n\n40\n\n80\n\n30\n\n5000\n\n-20\n\n20\n\n60\n10\n50\n\n3000\n40\n2000\n\nSZA ( °)\n\nX H O (ppm)\n2\n\n-10\n\n°C)\n\n4000\n\nSurface temperature (\n\n70\n\n0\n\n30\n20\n\n1000\n\n0\nJan Feb Mar Apr May Jun Jul Aug\n\n10\n\n-30\n\n0\n\n-40\n\n2019\nFigure 16. The three dates chosen for the error budget calculations are from East Trout Lake on February 18 (blue), June 11 (red), and July\n23 (yellow), 2019. These dates were chosen to span a range of water vapor, solar zenith angle, and surface temperature. In the left panel, the\nblack data points show the full East Trout Lake record between Jan and Aug 2019 for reference.\n\n8 Uncertainty budget\nTo calculate an uncertainty in the GGG2020 dataset, we selected three days from the East Trout Lake dataset spanning a\n705\n\nrange of atmospheric water vapor, surface temperature and solar zenith angle (Figure 16). Each known source of uncertainty is\nmodeled or perturbed by a realistic amount in the GFIT forward model (the quantitative amounts are described in the following\nparagraphs), and we compute the percent fractional difference in Xgas between the perturbed and unperturbed value. The total\nuncertainty is computed as the sum in quadrature of the individual uncertainties. For each gas, we have plotted the contributions\nof each source as a function of solar zenith angle for the June 11, 2019 date in Figures 18–20. The same figures for cold, dry\n\n710\n\nFebruary 18 are in the Appendix in Figures B1–B3, and for warm, wet July 23 are in Figures B4–B6. The sum in quadrature\nof all the sources of error for each gas are plotted for the three days together in Figures 21–23. Each source of uncertainty\nincluded in our error budget is described below.\nField of view\nThe field of view (FOV) is the maximum solid angle viewed by the detector element, and its value is set by the field stop\n\n715\n\ndiameter inside the instrument. It is an important parameter in the GFIT forward model because it defines the extent of off-axis\nrays that pass through the interferometer, ultimately limiting the spectral resolution of a spectrum. The field stop diameter is\n\n35\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nset by a physical pinhole ranging from 0.5-1.3 mm drilled into a thin plate within the instrument, and its size can be in error by\na few percent. Here, we increase FOV by 7% to reflect any uncertainty in the field stop diameter.\nContinuum basis functions\n720\n\nIn GGG2020, the number of continuum basis functions has been optimized to improve the spectral fits without over fitting the\ndata (see §6). Here, we increase the number of continuum basis functions fitted by 1 in all windows that have widths >5 cm−1\nto assess the sensitivity of our choice of the number of basis functions to the retrieved Xgas value. The gases excluded from\nthis test because of their fitting window widths are HF, HCl, and some H2 O and HDO windows.\nSolar pointing\n\n725\n\nThe observer-sun Doppler stretch (OSDS) is a calculation made by GFIT based on the Earth-Sun radial velocity and the\nEarth’s rotational velocity component, under the assumption that the solar tracker is imaging the centre of the Sun. It defines\nthe Doppler stretch of the solar absorption lines relative to the telluric (atmospheric) absorption lines. If the solar tracker is not\nimaging the exact centre of the Sun, the solar lines may be Doppler-shifted relative to the telluric lines, creating systematic\nresiduals in the spectral fits. Here we increase the OSDS by 2 ppm to assess the sensitivity of the retrievals to a small pointing\n\n730\n\nerror from the Doppler stretch component alone. This error affects carbon monoxide more than the other gases because for\nevery telluric CO line in the spectrum, there is also a solar CO absorption line beneath, making it difficult to distinguish solar\nfrom telluric CO absorption. In GGG2014 and previous versions, this was a particular problem, because the pointing was\nassumed to be in the centre of the solar disk. In GGG2020, however, the solar-gas stretches are now fitted, reducing the impact\nof an OSDS error on the CO retrievals (see Wunch et al., 2015, Fig. 13).\n\n735\n\nSolar tracker pointing offsets also affect the ray tracing in GFIT, causing errors in the airmasses calculated for a given\nspectrum. This error impacts all gas retrievals, but should mostly cancel in the ratio between the gas of interest and oxygen.\nHere, we add a 0.05 degree pointing offset (poff), which represents a pointing error of about 20% of the solar radius.\nPrior\nWe modify the priors in several ways to estimate the uncertainties caused by various errors in the a priori profiles.\n\n740\n\n– A priori pressure profile (prior pressure). We multiplied the pressure at each atmospheric level in the prior by 1.002 to\nscale up the pressure by 0.2% at all altitudes. For the HCl cell pressure error, we added 0.14 hPa (0.138 atm) to the cell\npressure, following the “pessimistic” uncertainty budget in Hase et al. (2013, P3565). (The purpose of the HCl cells will\nbe described in §8.10.)\n– A priori temperature profile (prior temperature). We added 1 K to each atmospheric level in the prior.\n\n745\n\n– A priori profile shape (prior shift). We shifted the a priori profiles down by one atmospheric level. In GGG2014, we\nshifted the priors down by 1 km, so this is a slightly different approach, but the level spacing is about 1 km in altitude\nnear the tropopause, where this shift is most important for well-mixed tropospheric gases like N2 O and CH4 , and HF, a\nstratospheric gas. H2 O and HDO are not shifted as part of this process, but are modified in an independent test.\n\n36\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– A priori boundary layer CO (prior CO enhanced). The GEOS FP-IT CO profiles are created using an old emission\ninventory, and tend to significantly overestimate emissions in urban regions that have reduced their emissions over time\n\n750\n\n(e.g., Los Angeles). However, because of the coarse spatial resolution of GEOS FP-IT, sites that are located near to an\nurban centre can be affected by the urban enhancements in the model. We therefore add an additional test that affects\nonly the CO error budget, in which we add 25 ppb to the altitudes below 2 km to estimate the uncertainty caused by the\nincorrect lower atmosphere shape in the GGG2020 CO prior profiles.\n755\n\n– A priori H2 O and HDO (prior h2o/hdo). We modified the water and HDO profiles by reducing the values in the first\n1 km by 50%.\nSurface pressure\nThe surface pressure measurements we collect as part of our on-site meteorological data are important for calculating the total\ncolumn of air overhead. The largest surface pressure uncertainty permitted by the TCCON data protocol is 0.3 hPa, but we\n\n760\n\nhave seen these instruments drift by up to 1 hPa. Here, we add 1 hPa to the surface pressure (pout) to calculate the sensitivity\nof the retrievals to this error.\nNonlinearity\nDetector nonlinearities, described in §5.1, cause a discrepancy between the low-resolution spectral envelope and the high\nresolution spectral lines, resulting in an offset at zero in the spectrum. These zero level offsets are most readily observed in\n\n765\n\nregions of the spectrum where strong absorption lines absorb all the incident light (Abrams et al., 1994). Here, we add 0.001\n(0.1%) to the zero level offset (ZLO) parameter in GFIT, a large ZLO observed in the network.\nInstrument line shape\nThe instrument line shape (ILS) of a Fourier transform spectrometer quantifies the optical alignment of the instrument, and is\nindependent of the alignment of the solar image. The ILS is characterized by two parameters: the modulation efficiency and\n\n770\n\nphase error. The modulation efficiency is the broadening or narrowing of the ideal spectral line width in the instrument, and the\nphase error is the asymmetrical component of the spectral line that is caused by the misalignment. It is not currently possible\nto model phase error within GFIT, but we can model imperfect modulation efficiency. The TCCON data protocol requires that\nthe instrument modulation efficiencies must be within 5% of a perfect alignment. The modulation efficiency of a perfectly\naligned interferometer is defined as a value of 1.0 at all optical path differences, taking self-apodization into account, and\n\n775\n\ntherefore the maximum and minimum modulation efficiency acceptable in the network is 1.05 and 0.95, respectively. Here we\nmodel two cases: a “shear” misalignment, where the modulation efficiency of the spectrometer increases linearly to 1.05 as a\nfunction of optical path difference, and an “angular” misalignment, where the modulation efficiency drops linearly to 0.95 as a\nfunction of optical path difference. We confirmed the misalignment by passing synthetic spectra generated by GFIT with these\nmisalignments through LINEFIT (v14.8 Hase et al., 1999), a program designed to assess instrument line shapes (see Figure\n\n780\n\n17).\nBecause GGG2020 cannot model phase errors, these sensitivity studies are likely to underestimate the full effect of ILS\nerrors, and therefore we include both the “shear” and “angular” misalignment in the sum.\n37\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure 17. Synthetic spectra were generated using GFIT to simulate shear and angular misalignment with 5% change from the ideal line\nshape at a maximum optical path difference of 45 cm. These spectra were then passed through LINEFIT 14.8 to confirm that the modulation\nefficiency and phase errors were as expected.\n\n8.1\n\nGeneral comments on the results\n\nThe results of this error budget analysis only account for changes using a single instrument, and therefore cannot assess\n785\n\nimprovements to GGG2020 that affect inter-instrument precision, such as consistent continuum fitting across the network,\nchannel fringe fitting when needed, a priori shape improvements, and so on. Site-to-site variability have been assessed in\nsections §7.1–§7.3. The results in this section quantify the errors incurred by uncertainties in a single instrument setup.\nThe method of simulating modulation efficiency errors in GGG2014 (Wunch et al., 2015) was incorrect, resulting in an\ninferred uncertainty from ILS errors that is too large, likely by about a factor of 2 (see Appendix B1 for details). The change\n\n790\n\nfrom the errant ILS modeling to our current model, on its own, will produce an apparent overall uncertainty reduction for\nGGG2020 when compared with GGG2014, but there have been no improvements in GGG2020 with respect to fitting imperfect\nILS. However, there are several other improvements in GGG2020 that have resulted in systematic reductions in the uncertainty,\nincluding higher order continuum fitting (§6), solar-gas stretch fitting (§8), and gas-specific spectroscopy (§3.1) and line shape\nfitting improvements (§3.2).\n\n795\n\nIn GGG2014, our retrievals were performed on a 1 km grid, and we shifted the profiles down by 1 level (or 1 km at all\naltitudes). In GGG2020, our retrievals are on a grid that increases in spacing with altitude, and a shift down by 1 level is\n\n38\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190611\n\nxluft - 20190611\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190611\n\nxch4 - 20190611\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 18. June 11, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. “Sum” in the legend means the quadrature sum of the other terms. The retrievals\nplotted here are Xluft , XCO2 , XCH4 , and XCO .\n\n39\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190611\n\nxhdo - 20190611\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190611\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190611\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 19. As in Figure 18, but for XH2 O , XHDO , XN2 O , and XHF .\n\nroughly 1 km at the tropopause, but smaller below and larger above. This change is most likely to affect the retrievals of gases\nfor which there is a rapid change in abundance near the tropopause and above: N2 O, CH4 , and HF. Therefore, our shift for the\nGGG2020 error budget represents a larger perturbation to the a prior shape for these gases, which will cause larger errors in\n800\n\nretrievals. However, because HF is a species found primarily in the stratosphere, and N2 O and CH4 are species found primarily\nin the troposphere, retrievals of HF can be used to diagnose and reduce the impact of the profile shift errors on XN2 O and XCH4\n(e.g., Washenfelder et al., 2003; Saad et al., 2014, 2016; Wang et al., 2014).\nIn each section below, we will discuss the results for each gas, keeping in mind the reductions in error from the ILS model,\nand the inflation of error from the prior shifts.\n\n40\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190611\n\nxlco2 - 20190611\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190611\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 20. As in Figure 18, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n805\n\n8.2\n\nXluft\n\nXluft is the column-averaged amount of dry air, and is equivalent to the parameter Xair in GGG2014. The error budget for\nXluft (Figures 18 and 21) is very similar to that of Xair in GGG2014, with uncertainties smaller than 0.7% for all solar zenith\nangles less than 82◦ . The error is dominated by pointing offsets at large solar zenith angles, and zero level offsets contribute\nsignificantly to the error at all solar zenith angles.\n810\n\n8.3\n\nXCO2\n\nThe XCO2 error budget is smaller than for GGG2014 (Wunch et al., 2015), mostly from the reduced continuum fitting errors.\nThe GGG2020 errors are below 0.16% (∼0.6 ppm) for solar zenith angles less than 82◦ , though if extrapolated linearly to\n41\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nsmaller solar zenith angles, the error could become larger than 0.15% at 0 degrees (Figures 18 and 21). The largest sources\nof error at lower solar zenith angles are from prior pressure offsets and misalignment. At larger solar zenith angles, the error\n815\n\nbecomes dominated by prior temperature errors and zero level offsets.\n8.4\n\nXCH4\n\nThe XCH4 error budget is smaller than for GGG2014 (Wunch et al., 2015). There is a significant reduction in the errors\nassociated with observer-sun Doppler stretch (OSDS) offsets and continuum fitting errors. The GGG2020 errors are below\n0.4% (∼7 ppb) for solar zenith angles less than 82◦ (Figures 18 and 21). The largest sources of error at lower solar zenith\n820\n\nangles are from prior profile shifts and prior pressure errors. At larger solar zenith angles, the error is dominated by prior\nprofile shifts. Errors caused by profile shifts can be mitigated by extracting the tropospheric partial column of XCH4 using the\nSaad et al. (2014) or Wang et al. (2014) methods.\n8.5\n\nXCO\n\nThe XCO spectral fitting has been substantially improved in GGG2020, largely because of our reduced sensitivity to errors in\n825\n\nthe observer-sun Doppler stretch (OSDS), and also because we removed one of the fitted windows from our standard analysis\nin GGG2020 that had relatively poorer spectral fits. The GGG2020 errors are below 2% (∼ 2 ppb assuming a 100 ppb column)\nfor all SZA < 82◦ . The largest sources of error are the prior CO enhancement, the prior shift, prior temperature, and shear\nmisalignment (Figures 18 and 21).\n8.6\n\n830\n\nXH2 O and XHDO\n\nThe error budget for water and HDO is roughly the same as for GGG2014 and earlier, with total errors under 2% in XH2 O and\n3% in XHDO over all solar zenith angles less than 82◦ . The largest component of the error budget for water vapor and HDO is\nthe shape of the a priori profile, which dominates the error budget for all solar zenith angles below 75◦ for water, and over all\nsolar zenith angles below 82◦ for HDO (Figures 19 and 22).\n8.7\n\n835\n\nXN2 O\n\nThe XN2 O error budget is roughly the same as in GGG2014, with total errors less than 1.25% (∼4 ppb) over all solar zenith\nangles. The largest source of error is the prior shift, which is not surprising, given the rapid chemical destruction of N2 O above\nthe tropopause, though the magnitude of the error is about twice as large as it was for GGG2014. As discussed above, this\nis likely caused by differences in the way we shift the profile, and could be mitigated by extracting the tropospheric partial\ncolumn by adapting the Saad et al. (2014) approach. Other contributors to the total error include the prior pressure, and shear\n\n840\n\nand angular misalignments (Figures 19 and 22).\n\n42\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n8.8\n\nXHF\n\nHF has only a single absorption line (4038.96 cm−1 ) that is located on the wing of a strong water absorption feature, so the\nretrievals tend to be noisy, especially at high solar zenith angles and under wet conditions. The XHF error budget has reduced\nin GGG2020 compared with GGG2014, with total errors now less than 5% over all solar zenith angles. In GGG2014, the errors\n845\n\nwere typically below 8%, but that error was dominated by the much larger shear misalignment. The largest source of error in\nGGG2020 is the prior shift, followed closely by shear misalignment (Figures 19 and 22).\n8.9\n\nXlCO2 and XwCO2\n\nIn GGG2014 and previous versions, we did not retrieve strong (“lCO2 ”) and weak (“wCO2 ”) CO2 bands. The strong CO2\nretrieval errors are dominated by prior temperature errors, and the weak CO2 errors are dominated by both shear and angular\n850\n\nmisalignments, errors in the prior pressure, adjustments to the continuum curvature, and zero level offsets (Figures 20 and 23).\nThe strong lCO2 retrieval errors are less than 0.3% over all solar zenith angles, and the weak wCO2 retrievals have around\n0.5% errors at all solar zenith angles, declining slightly at higher angles.\n8.10\n\nVSF HCl\n\nIn this error budget, we have included the scale factors retrieved for HCl (vsf_hcl in Figs. 20 and 23). In the East Trout Lake\n855\n\ninstrument and most others in the network, a sealed HCl cell filled with a known quantity of gas (Hase et al., 2013) is placed\npermanently in the solar beam inside the evacuated spectrometer to monitor long-term changes in ILS. Because the quantity\nof gas in the cell is significantly larger than the atmospheric abundance, the atmospheric component is negligible and largely\nindependent of surface pressure or other atmospheric adjustments. To assess the HCl retrieval sensitivity to changes in ILS and\nother parameters, we include the HCl scale factors in our error budget.\n\n860\n\nThe retrieval errors in the scaling factors retrieved for HCl in a sealed cell are dominated by errors in the instrument line\nshape with no significant solar zenith angle dependence. This is a comforting result, showing that our HCl retrievals are a good\ndiagnostic for instrument line shape drift. The HCl retrievals are not included in the standard public data files as they are used\nprimarily for diagnostic purposes.\n8.11\n\n865\n\nUncertainty estimate comparison\n\nFor six products (XCO2 , XwCO2 , XlCO2 , XCH4 , XCO , and XH2 O ) we can compare the uncertainty estimates derived from the\nerror budgets with those computed from in situ comparisons similar to those in §7.3 but with one difference: the comparisons\nin §7.3 use the in situ vertical profiles as the prior trace gas profiles in the TCCON retrievals; the in situ comparisons in this\nsection use standard TCCON GGG2020 prior profiles. For the in situ uncertainty, we use the median absolute deviation of the\nTCCON Xgas values from the in situ Xgas values after removing the mean bias for each Xgas (i.e. the correction factor in\n\n870\n\nTable 2). To convert the percent error from the error budget into a column-average mole fraction, we use the mean total percent\nerror across all three days used in the error budget (18 Feb, 11 June, and 23 July 2019) binned by SZA in 5° increments. We\n43\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2\n\nxluft\n0.16\n\n0.7\n20190218\n20190611\n20190723\n\n0.65\n\n20190218\n20190611\n20190723\n\n0.15\n\n0.6\n\n0.14\n\n0.55\n\n%\n\n%\n\n0.5\n\n0.13\n\n0.45\n\n0.12\n\n0.4\n0.35\n\n0.11\n0.3\n\n0.1\n\n0.25\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxco\n\nxch4\n\n2\n\n0.34\n20190218\n20190611\n20190723\n\n0.32\n\n10\n\n°)\n\n20190218\n20190611\n20190723\n\n1.9\n\n0.3\n\n1.8\n\n0.28\n\n1.7\n\n0.26\n\n%\n\n%\n\n1.6\n0.24\n\n1.5\n0.22\n\n1.4\n0.2\n\n1.3\n\n0.18\n\n1.2\n\n0.16\n\n1.1\n\n0.14\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 21. These figures show the sum in quadrature of all the errors plotted in Figure 18 for all three dates. The errors plotted here are for\nXluft , XCO2 , XCH4 , and XCO .\n\n44\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o\n\nxhdo\n\n1.8\n\n3\n20190218\n20190611\n20190723\n\n1.6\n\n20190218\n20190611\n20190723\n\n2.8\n2.6\n\n1.4\n2.4\n2.2\n\n%\n\n%\n\n1.2\n1\n\n2\n1.8\n\n0.8\n\n1.6\n0.6\n1.4\n0.4\n\n1.2\n\n0.2\n\n1\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\nxn2o\n1.2\n20190218\n20190611\n20190723\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf\n\n4.4\n\n1.15\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n20190218\n20190611\n20190723\n\n4.2\n4\n\n1.1\n3.8\n3.6\n\n1\n\n%\n\n%\n\n1.05\n\n3.4\n3.2\n\n0.95\n\n3\n\n0.9\n2.8\n\n0.85\n\n2.6\n\n0.8\n\n2.4\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 22. As in Figure 21, but for XH2 O , XHDO , XN2 O , and XHF . XHF values above 68° SZA are not available on 2019-07-23 because\nthe HF lines were blacked out by H2 O absorbance.\n\n45\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2\n\nxlco2\n0.48\n\n0.3\n20190218\n20190611\n20190723\n\n0.28\n\n20190218\n20190611\n20190723\n\n0.47\n0.46\n\n0.26\n\n0.45\n0.44\n\n%\n\n%\n\n0.24\n0.22\n\n0.43\n0.42\n\n0.2\n\n0.41\n0.18\n\n0.4\n0.16\n\n0.39\n0.38\n\n0.14\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl\n2.77\n20190218\n20190611\n20190723\n\n2.76\n2.75\n2.74\n\n%\n\n2.73\n2.72\n2.71\n2.7\n2.69\n2.68\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 23. As in Figure 21, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n\ninterpolate this to the mean SZA of all spectra used in the in situ comparison for that gas and multiply this interpolated mean\npercentage by the mean TCCON Xgas value across all the in situ comparisons. The results are presented in Table 3.\nIt is important to acknowledge that the error amounts calculated from the in situ comparison are (for most gases) conserva875\n\ntive, for several reasons. First, in situ profiles are usually taken when the target TCCON station is near optimal performance, so\nthose comparisons are unlikely to capture the full range of error sources. Second, the in situ profiles are heavily concentrated\nover certain TCCON sites, also limiting how representative they are. Finally, the TCCON Xgas values compared against the\nin situ values are averaged over a minimum of 2 hours. This will reduce sources of random error. However, we believe this\nis still a worthwhile evaluation of measurement accuracy because (a) there is real physical variation in the atmosphere during\n\n880\n\nthe in situ profile, and the time averaging is necessary to account for that and (b) many of the factors considered in the error\n\n46\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nGas\n\nSZA\n\nMean abs. dev.\n\nError budget\n\n\u000fin situ\n\n\u000fmeas\n\n\u000fFT\n\n\u000fstrat\n\nXCO2\n\n46°\n\n0.42 ppm\n\n0.47 ppm\n\n0.053 (0.30) ppm\n\n0.033 (0.16) ppm\n\n0.032 (0.12) ppm\n\n0.061 (0.072) ppm\n\nXwCO2\n\n46°\n\n0.43 ppm\n\n1.8 ppm\n\n0.062 (0.36) ppm\n\n0.037 (0.16) ppm\n\n0.038 (0.15) ppm\n\n0.075 (0.10) ppm\n\nXlCO2\n\n46°\n\n0.75 ppm\n\n0.66 ppm\n\n0.038 (0.24) ppm\n\n0.025 (0.14) ppm\n\n0.020 (0.067) ppm\n\n0.057 (0.060) ppm\n\nXCH4\n\n46°\n\n4.9 ppb\n\n3.9 ppb\n\n2.0 (9.6) ppb\n\n0.65 (3.1) ppb\n\n0.19 (0.49) ppb\n\n3.4 (6.3) ppb\n\nXCO\n\n43°\n\n8.1 ppb\n\n1.7 ppb\n\n2.8 (14.0) ppb\n\n1.9 (9.3) ppb\n\n0.13 (0.39) ppb\n\n0.24 (4.8) ppb\n\nXH2 O\n\n52°\n\n140 ppm\n\n33 ppm\n\n100 (950) ppm\n\n100 (950) ppm\n\n0 (0) ppm\n\n0 (0) ppm\n\nTable 3. A comparison of typical errors calculated from the differences between TCCON and in situ Xgas values (“Mean abs. dev.” in the\ntable) and errors calculated from the error budget (“Error budget” in the table). The text gives details on how each error metric was computed.\n“SZA” gives the solar zenith angle for which the error budget percent was taken to calculate the “Error budget” column. The remaining four\ncolumns give the total 2σ uncertainty on the in situ data (\u000fin situ ), followed by the 2σ uncertainty components coming from the in situ measurement itself (\u000fmeas ), the unmeasured free troposphere (\u000fFT ), and the unmeasured stratosphere (\u000fstrat ). The last two components are 0 for\nXH2 O because the radiosonde measurements used always cover the free troposphere, and we assume that error in the meteorological model\nused to obtain the stratospheric H2 O profile is negligible. The parenthetical numbers give the mean value per TCCON/in situ comparison\nfor each uncertainty component; the non-parenthetical errors are smaller because they are calculated by formally propagating the error from\n√\nindividual comparisons to the mean absolute deviation, thus reducing by n. Appendix C6 describes how the uncertainty components from\nthe last 3 columns are calculated and combined to give \u000fin situ in the fifth column.\n\nbudget will not average out over the coincidence window. For example, angular or shear misalignment of the instrument would\nbe essentially constant over an entire day.\nFor three Xgas products (XCO2 , XlCO2 , and XCH4 ) the in situ and error budget estimates are similar, which gives us\nconfidence in the error budget estimates. For XwCO2 , the error budget estimate is much larger than the in situ error estimate.\n885\n\nIt may be that the error budget tested larger errors in the stratosphere temperature or VMR prior profile than were observed\nduring the in situ comparisons, as the XwCO2 product is more sensitive to the upper atmosphere than the other CO2 products\nin GGG2020. (Pressure errors could be another source of the overestimate, but the pressure perturbation test was designed to\navoid introducing an overly large perturbation to the stratosphere.) As we treat the in situ-derived errors as conservative, this\nsituation is acceptable, but will be investigated in the future.\n\n890\n\nBoth XCO and XH2 O had larger errors in comparison with in situ data than through the error budget. For XCO , the difference\nin error estimates is 6.4 ppb. Almost half of that is attributed to uncertainty in the in situ measurements. The uncertainty in\nindividual comparisons (the parenthetical numbers in Table 3) is quite a bit larger; if part of this error is systematic (such as\nfrom drift in calibration tanks, e.g., Andrews, 2019), that could explain the remaining difference. For XH2 O , this is because of\nuncertainty in the radiosondes used to compare against. The radiosondes used at ARM have a 4 or 5% uncertainty in relative\n\n895\n\nhumidity (https://www.arm.gov/publications/tech_reports/handbooks/sonde_handbook.pdf, last accessed 10 Apr 2023). When\nwe propagate this uncertainty to the mean absolute deviation, it works out to 103 ppm—very nearly the missing 110 ppm\nbetween the two error estimates.\n47\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n9\n\nMiscellaneous changes\n\n9.1\n900\n\nAK binning\n\nThe public GGG2020 TCCON files now include one averaging kernel (AK) per observation. This is a change from GGG2014,\nwhere the public files included a table of canonical AKs for a limited set of SZAs, and users were required to interpolate the\nAKs to the SZA of each spectrum. This was done in response to user requests to simplify the use of the averaging kernels. This\ndoes not mean that averaging kernels are computed by GGG for every TCCON observation (they are not). Internally, we still\nuse a table of precomputed AKs, which are interpolated as needed to provide per-spectrum AKs in the public files. This affords\n\n905\n\nsignificant saving in data storage, as the files GGG requires for AK calculation are very large.\nThough users of public TCCON data no longer need to know how the AK tables work, there are two changes from GGG2014\nthat we wish to document here.\nFirst, in GGG2020, the bin coordinate has changed from solar zenith angle (SZA) to “slant Xgas ,” which is defined as:\n\nSlant Xgas = airmass · Xgas\n910\n\n(11)\n\nwhere “airmass” is the airmass calculated by GGG in the O2 window and “Xgas ” is the column average mole fraction of\nthe gas of interest. Using slant Xgas as the bin coordinate correctly accounts for cases where the dynamic range of a gas’s\nconcentrations is large enough to change the AK at a single SZA. This can be seen in Fig. 24. For CO2 (Fig. 24a,b), the AKs\nvary smoothly and monotonically with either SZA or slant XCO2 . However, for H2 O, the AKs do not vary monotonically with\nSZA (Fig. 24c) but do with slant XH2 O (Fig. 24d). Therefore, slant Xgas was adopted as the binning coordinate for all AKs for\n\n915\n\nconsistency.\nSecond, in order to provide per-spectrum AKs in the public TCCON data files without significantly increasing the file size,\nit was necessary to ensure that observations with similar slant Xgas values had identical AKs so that the netCDF compression\nalgorithm could operate effectively. We achieved this by “quantizing” the slant Xgas values that we interpolated the AKs to;\nthat is, we select 500 slant Xgas values that cover the expected range of slant Xgas , plus 50 additional points to cover extreme\n\n920\n\nvalues. Each observation then uses the AK corresponding to the one of those 550 slant Xgas values closest to its true slant Xgas\nvalue. This scheme keeps the difference between the quantized and full resolution AKs to < 1% in 90% of observations while\nonly increasing file size by ∼ 20%.\n9.2\n\nA priori profiles and AK corrections\n\nAs described in §4.3, the a priori profiles reported in the published GGG2020 netCDF files are in wet mole fraction. When\n925\n\napplying an averaging kernel correction to calculate the Xgas value that would be retrieved by TCCON for an arbitrary gas\nprofile, that gas profile must be converted into wet mole fraction. This can be done using either the TCCON H2 O a priori\nprofile provided or an H2 O profile measured or modeled coincidentally with the gas profile for which an Xgas value is desired.\n\n48\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n90\n\n0.0\n\nlog10(XCO2 airmass)\n\n50\n\n2.8\n\nSZA\n\nPressure (atm)\n\n2.6\n\n60\n0.4\n\n40\n\n0.6\n\n3.0\n\n30\n\n0.8\n\n20\n\n3.2\n\n10\n\n1.0\n0.2\n\n0.4\n\n0.6 0.8 1.0\nCO2 Column AK\n\n1.2\n\n1.4\n\n0\n\n0.2\n\n90\n\n0.0\n\n0.4\n\n0.6 0.8 1.0\nCO2 Column AK\n\n1.2\n\n1.4\n\n(d)\n\n1.2\n\n80\n\n1.4\n\n70\n\n0.2\n\n1.6\n\n60\n0.4\n\n50\n\n1.8\n\n40\n\n2.0\n\n30\n\n2.2\n\nSZA\n\nPressure (atm)\n\n2.4\n\n70\n\n0.2\n\n(c)\n\n(b)\n\n80\n\nlog10(XH2O airmass)\n\n(a)\n\n0.6\n0.8\n\n20\n\n2.4\n\n10\n\n1.0\n0.2\n\n0.4\n\n0.6\n0.8\nH2O Column AK\n\n1.0\n\n1.2\n\n2.6\n\n0\n\n0.2\n\n0.4\n\n0.6\n0.8\nH2O Column AK\n\n1.0\n\n1.2\n\nFigure 24. CO2 and H2 O AKs from four days’ measurements at the TCCON site in Lamont, OK, USA. (a) CO2 AKs binned by SZA. (b)\nCO2 AKs binned by slant XCO2 . (c) H2 O AKs binned by SZA. (d) H2 O AKs binned by slant XH2 O .\n\nUsers who are unsure which is appropriate for their application are encouraged to reach out to the TCCON network chairs\n(listed at https://tccon-wiki.caltech.edu/Main/SteeringCommitteeMembership) for assistance.\n930\n\n9.3\n\nChanges to quality flags\n\nAs in GGG2014, a spectrum is flagged as being poor quality if any of the retrieved Xgas or Xgas error values, or ancillary\nvariables pertaining to instrument operation or local observation conditions are outside of expected ranges. Such spectra are\nnot included in the public data files. In GGG2020, spectra may also be flagged as poor quality and withheld if:\n– the staff at the TCCON site identify a hardware issue affecting that spectrum\n935\n\n– during pre-release data review, a time period containing that spectrum is identified as out-of-family for TCCON data.\nThe latter case focuses on a smoothed timeseries of Xluft and DIP. As shown in §7.3 and §8, deviation of Xluft from the\nnetwork median correlate with bias in the other Xgas products. (See §3.3 for a definition of Xluft .) Therefore, when a 500spectrum rolling median of Xluft falls consistently outside the nominal range of 0.995 to 1.003, that time period is rejected,\nas the Xgas products will likely have biases exceeding the expected TCCON accuracy. Likewise, DIP is a measure of detector\n\n940\n\nnonlinearity (§5.1), and testing has shown that increasing magnitude of DIP increases bias in XCO2 (Fig. 26). Thus, data where\nDIP consistently exceeds ±5 × 10−4 are removed in order to keep the XCO2 bias less than 0.25 ppm.\n49\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n104\n\n0.2\n\n0.4\n\n0.6 0.8 1.0 1.2\nXCO2 column AK (unitless)\n\n1.4\n\n104\n\n400\n\n103\n\n600\n800\n\n102\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXlCO2 column AK (unitless)\n\n104\n103\n\n400\n600\n\n102\n\n800\n0.0\n\n0.2\n\n0.4 0.6 0.8 1.0\nXHF column AK (unitless)\n\n1.2\n\n1.4\n\n104\n\n200\nSlant XN2O\n\nPressure (hPa)\n\n(g) 0\n400\n\n103\n\n600\n800\n1000\n\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25 2.50\nXN2O column AK (unitless)\n\nSlant XH2O\n\nPressure (hPa)\n\n400\n\n104\n\n600\n800\n1000\n\n0.2\n\n0.4 0.6 0.8 1.0 1.2\nXH2O column AK (unitless)\n\n1.4\n\nSlant XwCO2\n\n800\n0.5\n\n0.6\n\n0.7 0.8 0.9 1.0 1.1\nXCH4 column AK (unitless)\n\n1.2\n\n107\n\n400\n\n106\n\n600\n800\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXO2 column AK (unitless)\n\n105\n104\n\n200\n\n103\n\n400\n600\n\n102\n\n800\n0.6\n\n0.8\n\n1.0 1.2 1.4 1.6 1.8\nXCO column AK (unitless)\n\n101\n\n2.0\n\n105\n\n(j) 0\n200\n400\n\n104\n\n600\n800\n1000\n\n103\n\n103\n\n200\n\n1000\n\n102\n\n200\n\n104\n\n600\n\n(h) 0\n\n105\n\n(i) 0\n\n400\n\n1000\n\n101\n\nPressure (hPa)\n\n1000\n\n105\n\n(f) 0\nPressure (hPa)\n\n200\n\nSlant XHF\n\nPressure (hPa)\n\n(e) 0\n\n102\n\n200\n\n1000\n\nPressure (hPa)\n\n1000\n\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25\nXwCO2 column AK (unitless)\n\n(d) 0\nPressure (hPa)\n\n200\nSlant XlCO2\n\nPressure (hPa)\n\n(c) 0\n\n800\n1000\n\n102\n\n103\n\n600\n\nSlant XCH4\n\n800\n1000\n\n400\n\nSlant XO2\n\n600\n\n200\n\nSlant XCO\n\n103\n\nSlant XHDO\n\n400\n\n104\n\n(b) 0\nPressure (hPa)\n\n200\nSlant XCO2\n\nPressure (hPa)\n\n(a) 0\n\n1.0\n\n1.2\n1.4\n1.6\n1.8\nXHDO column AK (unitless)\n\n2.0\n\n103\n\nFigure 25. Precomputed column AKs for TCCON Xgas products: (a) XCO2 , (b) XwCO2 , (c) XlCO2 , (d) XCH4 , (e) XHF , (f) XO2 , (g)\nXN2 O , (h) XCO , (i) XH2 O , and (j) XHDO .\n\n50\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure 26. Detector nonlinearity can cause a bias in XCO2 . This figure shows an example of the difference between the XCO2 retrieved after\ncorrecting the nonlinearity and prior to the nonlinearity correction as a function of the DIP parameter, that is a proxy for nonlinearity. Prior\nto correction, the Indianapolis data had DIP values that were almost exclusively negative. To limit the XCO2 bias caused by nonlinearity to\nless than 0.25 ppm, the absolute value of the DIP must be smaller than 0.5×10−3 .\n\n10\n\nConclusions\n\nThe GGG2020 TCCON data product incorporate numerous improvements to the GGG retrieval, based both on first-principle\nunderstanding and empirical evaluation. To review:\n945\n\n– The interferogram-to-spectrum conversion has added checks and diagnostics for detector nonlinearity or saturation, as\nwell as a modification to the phase correction that reduces bias between forward and reverse scans of the interferometer.\n– The solar and telluric spectroscopic linelists used in the GGG forward model have been updated to reflect new laboratory\nand atmospheric/solar observing studies, to include non-Voigt lineshapes, and to reduce an observed temperature and\nwater dependence in the O2 column amounts.\n\n950\n\n– The a priori inputs of atmospheric state (temperature, pressure, and composition) have increased temporal resolution and\nthe trace gas profiles have been updated to better reflect both atmospheric growth rates of key species and gradients in\ntheir mixing ratios across the tropopause.\n– Improvements to fitting the continuum and channel fringes in the spectra.\n– A more flexible airmass correction applied to Xgas value from individual spectral windows, rather than multi-window\n\n955\n\naverages of said values.\n– A change to how retrieved Xgas values from multiple spectral windows measuring the same gas are averaged together\nthat eliminates a dependence on how many observations were averaged at once.\n51\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– An updated in situ correction factor that increases the number of profiles used to tie TCCON to the calibration scales\nused by in situ GHG measurements.\n– Improvements to user-friendliness in how AKs and prior profiles are reported in public files.\n\n960\n\nThere remains work to be done to further improve the TCCON data product. Implementing the capability in GGG to account\nfor errors in ILS remains a high priority. This was planned for inclusion in GGG2020, but could not be completed in time. It\nis expected that this capability will be an important tool to eliminate the XCO2 bias seen in comparison with in situ profiles\nas Xluft deviates from its nominal 0.999 value. A second high priority objective is to investigate the temperature dependence\n965\n\nseen in the N2 O and (to a much lesser extent) CH4 data and correct the underlying spectroscopic terms.\nWe currently plan to develop a minor release, GGG2020.1, within the next several years that will include additional postprocessing bias corrections to address the bias of XCO2 versus Xluft and XN2 O and XCH4 versus temperature. We expect these\nwill allow us to release data from the early years of several sites, which is currently flagged as poor quality due to out-of-bounds\nXluft as well as improve the XN2 O data substantially. As this would be a post-processing-only update, the reprocessing could\n\n970\n\nbe completed very rapidly.\nAt time of writing, 26 TCCON sites have reprocessed their existing data with GGG2020. Several sites are still in the process\nof carrying out this reprocessing, in many cases to improve the data quality based on new diagnostics available in GGG2020.\nWork is ongoing towards completing these sites’ reprocessing. Extensions to the existing data records will be released monthly\ngoing forward.\n\n975\n\n11\n\nCode and data availability\n\nAll TCCON GGG2020 data is linked through tccondata.org and stored as DOI-tagged datasets on CaltechDATA (data.caltech.\nedu). Each TCCON site has a separate repository and DOI on CaltechDATA; these are listed in Table 1. If a future correction\nrequires a revision of previously published data, that revision will receive a new DOI. Users are encouraged to check tccondata.\norg for the latest revisions of data rather than relying on Table 1. A repository containing the full set of TCCON GGG2020\n980\n\ndata is also available on CaltechDATA with the DOI 10.14291/TCCON.GGG2020 (Total Carbon Column Observing Network\n(TCCON) Team, 2022). Users are asked to cite the individual sites’ data records rather than the combined record as this\nhelps track usage of site data and thus support the ongoing operation of these sites. We provide a citation generator at https:\n//tccondata.org/metadata/siteinfo/genbib/. All data is provided in netCDF format, and additional documentation for the data is\navailable at https://tccon-wiki.caltech.edu/. The GGG2020 retrieval software is archived on CaltechDATA (Toon, 2023) as well\n\n985\n\nas publicly available through GitHub at https://github.com/TCCON/GGG.\nAppendix A: Abbreviations\nAbbreviations used in this paper are listed in Table A1.\n\n52\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nAbbreviation\n\nMeaning\n\nNotes\n\nADCF\n\nAirmass dependent correction factor\n\nSee SZA note\n\nAICF\n\nAirmass independent correction factor\n\nAlso call the “in situ correction factor”\n\nAK\n\nAveraging Kernel\n\nRefers to column averaging kernels unless otherwise indicated\n\nCBF\n\nContinuum basis function\n\nFT\n\nFree troposphere\n\nFFT\n\nFast Fourier transform\n\nFOV\n\nField of view\n\nFTIR\n\nFourier transform infrared\n\nFTS\n\nFourier transform spectrometer\n\nFVSI\n\nFraction variation in solar intensity\n\nILS\n\nInstrument line shape\n\nIR\n\nInfrared\n\nGGG\n\n-\n\nGHG\n\nGreenhouse gas\n\nLM\n\nLine mixing\n\nMIR\n\nMid infrared\n\nMOPD\n\nMaximum optical path difference\n\nMOPITT\n\nMeasurements of Pollution in the Troposphere\n\nNDIR\n\nNondispersive infrared\n\nNIR\n\nNear infrared\n\nOSDS\n\nObserver-sun Doppler stretch\n\nRH\n\nRelative humidity\n\nRMS\n\nRoot mean square/squared\n\nqSDV\n\nQuadratice speed-dependent Voigt\n\nSZA\n\nSolar zenith angle\n\nTCCON\n\nTotal Carbon Column Observing Network\n\nUTC\n\nCoordinated Universal Time\n\nVMR\n\nVolume mixing ratio\n\nVSF\n\nVMR scale factor\n\nXgas\n\nColumn-average mole fraction\n\nZLO\n\nZero level offset\n\nZPD\n\nZero path difference\n\nThe name of the retrieval, not an abbreviation\n\nAn instrument on the Terra satellite\n\n“SZA-” and “airmass-dependence” are used equivalently\n\n“Xgas ” is generic; “XCO2 ”, “XCH4 ”, etc. are specific\n\nTable A1. Abbreviations used in this paper.\n\n53\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190218\n\nxluft - 20190218\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190218\n\nxch4 - 20190218\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B1. February 18, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. The retrievals plotted here are Xluft , XCO2 , XCH4 , and XCO .\n\nAppendix B: Error budget\nFor completeness, we include the error budget figures equivalent to Figures 18–20 for February and July at East Trout Lake in\n990\n\nFigs. B1 to B6. February is extremely cold (-30 to -15◦ C) and dry (<500 ppm XH2 O ), with short days and large solar zenith\nangles. July is warm (20 to 30◦ C) and humid (3000 to 4500 ppm XH2 O ), causing the HF absorption feature to be blacked out\nby adjacent H2 O lines at higher solar zenith angles, causing unreliable retrievals of HF.\n\n54\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190218\n\nxhdo - 20190218\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190218\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190218\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure B2. As in Figure B1, but for XH2 O , XHDO , XN2 O , and XHF .\n\nB1\n\nILS\n\nWe created synthetic spectra in GGG2020 with different ILS errors, following the formulation for the “shear” and “angular”\n995\n\nmisalignments tested for the GGG2014 error budget, and for the new formulation in GGG2020. We then passed these synthetic\nspectra through an ILS quantification program called LINEFIT (v14.8) (Hase et al., 1999), which calculates the modulation\nefficiency and phase error of the spectra. Here, we plot the LINEFIT-derived modulation efficiencies for these four cases\nin Figure B7. The GGG2020 shear and angular misalignments represent a ramp-up and ramp-down from 1.0 at zero path\ndifference to 5% offsets at 45 cm optical path difference, as expected. Unfortunately, the GGG2014 “shear” and “angular”\n\n1000\n\nmisalignments both model shear misalignments of different magnitudes. The GGG2014 “shear” case is, in fact, more like a\n\n55\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190218\n\nxlco2 - 20190218\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190218\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B3. As in Figure B1, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n\n15% ramp up as a function of optical path difference, and the GGG2014 “angular” case is more like a 3% ramp up. This will\nessentially double the inferred error from the ILS in GGG2014, when compared with GGG2020.\nAppendix C: AICF profile selection\nC1\n1005\n\nCO2 , CH4 , CO\n\nIn situ profiles for CO2 , CH4 , and CO were drawn primarily from the NOAA CO2 ObsPack (Cooperative Global Atmospheric\nData Integration Project, 2019), NOAA CH4 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020),\nNOAA AirCore dataset (Baier et al., 2021), additional AirCore launches at the Sodanklyä and Nicosia TCCON sites, the\n\n56\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190723\n\nxluft - 20190723\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190723\n\nxch4 - 20190723\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B4. July 23, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. The retrievals plotted here are Xluft , XCO2 , XCH4 , and XCO .\n\n57\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190723\n\nxhdo - 20190723\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190723\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190723\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure B5. As in Figure 18, but for XH2 O , XHDO , XN2 O , and XHF .\n\nInfrastructure for Measurement of the European Carbon Cycle (IMECC) campaign, and the GO-AMAZON campaign. The\nObsPack contains data from numerous providers across different institutions; Tables C1 and C2 provide a detailed breakdown.\n1010\n\nFor the NOAA ObsPack Aircraft and AirCore profiles, the procedure used to match these data to TCCON sites will be detailed\nin the following subsections. For the remaining sources, the profiles were already associated with specific TCCON sites, so no\ncolocation was required.\nAll airborne data sources used for these profiles are listed in Tables C1 and C2. Ground data used to extend some of the\nprofiles to the surface are listed in Table C3.\n\n58\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190723\n\nxlco2 - 20190723\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190723\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B6. As in Figure B4, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n1015\n\nC1.1\n\nObsPack\n\nThe ObsPack data is provided as a single time series per measurement campaign or similar source. To extract individual profiles\nfrom these files, we:\n1. Scan all files for data points within 2° (total distance) of an active TCCON site. When one is found, we store the list of\ndata points surrounding it in time that fall a box 10° longitude width and 5° latitude tall centered on the TCCON site as\n1020\n\na “chunk.” A chunk extends forward and backward in time from the point closest to the TCCON site and stops at the\nfirst data point in each direction that is outside the 10◦ × 5◦ box. Any profiles derived from this chunk are assigned to\n\nthe TCCON station it passes closest to.\n\n59\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure B7. The modulation efficiencies tested in GGG2014 and GGG2020.\n\n2. Further filter the chunks based on the lowest altitude, highest altitude, number of data points, and minimum distance to\na TCCON site. This step was done interactively to find the filtering criteria that gave the best balance between number\n1025\n\nof chunks retained and the usefulness of the profile(s) within the chunk. The final criteria used were:\n– Minimum altitude below 2000 m\n– Maximum altitude above 7500 m\n– At least 20 data points\n– Approached within 0.1° of a TCCON station\n\n1030\n\n3. These filtered chunks were then individually evaluated and specific data points within them chosen by hand to use as\nprofiles. In this process, we considered the latitude/longitude position of the aircraft, the profile of altitude versus time,\nand the profile of CO2 or CH4 versus altitude. We generally selected as profiles times when the aircraft was consistently\nascending or descending, and excluded times of level flight. However, this had to be handled on a case-by-case basis to\nallow for profiles with a period of level flight in between two legs of an ascent or descent. If a chunk contained multiple\n\n1035\n\nascending/descending legs, we would split them if:\n– there was a clear separation in time, or\n– the legs measured different airmasses (evidenced by different CO2 or CH4 mole fractions)\n4. For each profile, we check for ground data in the ObsPack that can be used to extend the profile to the surface. We\nidentified which ground files in the ObsPack are near which TCCON sites by hand. We interpolate any data within 4\n60\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C1. Airborne profile data used in the AICF calculation. “CO2 Obspack” is the CO2 GLOBALVIEWplus v5.0 ObsPack (Cooperative\nGlobal Atmospheric Data Integration Project, 2019) and “CH4 ObsPack” the CH4 GLOBALVIEWplus v2.0 ObsPack (Cooperative Global\nAtmospheric Data Integration Project, 2020). The “TCCON sites” column indicates at which sites profiles were used; the IDs are mapped\nto locations in Table 1 and numbers of profiles per site are given in Tables C4 and C5. In the “Providers” column, affiliations are given\nin parentheses. If only one affiliation is listed, it applies to all individuals named. Abbrevations: NASA = National Aeronautics and Space\nAdministration; LaRC = Langley Research Center; Harvard U. = Harvard University; CSUSB = California State University San Bernadino;\nGSFC = Goddard Space Flight Center; NCAR = National Center for Atmospheric Research; NOAA = National Oceanic and Atmospheric\nAdministration; GML = Global Monitoring Laboratory; FMI = Finnish Meteorological Institure; CARE-C = Climate and Atmosphere Research Center; LSCE/IPSL = Laboratoire des Sciences du Climat et de l’Environnement.\nSource\n\nCampaign or ID\n\nProviders\n\nTCCON sites\n\nCO2 ObsPack\n\nCO2 Budget and Regional Airborne Study -\n\nSteve Wofsy (Harvard U.)\n\npa\n\nDeep Convective Clouds & Chemistry\n\nAndreas Beyersdorf (CSUSB) & Yonghoon\n\noc\n\n(DC3), DC8 aircraft\n\nChoi (SSAI)\n\nCO2 ObsPack\n\nGoddard Space Flight Center (GSFC)\n\nStephan Randolph Kawa, James Brice Ab-\n\nCO2 ObsPack\n\nHIAPER\n\nMaine (COB2004)\nCO2 ObsPack\n\ndf, pa\n\nshire, & Haris Riris (NASA GSFC)\n\nCO2 ObsPack\nCO2 ObsPack\nCO2 ObsPack\n\nPole-to-Pole\n\nObservations\n\nSteve Wofsy (Harvard U.), & Britton\n\n(HIPPO)\n\nStephens (NCAR)\n\nIntercontinental Chemical Transport Exper-\n\nStephanie A. Vay (NASA LaRC) &\n\niment - North America (INTEX-NA)\n\nYonghoon Choi (SSAI)\n\nKorea-United States Air Quality Study\n\nJoshua P. DiGangi, & Yonghoon Choi\n\n(KORUS-AQ)\n\n(SSAI)\n\nO2 /N2 Ratio and CO2 Airborne Southern\n\nBritton Stephens (NCAR), Colm Sweeney\n\nOcean Study (ORCAS)\n\n(NOAA GML), Kathryn McKain (NOAA\n\nll, wg\npa\nan, df, rj\noc\n\nGML), Eric Kort (U. Michigan)\nCO2 ObsPack\n\nStudies of Emissions and Atmospheric\n\nSteve Wofsy (Harvard U.)\n\ndf\n\nStudies of Emissions and Atmospheric\n\nAndreas Beyersdorf (CSUSB) & Yonghoon\n\noc\n\nComposition, Clouds and Climate Coupling\n\nChoi (SSAI)\n\nComposition, Clouds and Climate Coupling\nby Regional Surveys (SEAC4RS), ER-2 aircraft\nCO2 ObsPack\n\nby Regional Surveys (SEAC4RS), DC8 aircraft\n\n1040\n\nhours of the lowest altitude measurement in a profile to the time of the lowest altitude profile measurement. In cases\n\n61\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C2. Table C1, continued. ARM = Atmospheric Radiation Monitoring facility.\nSource\n\nCampaign or ID\n\nProviders\n\nTCCON sites\n\nCO2 ObsPack\n\nStratosphere-Troposphere Analyses of\n\nSteve Wofsy (Harvard U.)\n\npa\n\nKathryn McKain (NOAA GML), Colm\n\nae, df, eu, ll, oc,\n\nSweeney (NOAA GML), Steve Wofsy\n\npa\n\nRegional Transport (START-08)\nCO2 ObsPack\n\nAtmospheric\n\nTomography\n\nMission\n\n(ATom)\n\n(Harvard U.), Bruce Daube (Harvard\nU.), Roisin Commane (Harvard U.)\nOther CO2\n\nNOAA Manaus\n\nJohn Miller (NOAA GML)\n\nma\n\nCH4 ObsPack\n\nHIAPER Pole-to-Pole Observations\n\nSteve Wofsy, Greg Santoni, & Jasna\n\nll,oc,pa,wg\n\n(HIPPO)\n\nPittman (Harvard U.)\n\nStratosphere-Troposphere Analyses of\n\nSteve Wofsy (Harvard U.)\n\npa\n\nKathryn McKain & Colm Sweeney\n\nae,ci,df,eu,ll,oc,pa\n\nCH4 ObsPack\n\nRegional Transport (START08)\nCH4 ObsPack\nIMECC\n\nAtmospheric\n\nRepository\n\nTomography\n\nMission\n\n(ATom)\n\n(NOAA GML)\n\nInfrastructure for Measurement of the\n\nVarious\n\nbi,br,gm,je,ka,or\n\nBianca Baier & Colm Sweeney (NOAA\n\ndf,oc,pa,so\n\n(CO2 , CH4 , CO)\n\nEuropean Carbon Cycle (IMECC)\n\nNOAA AirCores (CO2 ,\n\nN/A\n\nCH4 , CO)\nSodankylä\n\nGML)\nAirCores\n\nN/A\n\nHuilin Chen (RUG) & Rigel Kivi (FMI)\n\nso\n\nN/A\n\nPierre-Yves Quéhé (CARE-C, Cyl) &\n\nni\n\n(CO2 , CH4 , CO)\nNicosia AirCores (CO2 ,\nCH4 , CO)\nRadiosondes (H2 O)\n\nThomas Laemmel (LSCE/IPSL)\nSouthern Great Plains (SGP) Lamont\nCentral Facility and Tropical Western\nPacific (TWP) Darwin Facility\n\n62\n\nARM\n\ndb, oc\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwhere ground data is only available before or after the lowest profile measurement, we use the closest ground data in\ntime.\nC1.2\n\nAirCore\n\nAs AirCore data intrinsically provides discrete profile, matching these data to TCCON sites was much simpler. For NOAA\n1045\n\nAirCores, we search all files for those where the mean latitude and longitude of the profile were within 1° (total distance) of\na TCCON site. We use a looser distance compared to the aircraft as it is unlikely that an AirCore would be within 1° of a\nTCCON site by happenstance if it was not intended to match with that TCCON. However, since it is possible that the balloon\ntrajectory drifted significantly depending on the winds, we use the looser distance criterion to allow for that.\nC2\n\n1050\n\nH2 O\n\nProfiles for the H2 O AICF come from radiosonde data provided by the Department of Energy Atmospheric Radiation Measurement (ARM) facility (Keeler and Burk). The data were downloaded from https://adc.arm.gov/discovery/#/results/instrument_\nclass_code::sonde%2Fprimary_meas_type_code::atmtemp in March 2021. Two ARM sites are close enough to TCCON locations to be useful: the Southern Great Plains (SGP) site’s Central Facility (facility code C1) is near the Lamont, OK, USA\nTCCON site, and the Tropical Western Pacific (TWP) site’s Darwin facility (code C3) is near the Darwin, Australia TCCON\n\n1055\n\nsite.\nThese facilities produce more radiosonde observations than we can feasibly use in the AICF calculation, so we must choose\na subset. We use the following steps for each site:\n1. Identify radiosonde profiles that are coincident with another trace gas profile (CO2 , CO, CH4 , or N2 O).\n\n1060\n\n2. Identify radiosonde profiles not in the set identified in Step 1 that have at least 30 TCCON spectra within ±3 hours of\nthe time of the profile’s lowest altitude measurement and\n\n3. Combine the profiles from step 1 with randomly selected profiles from step 2 to collect 50 total profiles. (We use a seed\nof 42—chosen in reference to “The Hitchhiker’s Guide to the Galaxy”—to ensure repeatability across runs.)\n4. Finally, remove any profiles from this set of 50 that have a maximum altitude < 15 km.\nOnce we have assembled a pool of radiosonde profiles, we convert the relative humidity (RH) values stored in the files to\n1065\n\nwater mole fractions. Based on the convention described in Miloshevich et al. (2006), we assume that the definition of RH\nis the ratio of water vapor pressure to the saturation water vapor pressure over liquid water and calculate the H2 O dry mole\nfraction as\nRH · SVP\np\nfH2 O,wet\nfH2 O,dry =\n1 − fH2 O,wet\n\nfH2 O,wet =\n\n(C1)\n(C2)\n\n63\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1070\n\nwhere RH is the relative humidity as a fraction (i.e. 0 to 1), SVP is the saturation vapor pressure of water over liquid water\ncalculated using Eq. 6 of Miloshevich et al. (2004) (see also Eq. 15 of Wexler, 1976), and p is the atmospheric pressure (in the\nsame units as SVP).\nC3 Constructing full profiles\nIn order to ensure a proper comparison between the in situ and TCCON column amounts, the in situ profiles must extend to the\n\n1075\n\ntop of the TCCON retrieval altitude grid, 70 km. No aircraft or balloon-borne profile reaches this altitude, therefore, similarly\nto Wunch et al. (2010), we extend the in situ profiles using the GGG2020 prior profiles (Laughner et al., 2023).\nThe differences between Wunch et al. (2010) and our approach stem from (1) the GGG2020 priors do a better job of\nrepresenting trace gas profiles in the stratosphere and (2) we have enough additional profiles over TCCON sites to be selective\nabout which ones we use. This is why we filtered the ObsPack data to “chunks” that have data up to at least 7500 m altitude\n\n1080\n\n(§C1.1), to limit the altitude that needs to be filled in above the top of the profile.\nThere are three ways that profiles are extended up to 70 km altitude, depending on their top altitude:\n1. If the profile’s top is above 380 K potential temperature (i.e. reaches the stratospheric overworld), then we append the\nGGG2020 priors for levels above the profile top.\n2. If the profile’s top is below 380 K potential temperature but at or above 7.5 km, then the in situ profile’s values are\n\n1085\n\nbinned to the same altitude grid (see below) and then we do a constant value extrapolation of the top binned value up\nto the tropopause altitude. We use the GGG2020 prior above 380 K potential temperature again, and connect the two\nparts of the profile by linearly interpolating the trace gas mole fractions with respect to potential temperature between\nthe tropopause and 380 K. This case covers profiles where the top of the measured profile is expected to be a better\nrepresentation of the unmeasured free troposphere than the GGG2020 priors.\n\n1090\n\n3. If the profile’s top is below 7.5 km, then we use the GGG2020 priors for all levels above the profile top. The case assumes\nthat profiles that do not reach above 7.5 km do not constrain the free troposphere well enough to supplant the GGG2020\npriors. While we filtered the ObsPack data for “chunks” that have data above 7.5 km, we still have a few profiles with\nceilings below 7.5 km from chunks that needed to be split into multiple profiles.\nFor #2, we calculate the binned in situ profile values for the highest altitude of the GGG retrieval grid below the in situ\n\n1095\n\nprofile’s ceiling (zGGG,k ) as:\nPnobs\nwf\nPnobsi obs,i\nf obs = i=1\ni=1 wi\n\n\n\n(zobs,i − zGGG,k−1 )/(zGGG,k − zGGG,k−1 ) if zGGG,k−1 ≤ zobs,i < zGGG,k\nwi = (zGGG,k+1 − zobs,i )/(zGGG,k+1 − zGGG,k ) if zGGG,k ≤ zobs,i < zGGG,k+1\n\n\n\n0\notherwise\n64\n\n(C3)\n\n(C4)\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n5000\n\nGGG altitude grid level\nObservation weighting\n\nAltitude (km)\n\n4000\n3000\n2000\n1000\n0.0\n\n0.1\n\n0.2\n0.3\nWeight\n\n0.4\n\n0.5\n\n0.6\n\nFigure C1. An example of the weighting functions from Eq. (C4). Lines indicate the weights applied to the observed mole fractions and\ncircles indicate the GGG altitude grid levels that correspond to those weights—like colors match.\n\nFigure C1 shows an example of the weights for one short profile at the Armstrong TCCON site.\nThere is a special case for CH4 applied when integrating the in situ profile to calculate the in situ-derived XCH4 . Previous\n1100\n\nwork (e.g. Washenfelder et al., 2003; Saad et al., 2014, 2016) established that there is a strong correlation between CH4 and\nHF in the stratosphere. Since this correlation is encoded into the GGG2020 priors (Laughner et al., 2023), we can use the\ndifference between the prior and posterior HF column (which is almost entirely found in the stratosphere) from the TCCON\nretrievals to adjust the levels in the in situ CH4 profiles that use the GGG2020 profiles.\nSpecifically, when calculating the in situ XCH4 , we get the slope of CH4 vs. HF mixing ratios used by the GGG2020 priors\n\n1105\n\nfor the year and region (tropics, midlatitudes, or polar vortex) of the profile (see §3.5 and Fig. 11 of Laughner et al., 2023). We\nthen multiply this slope by the difference between the prior and median posterior HF profile of all the TCCON observations\nmatched with the in situ profile in question in order to get the expected change in the CH4 priors to better match the true\nstratospheric profile. Finally, we multiply this profile difference by the TCCON AK and integrate only the levels in the total in\nsitu profile obtained from the GGG2020 priors. The integration uses Eq. (8) and add the integrated change to the in situ XCH4\n\n1110\n\nas a posterior adjustment.\nAgain, note that this correction is only applied when integrating the in situ profiles to obtain the true XCH4 value to compare\nthe TCCON retrievals against. When using the in situ profiles as priors in the TCCON retrievals, the levels taken from the\nGGG2020 priors are not adjusted in this fashion.\nC4 Grouping temporally proximate profiles\n\n1115\n\nThere are several cases where multiple profiles are available within a short time of each other (such as different legs of a\nmissed approach or duplicate AirCore launches). Because we use the observed profiles as the prior in the TCCON retrievals\nfrom which the AICF is derived, this presents a technical challenge. Ideally, we want to use the same prior for all retrievals\nmatched up with a given profile for comparison. Our temporal coincidence criterion can be up to ±3 hours, therefore, in cases\n65\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwith two or more profiles within a few hours, if for each TCCON retrieval we used the observed priors closest in time to it, this\n1120\n\nwould result in a change of prior partway through our coincidence window.\nOur solution was to merge profiles close enough in time for this to occur, but only for use as priors. Each individual observed\nprofile still contributes one point on Fig. 11. This does mean that the prior will not exactly match any of the observed profiles\nthose retrievals are compared against, but we consider that an acceptable error, given that we do apply an AK correction to the\nintegrated in situ profile.\n\n1125\n\nTo find profiles that need to be merged, we first identify which TCCON observations would match with that profile. We ignore\nthe quality filtering criteria from §7.3.1 during this step, and only try to find the time window (± 1, 2, or 3 hours) necessary\nto match at least 30 TCCON observations to each profile. If any two profiles from the same TCCON site are matched to any\nof the same TCCON observations, they are grouped together in the list of profiles, to be averaged together when creating the\ncustom priors in §C5. This initial list is written out to a text file so that it can be modified by hand later, as needed.\n\n1130\n\nC5 Running custom TCCON retrievals\nAs mentioned in §7.3, when we run the TCCON retrievals for the AICF calculation, we use as custom priors the in situ profiles\nthat a given TCCON observation will be compared against. This reduces error in the TCCON Xgas value that arises from an\nincorrect prior profile and thus improves the accuracy of the AICF. There are several technical considerations in how we handle\nthis matching. In order to make those considerations clear, let us first describe how the GGG retrieval accepts inputs describing\n\n1135\n\nboth the prior profiles and the TCCON observations to retrieve on.\nGGG takes a list of TCCON spectra to retrieve as input in the “runlog” file. This lists each spectrum on which to run the\nretrieval in order. For the AICF retrievals, we combined all the spectra from all the relevant TCCON sites into a single runlog.\nThe priors (including temperature and pressure as well as trace gas mixing ratios) are written to a “.mav” file. This file is\norganized into blocks. Each block indicates the first spectrum from the runlog which the priors contained in the .mav block\n\n1140\n\napply to. During the retrieval, GGG iterates through the spectra contained in the runlog. When it reaches the spectrum defined\nas the first spectrum of the next block in the .mav file, it loads the priors from that block before continuing.\nIn inserting the in situ profiles into the .mav file as priors, we had three objectives:\n1. Retain the standard priors for gases and times that we did not have in situ profiles available.\n2. Ensure that the in situ profiles were used as priors for any spectra that they might be compared against.\n\n1145\n\n3. Ensure that any in situ profiles were only applied to the TCCON site where and day when they were measured.\nTo meet these objectives, our approach to inserting the in situ profiles as priors was:\n– Divide the runlog into chunks by site and day, so that each chunk only has spectra from one site on one day.\n– For each unique site/day chunk, collect all the in situ profiles from that day.\n\n66\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– Average together any in situ profiles grouped together in the list created in §C4. For this, we used an approach that\nconsiders whether each in situ profile contributed observations to a given level in the regridded profile. For a level on the\n\n1150\n\nretrieval grid where none of the in situ profiles provided any data points (i.e. the observed profiles were extrapolated or\nhad the GGG2020 prior appended to it), both profiles are weighted equally. For a level where at least one of the in situ\nprofiles had observed data, each profile is weighted by the fraction of data for that level that came from observations.\n– For gases that only have one profile (after averaging) for that site/day, assign that profile to all the .mav blocks for that\nsite/day.\n\n1155\n\n– For gases that have multiple profiles that are not merged together (§C4), use the first profile in the day for all .mav blocks\nup until the first spectrum that could be compared with the second profile in the day (for our coincidence criteria, this\nwill be the spectra 3 hours before the floor time of the second profile). Introduce a new .mav block on that profile that\nswitches to the second profile. Repeat for third, fourth, etc. profiles if present. Assign the last profile to cover all .mav\nblocks through the end of the day.\n\n1160\n\nOnce the profiles are assigned to their .mav blocks, they must be averaged from their native vertical resolution to the GGG\nretrieval altitude grid and, if multiple profiles for the same gas were present for the same block, they must be averaged together.\nFor the vertical regridding, we use the same approach as described in §C3 where we do a weighted average of the observed\nmixing ratios, where the weights are maximized when the observed altitude equals the altitude of the GGG retrieval level they\n1165\n\nare being averaged to, and which decrease linearly to the adjacent GGG retrieval levels (Fig. C1, Eq. C4).\nWe found that it is crucial that we use geopotential height as the altitude for the regridding, as that did a better job ensuring\nthat the observed profiles followed hydrostatic balance. To compute geopotential height for the in situ profiles, we take pressure\nand geopotential height from the two GEOS FP-IT files (Lucchesi, 2015) that bound the profile’s lowest altitude in time and\naverage the GEOS FP-IT data, and weight each by the time difference between the GEOS FP-IT profile and the time of the\n\n1170\n\nlowest altitude measurement in the in situ profile, giving greater weight to profiles nearer in time to the in situ profile. We then\ninterpolate the GEOS FP-IT geopotential altitude on the logarithm of pressure to the pressures in the in situ profile.\nThe final consideration in preparing the custom priors is that we always retain the pressure and temperature profiles from\nthe standard GEOS FP-IT priors used in GGG2020. This is because our testing found it very difficult to maintain hydrostatic\nbalance if we used the observed pressure and temperature. This, in turn, caused greater error in the retrieved Xgas values, as\n\n1175\n\nthe air column would be incorrect.\nOnce the custom priors were generated, the TCCON retrievals could be run as normal. The standard post processing corrections for airmass dependence (§7.1) and window-to-window averaging (§7.2) were applied as well. AKs were calculated for\neach spectrum retrieved as used to smooth the in situ profiles and account for the TCCON vertical sensitivity (§7.3).\nC6\n\n1180\n\nUncertainty in TCCON/in situ comparisons\n\nFor the TCCON/in situ ratios in §7.3, we considered five sources of uncertainty for the comparisons:\n\n67\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1. In situ measurement error (\u000fmeas ): This accounts for the error in individual in situ measurements that make up the\nprofiles. To be conservative, we assume the worst-case scenario with 100% correlated error at all levels. The uncertainty in\nXgas is then calculated as:\nZ\nZ\n\u000fmeas = c(p) + 2σ(p) dp − c(p) dp\n1185\n\n(C5)\n\nwhere c(p) is the measured mixing ratio and σ(p) the uncertainty at each level. The integrals represent the pressure-weighted\nintegration, Eq. (8). The uncertainty values are those reported in the original data files where available or a typical value chosen\nin consultation with the data providers.\n2. Unmeasured free troposphere (\u000fFT ): This accounts for uncertainty due to the portion of the free troposphere not measured by a given profile. For each profile, we first calculate σobs,FT , the standard deviation of measurements above 750 hPa\n\n1190\n\nand below the tropopause (as determined by GEOS FP-IT meteorology). We then create a perturbed profile,\n\nc(p) + 2σ\nobs,FT if interp/extrap at p\nc0 (p) =\n\nc(p)\notherwise\n\n(C6)\n\nwhich adds this standard deviation to interpolated or extrapolated levels above the top of the measured profile. The uncertainty\nin Xgas is calculated as:\nZ\nZ\n\u000fFT = c0 (p) dp − c(p) dp\n\n1195\n\n(C7)\n\nThis error will be zero for profiles that do not require extrapolation or interpolation to reach the stratospheric overworld (i.e.\naltitudes with potential temperature ≥ 380 K).\n\n3. Bias in stratospheric prior (\u000fstrat ): This represents expected bias in the column from the use of GGG2020 priors for\n\nlevels in the stratosphere. This uses the retrieved vs. prior HF column as a proxy for error in the stratospheric prior. As discussed\nin §7.3.3, HF is predominately found in the stratosphere, so the difference between the retrieved and prior HF columns gives\n1200\n\ninformation about whether the stratospheric profile was biased high or low. We calculate the bias as:\n\u000fstrat = 2 · (XHF,post − XHF,prior ) ·\n\n∂Xgas\n∂XHF\n\n(C8)\n\nThe derivative ∂Xgas /∂XHF has to be calculated for each gas. For CO2 we use 8.09×103 , which was derived from East Trout\nLake TCCON data by comparing prior and posterior wCO2 and HF columns. (East Trout Lake is positioned to see significant\nstratospheric variability due to the polar vortex, and wCO2 is the GGG2020 CO2 product with enhanced sensitivity to the\n1205\n\nstratosphere.) For CH4 , this is drawn from the CH4 :HF slopes used in the GGG2020 priors (Laughner et al., 2023).\nAirCore profiles are treated specially, as they always reach into the stratosphere. For these profiles, we create a perturbed\nprofile, c0 (p), where the levels in the stratosphere filled by the GGG2020 priors have the difference between the top of the\nAirCore profile and the corresponding level in the prior added to them. The difference between the integral of these profiles\n\n68\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nbecome the stratospheric error. Mathematically, that is\n\nc(p) + 2[c\nprior (pobs. top ) − cAirCore (pobs. top )]\n1210\nc0 (p) =\n\nc(p)\nZ\nZ\n\u000fstrat,AirCore = c0 (p) dp − c(p) dp\n\nif using prior at p\n\n(C9)\n\notherwise\n\n(C10)\n\n4. Random error in TCCON Xgas value (\u000fstd. xgas ): This represents random error in the TCCON observations. Because we\nrequire at least 30 TCCON observations coincident with a profile for a valid comparison, we use twice the standard deviation\namong those coincident observations as the metric of random error. The coincidence windows vary between 2 and 6 hours\n1215\n\nwide, so the standard deviation likely includes some true change in the data, and can therefore be considered conservative.\n5. Bias in TCCON derived from Xluft (\u000fXluft ): This represents bias in retrieved Xgas values resulting from instrument\nhardware issues diagnosed from deviations in Xluft from the nominal network value (0.999, see §7.3). The bias is calculated\nas:\n\u000fXluft =\n\n1220\n\n∂r\n· (Xluft,median − 0.999) · Xgas,median\n∂Xluft\n\n(C11)\n\nHere, Xluft,median and Xgas,median are the median values of TCCON Xluft and the target Xgas across the 30+ coincident\nobservations for the comparison. 0.999 is the nominal value of Xluft that represents a well-operating instrument. The ∂r/∂Xluft\nvalue is how the TCCON/in situ ratio changes with Xluft , and was derived for XCO2 , XwCO2 , XlCO2 , and XCH4 by an\nunweighted robust fit through similar plots of TCCON/in situ ratio vs. Xluft as Fig. 11, but with TCCON retrievals that used\nthe standard trace gas priors instead of custom ones built from the in situ profiles. The values used are given in Table C6.\n\n1225\n\nFull error calculation: As the error terms include a mix of random (\u000fmeas , \u000fFT , \u000fstd. xgas ) and systematic (\u000fstrat , \u000fXluft )\nerrors, the in situ and TCCON total errors are calculated as:\nq\n\u000fin situ = \u000f2meas + \u000f2FT + |\u000fstrat |\nq\n\u000fTCCON = \u000f2std. xgas + |\u000fXluft |\n\n(C12)\n(C13)\n\nThe first term in the second equation is written as a root of a square to indicate that if additional random TCCON error terms\n1230\n\nwere to be added in the future, they should add in quadrature. The uncertainty in the TCCON/in situ ratio (Xgas,TCCON /Xgas,in situ )\nP\nfollows standard error propagation (\u000ftotal = i (σx · ∂f (x)/∂x)2 ):\n\u000ftotal =\n\n2\n\u000f2TCCON \u000f2in situ Xgas,TCCON\n+\n\u000f2in situ\n\u000f4in situ\n\n(C14)\n\nNote that Eq. (C12) is applied to each individual TCCON/in situ comparison, while the statistics in Table 3 are averaged\nover all the comparisons for a given gas. Therefore, the values of \u000fin situ , \u000fmeas , \u000fFT , and \u000fstrat in Table 3 do not directly relate\n1235\n\nto each other through Eq. (C12). As noted in the caption for Table 3, the non-parenthetical values in the last four columns\n\n69\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nformally propagate the error from the individual comparisons, such that the values shown in the table (which we will denote\ngenerally as \u000fformal ) are calculated from the individual comparisons’ values with\n\n\u000f2formal =\n\nn \u0012\nX\n1\ni=1\n\nn\n\n\u000findiv,i\n\n\u00132\n\n(C15)\n\nwhere \u000findiv,i denotes individual comparisons’ error values and n is the number of individual observations. Conversely, the\n1240\n\nparenthetical numbers in Table 3 give the simple mean, i.e.:\nn\n\n1X\n\u000fmean =\n\u000findiv,i\nn i=1\n\n(C16)\n\nAppendix D: Comparison between TCCON and NOAA surface N2 O\nFor Fig. 14, we constructed N2 O profiles to compare TCCON XN2 O against using NOAA surface data. This approach takes\nadvantage of how well-mixed N2 O is in the troposphere to build a large set of comparison. The approach, in detail, is as\n1245\n\nfollows.\nThe TCCON vs. in situ comparison shown in Fig. 14 calculates an in situ XN2 O from N2 O profiles using Eq. (7) as with the\nother Xgas quantities in §7.3. These N2 O profiles are constructed using the NOAA surface N2 O VMR from the surface to the\ntropopause, the GGG2020 N2 O prior for levels with potential temperature greater than 380 K, and linearly interpolating the\nN2 O VMR with respect to potential temperature between the tropopause and 380 K level.\n\n1250\n\nFor the tropospheric N2 O VMRs, we obtained monthly average NOAA global N2 O data from https://gml.noaa.gov/hats/\ncombined/N2O.html (last access 10 May 2021). For sites at latitudes north of 23◦ N or south of 23◦ S, we use the northern and southern hemispheric averages, respectively (GML_NH_N2O and GML_SH_N2O in the combined NOAA N2 O file).\nFor equatorial latitudes between 23◦ S and 23◦ N, we used the average of the Mauna Loa and American Samoa N2 O data\n(GML_mlo_N2O and GML_smo_N2O in the combined file). For each comparison point in Fig. 14, we used the N2 O VMR\n\n1255\n\nfrom that month as the tropospheric VMR of the profile.\nThe comparisons selected for Fig. 14 meet the following criteria:\n– The difference between the prior and posterior HF column must be < 2 × 1014 molec. cm−2 in magnitude. Since HF is\n\nalmost entirely in the stratosphere, this limits the comparisons to cases where the GGG2020 prior stratospheric profiles\nare reasonably accurate, thus limiting error in the in situ XN2 O from an incorrect assumed stratosphere\n\n1260\n\n– Xluft must be in the range [0.996, 1.002). This ensures we are considering data when the TCCON instrument was well\naligned, as discussed in §7.3.1\n– FVSI must be ≤ 0.05. This limits the comparison to mostly cloud-free observations.\n\n70\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nAppendix E: Variable O2 mole fraction derivations\nE1\n1265\n\nTrends in O2 mole fraction from trends in XCO2\n\nThe derivation of Eq. (10) begins from the definition of fO2 :\n\nfO2 =\n\nNO2\nN + NO2 + NCO2\n\n(E1)\n\nwhere:\n– NO2 and NCO2 are the number of moles of O2 and CO2 , respectively,\n– N is the number of moles of gases other than O2 or CO2 in H2 O-free air, and\n– Ntot (used below) is N + NO2 + NCO2\n\n1270\n\nDefining α = ∂NO2 /∂NCO2 , taking the derivative of fO2 with respect to NCO2 , and simplifying gives:\n∂fO2\n=\n∂NCO2\n\n\u0012\n\nα(N + NCO2 ) NO2\n−\nNtot\nNtot\n\n\u0013\n\n·\n\n1\nNtot\n\n(E2)\n\nRecognizing that NO2 /Ntot = fO2 and (N + NCO2 )/Ntot = 1 − fO2 as well as converting the derivative to a ratio of small\n\nbut finite differences (represented by δ in place of ∂) gives:\n\n1275\n\n1\nδfO2\n= (α − α · fO2 − fO2 ) ·\nδNCO2\nNtot\nδNCO2\n⇒ δfO2 = (α − α · fO2 − fO2 ) ·\nNtot\n\n(E3)\n(E4)\n\nFinally, to convert δNCO2 /Ntot into terms of XCO2 and XCO2 ,ref , we start by defining:\n\nXCO2 ,ref =\n\nNCO2\nNtot\n\n(E5)\n\nand\n1280\n\nXCO2 =\n\nNCO2 + δNCO2\nNtot + δNCO2 + δNO2\n\n(E6)\n\nas well as δNO2 = α · δNCO2 . Substituting this and NCO2 = XCO2 ,ref · Ntot from Eq. (E5) in Eq. (E6) and rearranging gives:\nXCO2 − XCO2,ref\nδNCO2\n=\nNtot\n1 − XCO2 − α · XCO2\n\n(E7)\n\nSubstituting Eq. (E7) in Eq. (E4) yields the final version of Eq. (10).\n71\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nE2\n1285\n\nO2 mole fraction from O2 /N2 data\n\nMeasurements of atmospheric O2 concentration are commonly reported as 10−6 relative deviations in the O2 /N2 ratio (denoted\nδ(O2 /N2 ) and given in units of per meg) to avoid the complexities of diluation effects from changes in CO2 and other trace\nspecies on the O2 mole fraction. To convert from available measurements of trends in δ(O2 /N2 ), we must convert to units of\nppm and account for the diluting effect of trends in CO2 . The equation for the black line in Fig. 13, based on Scripps δ(O2 /N2 )\nand NOAA global mean CO2 data, is slightly different from Eq. (10). As above, the derivation starts with Eq. (E1), but now\n\n1290\n\nsince we have measured values for the change in NO2 and NCO2 , our change in fO2 will instead be:\n\nδfO2 =\n\n∂fO2\n∂fO2\n· δNO2 +\n· δNCO2\n∂NO2\n∂NCO2\n\n(E8)\n\nIn this case, both ∂NO2 /∂NCO2 and ∂NCO2 /∂NO2 are 0, since we have measurements of both O2 and CO2 and therefore\ncan treat their changes as orthogonal. That leads to the following expressions for the derivatives in Eq. (E8):\n\n1295\n\n1 − fO2,ref\n∂fO2\n=\n∂NO2\nNtot\nf\n∂fO2\nO\n= − 2,ref\n∂NCO2\nNtot\n\n(E9)\n(E10)\n\nInserting these into Eq. (E8) gives:\n\nδfO2 = (1 − fO2,ref ) ·\n\nδNCO2\nδNO2\n− fO2,ref ·\nNtot\nNtot\n\n(E11)\n\nδNO2 /Ntot can be expressed in terms of δ(O2 /N2 ) values by using the definition of δ(O2 /N2 ) (Keeling et al., 1998):\nδ(O2 /N2 ) =\n1300\n\n(O2 /N2 )sample\n−1\n(O2 /N2 )reference\n\n(E12)\n\nand assuming that the amount of N2 in the atmosphere does not change. Multiplying this definition by fO2,ref gives:\n\nδ(O2 /N2 ) · fO2,ref\n\n\u0014\n\n\u0015\n(NO2 + δNO2 )/NN2\nNO2\n=\n−1 ·\nNO2 /NN2\nNtot\nδNO2\n=\nNtot\n\n(E13)\n(E14)\n\nδNCO2 /Ntot can be expressed as in Eq. (E7) except with α = 0 (again, this is because we have measurements of mole\nfractions of CO2 and O2 ). The final equation used for the “best estimate” line in Fig. 13 is therefore:\n\n1305\n\nfO2 ,ref + δfO2 = fO2 ,ref + (1 − fO2 ,ref ) · δ(O2 /N2 ) · fO2 ,ref −\n\nXCO2 − XCO2 ,ref\n· fO2 ,ref\n1 − XCO2\n\n72\n\n(E15)\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwhere fO2 ,ref is the 0.209341 value obtained in §7.3.2 by adjusting Aoki et al. (2019). As noted in §7.3.2, the δ(O2 /N2 ) data\nused is a weighted average of the ALT, LJO, and CGO sites with weights of 41 , 14 , and 12 , respectively. Note that the NOAA\nglobal mean CO2 (rather than TCCON XCO2 ) is used for XCO2 and XCO2 ,ref in this equation.\n\nAuthor contributions. J.L. Laughner led the development of the new airmass correction (§7.1), window-to-window averaging (§7.2), in situ\n1310\n\nscaling (§7.3), and miscellaneous changes in §9. G.C. Toon is the main developer of GGG. J. Mendonca developed the non-Voigt treatment\nof the spectral line shape (§3.2). C. Petri contributed to the development of the phase correction update (§5.2). S. Roche developed the new\nretrieval grid (§4.1), meteorological resampler (§4.2), and netCDF writer. D. Wunch carried out the sensitivity tests (§8). D. Wunch, C.M.\nRoehl, G.C. Toon, P.O. Wennberg, and J.L. Laughner conducted the O2 study in §3.3. J.-F. Blavier is a key developer of I2S. D.W.T. Griffith\ncontributed to various aspects of GGG2020 development. P. Heikkinen, R. Kivi, and M.K. Sha first diagnosed the nonlinearity issue from\n\n1315\n\n§5.1 and developed a correction methodology. R.F. Keeling and B.B. Stephens consulted on the approaches to parameterize the change in O2\nmole fraction (§7.3.2). M. Kiel performed tests of the phase correction threshold (§5.2) and choices of NCBFs (§6) C.M. Roehl, N. Deutscher,\nP. Jeseck, D. Pollard, M. Rettinger, S. Roche, M.K. Sha, Y. Té and D. Wunch all participated in a beta test of GGG2020. N.M. Deutscher,\nJ. Gross, B. Herkommer, P. Jeseck, I. Morino, H. Ohyama, C. Petri, J. Notholt, D. Pollard, M. Rettinger, S. Roche, E. McGee, K. Strong,\nC.M. Roehl, M.K. Sha, K. Shiomi, R. Sussmann, Y. Té, V. Velazco, D. Wunch, and M. Zhou provided data used to derive the corrections in\n\n1320\n\n§7.1 and §7.2. B.C. Baier, B.B. Stephens, H. Chen, Y. Choi, X. Lan, T. Laemmel, K. McKain, J. Miller, H. Riris, C. Rousogenous, and S.C.\nWofsy provided in situ data used in §7.3. P.O. Wennberg provided input to all elements of this work. All authors reviewed the manuscript.\n\nCompeting interests. The authors declare no competing interests.\n\nAcknowledgements. The authors gratefully acknowledge the use of GNU Parallel (Tange, 2011) in the GGG processing. The authors also\nthank James Abshire for providing CO2 data used in deriving the in situ correction (§7.3). A portion of this research was carried out\n1325\n\nat the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with NASA (80NM0018D0004). Government\nsponsorship is acknowledged. Support for Caltech TCCON sites and partial support for JLL, MK, CMR, and POW provided by NASA grants\nNNX17AE15G and 80NSSC22K1066. Material from BBS and RFK is based upon work supported by the National Center for Atmospheric\nResearch, which is a major facility sponsored by the National Science Foundation under Cooperative Agreement No. 1852977.\nMR and RS acknowledge funding by the German Helmholtz Research Program “Changing Earth – Sustaining our Future” within the\n\n1330\n\nResearch Field “Earth and Environment”. The Paris TCCON site has received funding from Sorbonne Université, the French research center\nCNRS and the French space agency CNES. The Cyprus TCCON site and AirCore flights have received funding from the European Union’s\nHorizon 2020 research and innovation programme under grant agreement No. 856612 and the Cyprus Government. The TCCON site at\nRéunion Island has been operated by the Royal Belgian Institute for Space Aeronomy with financial support since 2014 by the EU project\nICOS-INIWRE (Grant agreement ID: 313169), the ministerial decree for ICOS (FR/35/IC1 to FR/35/C6), ESFRI-FED ICOS-BE project\n\n1335\n\n(EF/211/ICOS-BE) and local activities supported by LACy/UMR8105 and by OSU-R/UMS3365 – Université de La Réunion. The Eureka\nTCCON measurements were made at the Polar Environment Atmospheric Research Laboratory (PEARL) by the Canadian Network for the\n\n73\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nDetection of Atmospheric Change (CANDAC), primarily supported by the Natural Sciences and Engineering Research Council of Canada,\nEnvironment and Climate Change Canada, and the Canadian Space Agency. TCCON sites at Tsukuba, Rikubetsu and Burgos are supported\nin part by the GOSAT series project. Burgos is supported in part by the Energy Development Corporation Philippines.\n\n74\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1340\n\nReferences\nAbrams, M. C., Toon, G. C., and Schindler, R. A.: Practical example of the correction of Fourier-transform spectra for detector nonlinearity,\nAppl. Opt., 33, 6307–6314, https://doi.org/10.1364/AO.33.006307, 1994.\nAllen, D. 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T., Hase, F., Heikkinen, P., Hermans, C.,\n\n1565\n\nHoffmann, A., Huebner, M., Jones, N., Kivi, R., Langerock, B., Petri, C., Scolas, F., Tu, Q., and Weidmann, D.: Intercomparison of lowand high-resolution infrared spectrometers for ground-based solar remote sensing measurements of total column concentrations of CO2 ,\nCH4 , and CO, Atmospheric Measurement Techniques, 13, 4791–4839, https://doi.org/10.5194/amt-13-4791-2020, 2020.\nSherlock, V., Connor, B., Robinson, J., Shiona, H., Smale, D., and Pollard, D.: TCCON data from Lauder, New Zealand, 120HR,\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\n\n1570\n\nhttps://doi.org/10.14291/tccon.ggg2020.lauder01.R0, 2022a.\nSherlock, V., Connor, B., Robinson, J., Shiona, H., Smale, D., and Pollard, D.: TCCON data from Lauder, New Zealand, 125HR,\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\nhttps://doi.org/10.14291/tccon.ggg2020.lauder02.R0, 2022b.\nShiomi, K., Kawakami, S., Ohyama, H., Arai, K., Okumura, H., Ikegami, H., and Usami, M.: TCCON data from Saga, Japan,\n\n1575\n\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\nhttps://doi.org/10.14291/tccon.ggg2020.saga01.R0, 2022.\nStrong, K., Roche, S., Franklin, J., Mendonca, J., Lutsch, E., Weaver, D., Fogal, P., Drummond, J., Batchelor, R., and Lindenmaier, R.: TCCON data from Eureka, Canada, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.eureka01.R0, 2022.\n\n1580\n\nSussmann, R. and Rettinger, M.: TCCON data from Garmisch, Germany, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.garmisch01.R0, 2017a.\nSussmann, R. and Rettinger, M.: TCCON data from Zugspitze, Germany, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.zugspitze01.R0, 2017b.\nSweeney, C., McKain, K., Higgs, J., Wolter, S., Crotwell, A., Neff, D., Dlugokencky, E., Lang, P., Novelli, P., Mund, J., Moglia,\n\n1585\n\nE., and Crotwell, M.: NOAA Carbon Cycle and Greenhouse Gases Group aircraft-based measurements of CO2 , CH4 , CO,\nN2 O, H2\n\nSF6 in flask-air samples taken since 1992. NOAA Earth System Research Laboratory, Global Monitoring Division.,\n\nhttps://doi.org/10.7289/V5N58JMF, 2018.\nTange, O.: GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February, 42–47, 2011.\nTans, P.: System and method for providing vertical profile measurements of atmospheric gases., U.S. Patent 7,597,014, filed 15 Aug 2006,\n1590\n\nissued 6 Oct 2009, 2009.\nTe, Y., Jeseck, P., and Janssen, C.: TCCON data from Paris, France, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA,\nCalifornia Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.paris01.R0, 2022.\nToon, G.: Atmospheric Non-Voigt Line List for the TCCON 2020 Data Release (GGG2020.R0) [Data set]. CaltechDATA,\nhttps://doi.org/10.14291/TCCON.GGG2020.ATMNV.R0, 2022a.\n\n1595\n\nToon,\n\nG.:\n\nSolar\n\nLine\n\nList\n\nfor\n\nthe\n\nTCCON\n\n2020\n\nhttps://doi.org/TCCON.GGG2020.SOLAR.R0, 2022b.\n\n81\n\nData\n\nRelease\n\n(GGG2020.R0)\n\n[Data\n\nset].\n\nCaltechDATA,\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nToon, G.: Atmospheric Voigt Line List for the TCCON 2020 Data Release (GGG2020.R0) [Data set]. CaltechDATA,\nhttps://doi.org/10.14291/TCCON.GGG2020.ATM.R0, 2022c.\nToon, G.: TCCON/GGG – GGG2020, https://doi.org/10.14291/tccon.ggg2020.stable.R0, 2023.\n1600\n\nTotal\n\nCarbon\n\nColumn\n\nObserving\n\nNetwork\n\n(TCCON)\n\nTeam:\n\n2020\n\nTCCON\n\nData\n\nRelease\n\n(GGG2020),\n\nhttps://doi.org/10.14291/TCCON.GGG2020, 2022.\nTran, D., Delahaye, T., Armante, R., Hartmann, J.-M., Mondelain, D., Campargue, A., Fleurbaey, H., Hodges, J., and Tran, H.: Validation of\nspectroscopic data in the 1.27 µm spectral region by comparisons with ground-based atmospheric measurements, Journal of Quantitative\nSpectroscopy and Radiative Transfer, 261, 107 495, 2021.\n1605\n\nTran, D. D., Tran, H., Vasilchenko, S., Kassi, S., Campargue, A., and Mondelain, D.: High sensitivity spectroscopy of the O2 band at 1.27\nµm:(II) air-broadened line profile parameters, Journal of Quantitative Spectroscopy and Radiative Transfer, 240, 106 673, 2020.\nTran, H., Ngo, N. H., and Hartmann, J.-M.: Efficient computation of some speed-dependent isolated line profiles, Journal of Quantitative\nSpectroscopy and Radiative Transfer, 129, 199–203, 2013.\nWang, Z., Deutscher, N., Warneke, T., Notholt, J., Dils, B., Griffith, D. W., Schmidt, M., Ramonet, M., and Gerbig, C.: Retrieval of tropo-\n\n1610\n\nspheric column-averaged CH 4 mole fraction by solar absorption FTIR-spectrometry using N 2 O as a proxy, Atmospheric Measurement\nTechniques, 7, 3295–3305, 2014.\nWarneke, T., Messerschmidt, J., Notholt, J., Weinzierl, C., Deutscher, N., Petri, C., Grupe, P., Vuillemin, C., Truong, F., Schmidt, M., Ramonet, M., and Parmentier, E.: TCCON data from Orleans, France, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA,\nCalifornia Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.orleans01.R0, 2022.\n\n1615\n\nWashenfelder, R. A., Wennberg, P. O., and Toon, G. C.: Tropospheric methane retrieved from ground-based near-IR solar absorption spectra,\nGeophys. Res. Lett., 30, https://doi.org/10.1029/2003GL017969, 2003.\nWeidmann, D., Brownsword, R., and Doniki, S.: TCCON data from Harwell, Oxfordshire (UK), Release GGG2020.R0,\nhttps://doi.org/10.14291/tccon.ggg2020.harwell01.R0, 2023.\nWennberg, P. O., Roehl, C., Blavier, J.-F., Wunch, D., Landeros, J., and Allen, N.: TCCON data from Jet Propulsion Laboratory, Pasadena,\n\n1620\n\nCalifornia, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA,\nU.S.A., https://doi.org/10.14291/tccon.ggg2020.jpl02.R0, 2022a.\nWennberg, P. O., Roehl, C., Wunch, D., Toon, G. C., Blavier, J.-F., Washenfelder, R., Keppel-Aleks, G., Allen, N., and Ayers, J.: TCCON\ndata from Park Falls, Wisconsin, USA, Release GGG2020R1. TCCON data archive, hosted by CaltechDATA, California Institute of\nTechnology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.parkfalls01.R1, 2022b.\n\n1625\n\nWennberg, P. O., Wunch, D., Roehl, C., Blavier, J.-F., Toon, G. C., and Allen, N.: TCCON data from California Institute of Technology,\nPasadena, California, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.pasadena01.R0, 2022c.\nWennberg, P. O., Wunch, D., Roehl, C., Blavier, J.-F., Toon, G. C., Allen, N., Dowell, P., Teske, K., Martin, C., and Martin, J.: TCCON data\nfrom Lamont, Oklahoma, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\n\n1630\n\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.lamont01.R0, 2022d.\nWennberg, P. O., Wunch, D., Yavin, Y., Toon, G. C., Blavier, J.-F., Allen, N., and Keppel-Aleks, G.: TCCON data from Jet Propulsion\nLaboratory, Pasadena, California, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of\nTechnology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.jpl01.R0, 2022e.\n\n82\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nWexler, A.: Vapor Pressure Formulation for Water in Range 0 to 100◦ C. A Revision, J. Res. Nat. Bur. Stand. A Phys. Chem., 80A,\n1635\n\nhttps://doi.org/10.6028/jres.080A.071, 1976.\nWunch, D., Toon, G. C., Wennberg, P. O., Wofsy, S. C., Stephens, B. B., Fischer, M. L., Uchino, O., Abshire, J. B., Bernath, P., Biraud,\nS. C., Blavier, J.-F. L., Boone, C., Bowman, K. P., Browell, E. V., Campos, T., Connor, B. J., Daube, B. C., Deutscher, N. M., Diao,\nM., Elkins, J. W., Gerbig, C., Gottlieb, E., Griffith, D. W. T., Hurst, D. F., Jiménez, R., Keppel-Aleks, G., Kort, E. A., Macatangay, R.,\nMachida, T., Matsueda, H., Moore, F., Morino, I., Park, S., Robinson, J., Roehl, C. M., Sawa, Y., Sherlock, V., Sweeney, C., Tanaka,\n\n1640\n\nT., and Zondlo, M. A.: Calibration of the Total Carbon Column Observing Network using aircraft profile data, Atmos. Meas. Tech., 3,\n1351–1362, https://doi.org/10.5194/amt-3-1351-2010, 2010.\nWunch, D., Toon, G. C., Blavier, J.-F. L., Washenfelder, R. A., Notholt, J., Connor, B. J., Griffith, D. W., Sherlock, V., and Wennberg,\nP. O.: The Total Carbon Column Observing Network, Philosophical Transactions of the Royal Society A: Mathematical, Physical and\nEngineering Sciences, 369, 2087–2112, https://doi.org/10.1098/rsta.2010.0240, 2011.\n\n1645\n\nWunch, D., Toon, G. C., Sherlock, V., Deutscher, N. M., Liu, C., Feist, D. G., and Wennberg, P. O.: Documentation for the 2014 TCCON\nData Release, https://doi.org/10.14291/TCCON.GGG2014.DOCUMENTATION.R0/1221662, 2015.\nWunch, D., Wennberg, P. O., Osterman, G., Fisher, B., Naylor, B., Roehl, C. M., O'Dell, C., Mandrake, L., Viatte, C., Kiel, M., Griffith, D.\nW. T., Deutscher, N. M., Velazco, V. A., Notholt, J., Warneke, T., Petri, C., Maziere, M. D., Sha, M. K., Sussmann, R., Rettinger, M.,\nPollard, D., Robinson, J., Morino, I., Uchino, O., Hase, F., Blumenstock, T., Feist, D. G., Arnold, S. G., Strong, K., Mendonca, J., Kivi,\n\n1650\n\nR., Heikkinen, P., Iraci, L., Podolske, J., Hillyard, P. W., Kawakami, S., Dubey, M. K., Parker, H. A., Sepulveda, E., García, O. E., Te, Y.,\nJeseck, P., Gunson, M. R., Crisp, D., and Eldering, A.: Comparisons of the Orbiting Carbon Observatory-2 (OCO-2) XCO2 measurements\nwith TCCON, Atmospheric Measurement Techniques, 10, 2209–2238, https://doi.org/10.5194/amt-10-2209-2017, 2017.\nWunch, D., Mendonca, J., Colebatch, O., Allen, N., Blavier, J.-F. L., Kunz, K., Roche, S., Hedelius, J., Neufeld, G., Springett, S., Worthy, D., Kessler, R., and Strong, K.: TCCON data from East Trout Lake, Canada, Release GGG2020R0. TCCON data archive, hosted\n\n1655\n\nby CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.easttroutlake01.R0,\n2022.\nZhou, M., Wang, P., Nan, W., Yang, Y., Kumps, N., Hermans, C., and De Mazière, M.: TCCON data from Xianghe,\nhttps://doi.org/10.14291/tccon.ggg2020.xianghe01.R0, 2022.\n\n83\n\n\f84\n\nCRDS on tower\n\nFlask\n\nCRDS on tower\n\nLicor 7000 NDIR (CO2 ), in situ GHG FTS\n\nCH4 ObsPack\n\nCH4 ObsPack\n\nCH4 ObsPack\n\nNIWA (direct)\n\n(CH4 )\n\nProgrammable flask packages\n\nCH4 ObsPack\n\nLi-cor NDIR on tower\n\nCO2 ObsPack\n\nCRDS on tower\n\nProgrammable flask packages\n\nCO2 ObsPack\n\nCO2 ObsPack\n\nMeasurement type\n\nSource\n\nNIWA = National Institute of Water & Atmospheric Research Ltd.\n\nGreat\n\nDan Smale (NIWA)\n\nGreat\n\nPlains\n\nPlains\n\nPlains\n\nLauder, New Zealand\n\nARM site, OK, USA\n\nSouthern\n\nARM site, OK, USA\n\nBiraud (LBNL), & Margaret Torn (LBNL)\nSebastien Biraud & Margaret Torn (LBNL)\n\nSouthern\n\nGreat\n\nPark Falls, WI, USA\n\nPark Falls, WI, USA\n\nARM site, OK, USA\n\nSouthern\n\nPark Falls, WI, USA\n\nPark Falls, WI, USA\n\nLocation\n\nEd Dlugokencky (NOAA GML), Sebastien\n\nsai (U. of WI), & Dan Baumann (USGS)\n\nArlyn Andrews (NOAA GML), Ankur De-\n\nWI), & Dan Baumann (USGS)\n\nkencky (NOAA GML), Ankur Desai (U. of\n\nArlyn Andrews (NOAA GML), Ed Dlugo-\n\nSebastien Biraud & Margaret Torn (LBNL)\n\n(USGS)\n\nAnkur Desai (U. of WI), & Dan Baumann\n\nkencky (NOAA GML), Ken Davis (PSU),\n\nArlyn Andrews (NOAA GML), Ed Dlugo-\n\nWI), & Dan Baumann (USGS)\n\nwin, Ken Davis (PSU), Ankur Desai (U. of\n\nArlyn Andrews (NOAA GML), Peter Bak-\n\nProviders/partners\n\nll\n\noc\n\noc\n\npa\n\npa\n\noc\n\npa\n\npa\n\nTCCON site\n\nGeological Survey; LBNL = Lawrence Berkeley National Laboratory; ARM = Atmospheric Radiation Measurement; CRDS = cavity ring-down spectroscopy;\n\nand Atmospheric Administration Global Monitoring Laboratory; PSU = Pennsylvania State University; U. of WI = University of Wisconsin; USGS = United States\n\nparentheses. If only one affiliation is listed, it applies to all individuals named. Abbrevations: NDIR = Nondispersive infrared; NOAA GML = National Oceanic\n\n“TCCON sites” column indicates which sites profile were used at, the IDs are mapped to locations in Table 1. In the “Providers” column, affiliations are given in\n\nIntegration Project, 2019) and “CH4 ObsPack” the CH4 GLOBALVIEWplus v2.0 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020). The\n\nTable C3. Ground in situ data used in validating the priors. “CO2 Obspack” is the CO2 GLOBALVIEWplus v5.0 ObsPack (Cooperative Global Atmospheric Data\n\nhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C4. The number of profiles in the CO2 in situ correction from each campaign or other data source identified and used for each TCCON\nsite. The “Found” column gives the number of profiles identified for that campaign & site, the “Used” column gives the number of those\nprofiles which could be used in the in situ comparison after matching with TCCON data. The definitions of the site IDs can be found in Table\n1; “we” refers to an instrument in Jena, Germany for which GGG2020 data is not available at time of writing.\nCampaign\n\nSite\n\nFound\n\nUsed\n\nCampaign\n\nSite\n\nATom\n\nae\n\n4\n\ndf\neu\n\nFound\n\nUsed\n\n0\n\nINTEX-NA\n\npa\n\n3\n\n3\n\n1\n\n1\n\nKORUS-AQ\n\n2\n\n0\n\nan\n\n1\n\n1\n\ndf\n\n1\n\n1\n\nll\n\n4\n\n4\n\nrj\n\n2\n\n2\n\noc\n\n1\n\n0\n\nORCAS\n\noc\n\n1\n\n1\n\npa\n\n1\n\n1\n\nSEAC4RS\n\ndf\n\n1\n\n1\n\nCOB2004\n\npa\n\n5\n\n4\n\noc\n\n2\n\n0\n\nDC3\n\noc\n\n3\n\n2\n\nSTART-08\n\npa\n\n2\n\n0\n\nGO-Amazon\n\nma\n\n2\n\n1\n\nAirCore\n\ndf\n\n3\n\n3\n\nGSFC\n\ndf\n\n8\n\n7\n\nni\n\n3\n\n2\n\npa\n\n2\n\n2\n\noc\n\n19\n\n13\n\nll\n\n7\n\n5\n\npa\n\n2\n\n2\n\nwg\n\n1\n\n0\n\nso\n\n16\n\n9\n\nbi\n\n2\n\n2\n\nbr\n\n2\n\n0\n\ngm\n\n1\n\n1\n\nje\n\n1\n\n0\n\nka\n\n1\n\n0\n\nor\n\n2\n\n0\n\nHIPPO\nIMECC\n\n85\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C5. Same as Table C4 but for the CH4 in situ correction.\nCampaign\n\nSite\n\nATom\n\nae\n\nHIPPO\n\nFound\n\nUsed\n\n4\n\n0\n\nCampaign\n\nSite\n\nFound\n\nUsed\n\nIMECC\n\nbi\n\n2\n\n2\n\nci\n\n2\n\n1\n\nbr\n\n2\n\n0\n\ndf\n\n1\n\n1\n\ngm\n\n1\n\n0\n\neu\n\n1\n\n0\n\nje\n\n1\n\n0\n\nll\n\n1\n\n1\n\nka\n\n1\n\n0\n\noc\n\n1\n\n0\n\nor\n\n2\n\n0\n\npa\n\n1\n\n1\n\nSTART-08\n\npa\n\n2\n\n1\n\nll\n\n5\n\n3\n\nAirCore\n\ndf\n\n3\n\n3\n\noc\n\n4\n\n1\n\nni\n\n3\n\n2\n\npa\n\n1\n\n0\n\noc\n\n19\n\n13\n\nwg\n\n1\n\n0\n\npa\n\n2\n\n2\n\nso\n\n16\n\n9\n\nTable C6. Values of ∂r/∂Xluft in Eq. (C11). Gases not listed here use 0 for ∂r/∂Xluft .\nGas\n\n∂r/∂Xluft\n\nCO2\n\n0.363\n\nwCO2\n\n0.206\n\nlCO2\n\n0.928\n\nCH4\n\n0.0609\n\n86\n\n\f" | |
https://openalex.org/W2741431339 | https://www.nature.com/articles/s41598-017-07981-4.pdf | English | null | Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice | Scientific reports | 2,017 | cc-by | 10,713 | Three TF Co-expression Modules
Regulate Pressure-Overload
Cardiac Hypertrophy in Male Mice
Yao-Ming Chang 1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthur
Chun-Chieh Shih4 & Chien-Chang Chen2 Received: 20 March 2017
Accepted: 3 July 2017
Published: xx xx xxxx Received: 20 March 2017
Accepted: 3 July 2017
Published: xx xx xxxx Yao-Ming Chang 1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthu
Chun-Chieh Shih4 & Chien-Chang Chen2 Pathological cardiac hypertrophy, a dynamic remodeling process, is a major risk factor for heart
failure. Although a number of key regulators and related genes have been identified, how the
transcription factors (TFs) dynamically regulate the associated genes and control the morphological and
electrophysiological changes during the hypertrophic process are still largely unknown. In this study,
we obtained the time-course transcriptomes at five time points in four weeks from male murine hearts
subjected to transverse aorta banding surgery. From a series of computational analyses, we identified
three major co-expression modules of TF genes that may regulate the gene expression changes during
the development of cardiac hypertrophy in mice. After pressure overload, the TF genes in Module 1
were up-regulated before the occurrence of significant morphological changes and one week later were
down-regulated gradually, while those in Modules 2 and 3 took over the regulation as the heart size
increased. Our analyses revealed that the TF genes up-regulated at the early stages likely initiated the
cascading regulation and most of the well-known cardiac miRNAs were up-regulated at later stages
for suppression. In addition, the constructed time-dependent regulatory network reveals some TFs
including Egr2 as new candidate key regulators of cardiovascular-associated (CV) genes. Many heart related diseases, such as ischemic heart disease, hypertension, heart failure, and valvular heart dis-
ease, are accompanied by cardiac hypertrophy1. This type of cardiac hypertrophy, also called pathological hyper-
trophy, is associated with altered cardiac gene expression, fibrosis, and cardiac dysfunction and can progress to
heart failure eventually. In contrast, the other type of cardiac hypertrophy is physiological and occurs in response
to chronic exercise training that is reversible and characterized by normal cardiac morphology without fibrosis
or apoptosis2. The gene regulation network involved in the hypertrophic process is still largely unknown. Studies
using animal models have identified a few genes and regulators and verified some of their specific roles in cardiac
hypertrophy3–13. The development of cardiac hypertrophy is a dynamic process, and a few studies have taken this
fact into consideration14–16. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Results Animal model of cardiac hypertrophy, experimental design, and transcriptome data process-
ing. Adult male C57BL/6 J mice were anaesthetized and subjected to pressure overload by transverse aortic
banding (TAB) according to the method described previously18, 19. The RNAs of cardiac tissues were taken from
the left ventricles of mouse hearts subjected to TAB or sham operation at days 3, 5, 7, 14, and 28 after surgery
(Suppl. Fig. S1). The expression changes of mRNAs and miRNAs were measured by cDNA and miRNA microar-
rays, respectively. After the data processing and within and between sample normalizations (see Methods), the
total numbers of genes and miRNAs for this study are 16,152 and 928, respectively. The expression fold-changes
of each gene and miRNA at each time point were separately calculated by the log2 ratio of the normalized inten-
sity values with and without the pressure overload treatment (Suppl. File S1). Day 5 is the major transitional stage of transcriptome expression after pressure overload in
mouse hearts. We first calculated the Pearson correlation coefficient (PCC) of gene expressions between
sham and TAB at different time points. To reduce the bias that might arise from extremely high or low gene
expression levels, those genes with expression intensity values above the top 1% or below the bottom 1% of all
expressed genes at any time point were removed. Furthermore, to avoid the PCC being dominated by genes inde-
pendent of the TAB treatment, the genes with expression differences between the two conditions that were not
greater than one standard deviation in all time points were removed as well. Then, the PCCs of the total intensity
values of the filtered non-TF genes (6,579 genes) between two different conditions were calculated for each time
point (Suppl. Fig. S2). The same procedure was applied to 928 miRNAs and 606 TF genes to calculate their PCCs. For non-TF genes, the PCC between sham and TAB decreased from day 3 (0.77) to the minimum (0.68) at day 5
(blue line in Fig. 1). After day 5, the PCC increased from 0.78 at day 7, to 0.86 at day 14, and to 0.92 at day 28. The
PCCs for TF genes showed similar tendencies: they were 0.84, 0.71, 0.86, 0.91, and 0.96 for days 3, 5, 7, 14, and
28, respectively (red line in Fig. 1). www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 1. Pearson correlation coefficients (PCCs) of the expression intensity values of filtered non-TF genes
(with expressional differences greater than 1 standard deviation but excluding those at the top and bottom 1%
intensity values), TF genes, and microRNAs between with and without pressure overload in the cardiac samples
at days 3, 5, 7, 14, and 28. The blue, red, and green lines represent the PCCs for filtered non-TF genes, TF genes,
and microRNAs, respectively. Figure 1. Pearson correlation coefficients (PCCs) of the expression intensity values of filtered non-TF genes
(with expressional differences greater than 1 standard deviation but excluding those at the top and bottom 1%
intensity values), TF genes, and microRNAs between with and without pressure overload in the cardiac samples
at days 3, 5, 7, 14, and 28. The blue, red, and green lines represent the PCCs for filtered non-TF genes, TF genes,
and microRNAs, respectively. modularized? (3) What roles do these TFs or miRNAs play in stress-induced cardiac hypertrophy? To answer
these questions, we first conducted a time course experiments to collect mRNA and miRNA expression data at
five different time points from thoracic aortic banding (TAB)- and sham-operated (control) mouse hearts. Then,
we analyzed the time-course transcriptome data and integrated them with the regulatory information from public
bioinformatics databases. Based on the results, we attempted to answer the above questions one by one and iden-
tified the candidate TFs and miRNAs at different stages of cardiac hypertrophy. Three TF Co-expression Modules
Regulate Pressure-Overload
Cardiac Hypertrophy in Male Mice
Yao-Ming Chang 1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthur
Chun-Chieh Shih4 & Chien-Chang Chen2 For example, Friddle et al.14 conducted a time course experiment, taking a total RNA
sample from heart tissue of the drug-induced cardiac hypertrophy each day in two weeks, and identified dozens
of genes associated with cardiac hypertrophy. Van den Bosch et al.16 conducted another time course experiment
from aortic banding-induced cardiac hypertrophy at five time points in 8 weeks and found many differentially
expressed genes associated with metabolic activity for compensated hypertrophy. In addition, Sheehy et al.15 com-
pared the temporal change of transcriptomes measured in hearts subjected to either exercise-induced or aortic
banding–induced hypertrophy at different time points. As most studies took cardiac samples only at few time
points, a comprehensive study of how the transcription factors (TFs) dynamically regulate the associated genes
during the hypertrophic process is still lacking. Noting that heart undergoes morphological and electrophysiological changes to overcome a pressure over-
load, Meerson and colleagues divided cardiac remodeling into three stages: developing hypertrophy, compensa-
tory hypertrophy, and overt heart failure1, 17. However, how these morphological and electrophysiological changes
are regulated is still largely unknown. In this study, we raised three questions: (1) Which genes are involved in
the hypertrophic process, from developing hypertrophy to compensatory hypertrophy and to overt heart failure
stages? (2) Which TFs or miRNAs are responsible for inducing these changes and are they co-regulated and 1Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. 2Institute of Biomedical Sciences, Academia Sinica,
Taipei, Taiwan. 3Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA. 4Institute
of Information Science, Academia Sinica, Taipei, Taiwan. Correspondence and requests for materials should be
addressed to A.C.-C.S. (email: arthur@iis.sinica.edu.tw) or C.-C.C. (email: ccchen@ibms.sinica.edu.tw) SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 1 1 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 Results For miRNAs, the PCCs also decreased from day 3 (0.95) to day 5 (0.87), then
slowly increased from 0.91 at day 7 to 0.93 at day 14, but decreased to 0.86 at day 28, which was similar to that
for day 5 (green line in Fig. 1). Anatomically, the morphology of the heart after pressure overload still appeared
normally at day 3. The heart size started to increase from day 5 to day 7 and became significantly larger in the TAB
group (Suppl. Fig. S3A). The ratio of heart weight over body weight (HW/BW, an index of cardiac hypertrophy)
remained similar between the TAB and sham groups at day 3 after surgery in mice and started to increase from
day 5 to day 7 and reached a stable level at day 14 in TAB mice20, 21 (Suppl. Fig. S3B).i y
y
y
pp
g
In summary, we made three observations (Fig. 1): (1) the PCCs for filtered non-TF genes and TF genes in
murine hearts after pressure overload decreased from day 3 and reached the lowest at day 5. Then, the PCCs
slowly returned to the same level as in the case without pressure overload. Therefore, day 5 is the critical transi-
tional stage of gene regulation during the process of TAB-induced cardiac hypertrophy in male murine hearts. This observation is consistent with the result that most genes within the process of compensated hypertrophy
returned to basal expression levels one week after TAB16. (2) The PCCs for all filtered non-TF genes and for TF
genes showed similar tendencies of change, indicating that most non-TF gene expression changes may be directly
or indirectly regulated by TFs. (3) For miRNAs, its PCC after day 5 did not return to the normal level as those for
filtered non-TF genes and TF genes, but had a significant change at day 28. It seems that after day 5 the miRNA
expression may have different regulatory mechanisms than those for filtered non-TF genes and TF genes. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 2 www.nature.com/scientificreports/ Figure 2. Proportions of differentially expressed (DE) genes and miRNAs and the number of enriched GO
terms for DE genes at different time points. (A) Proportions of DE genes (blue bars) and miRNAs (red bars)
that first time occurred at a time point. (B) Number of enriched GO terms for DE genes at a time point. Results We confirmed some of the DE genes using quanti-
tative real-time RT-PCR and the results showed that Egr1, Egr2 and cMyc are indeed differentially expressed after
TAB surgery at different time points (Suppl. Fig. S5).ii f
Next, we inferred the enriched functions for identified DE genes. Using all identified DE genes as the queries
and all expressed genes as the background (see Methods), we found 76, 30, and 15 enriched GO terms belonging
to 20, 10, and 9 similar groups in the categories of biological process (BP), molecular function (MF), and cellular
component (CC), respectively (Suppl. Table S1). The enriched functions for the up-regulated DE genes, includ-
ing stimulus receptor on membrane, intracellular signal transduction, inflammatory response, and so on. These
observations are mostly consistent with previous studies22, 23. y
However, the numbers of enriched GO terms at different time points were not evenly distributed. We used
the DE genes identified at each time point and inferred their enriched GO functions. After collecting the GO
categories, we found 78, 426, 308, 46, and 25 GO terms enriched at days 3, 5, 7, 14, and 28, respectively (Fig. 2B). The numbers of enriched GO terms at days 5 and 7 were several times higher than those for the other three
time points, although the numbers of DE genes between different time points did not differ significantly (Suppl. Fig. S4A and C). This result indicates that the DE genes at days 5 and 7 had more enriched functions related to
pressure-overload induced cardiac hypertrophy. We then asked whether the enriched functions were derived from the DE genes that were already up-regulated
before or at that time point. We divided the up-regulated DE genes at a time point into two sets: (1) up-regulated
for the first time at that time point; these genes were classified in the New+ set (purple bars in Fig. 2C) and (2)
already up-regulated at a previous time point(s); these genes were classified in the Old+ set (orange bars in
Fig. 2C). After the functional enrichment analysis, we found that the total numbers of enriched GO terms for the
DE genes in the New+ and Old+ sets were almost the same in day 5, but those for day 7 were mostly from the
Old+ set (Fig. 2D). Results (C)
Numbers of up-regulated DE genes with first time up-regulation (New+ set; purple bars) at a time point and DE
genes up-regulated at a previous time point (Old+ set; orange bars). (D) Numbers of enriched GO terms for DE
genes from the New+ set (purple bars) and DE genes from the Old+ set (orange bars) at a time point. Figure 2. Proportions of differentially expressed (DE) genes and miRNAs and the number of enriched GO
terms for DE genes at different time points. (A) Proportions of DE genes (blue bars) and miRNAs (red bars)
that first time occurred at a time point. (B) Number of enriched GO terms for DE genes at a time point. (C)
Numbers of up-regulated DE genes with first time up-regulation (New+ set; purple bars) at a time point and DE
genes up-regulated at a previous time point (Old+ set; orange bars). (D) Numbers of enriched GO terms for DE
genes from the New+ set (purple bars) and DE genes from the Old+ set (orange bars) at a time point. Functional enrichments of genes and miRNAs differentially expressed at early stages. The
genes and miRNAs whose expression levels differed significantly between sham and TAB at least at one time point
were defined as differentially expressed (DE) genes and miRNAs, respectively. We identified the DE genes and
miRNAs from the whole transcriptome data for each time point and used the DE genes to predict their potential
functions by Gene Ontology (GO) term enrichment analysis (see Methods).ih y
gy
y
We identified 2,853 DE genes and 148 DE miRNAs. There were 851, 917, 911, 908, and 948 genes and 64,
61, 67, 48, and 63 miRNAs differentially expressed at days 3, 5, 7, 14, and 28, respectively (Suppl. Fig. S4). There
was no significant difference in the numbers of either DE genes or DE miRNAs between different time points. However, if we only considered the DE genes and miRNAs that were either up- or down-regulated for the first
time at a specific time point, the proportions were 30%, 20%, 15%, 17%, and 18% of DE genes and 43%, 23%, 7%,
18%, and 9% of DE miRNAs at days 3, 5, 7, 14, and 28, respectively (Fig. 2A). Thus, half of DE genes and more
than half of DE miRNAs arose for the first time at day 3 or 5. Results That is, the number of up-regulated TF genes in Module
1 increased from day 3 to day 7 and then decreased, while those in Module 2 increased from day 14 to day 28
(Fig. 3C). For down-regulated TF genes, in contrast, the number in Module 1 increased from day 7 to day 14,
while that in Module 2 decreased from day 3 to day 7 and that in Module 3 increased at day 7 and then decreased
(Fig. 3D). Next, the enriched functions for the TF genes and their coexpressed DE genes in each module were predicted. We first defined a DE gene as coexpressed with a TF gene if its intensity profile was positively correlated with
that of the TF gene (PCC ≥ 0.9). After identifying the coexpressed genes, we conducted a functional enrichment
analysis with GO-Slims, a cut-down version of the GO ontologies, for the three modules at each time point. We
found 8, 28, 14, 11, and 14 GO-Slim terms enriched for days 3, 5, 7, 14, and 28, respectively, so the maximum
number of enriched functions occurred at day 5 (Suppl. Fig. S7). The coexpressed DE genes in Module 1 had
more enriched GO-Slim terms than those in the other two modules. Moreover, most of the GO-Slim terms for
day 5 covered more than 75% of the total enriched functions for all time points. This result indicates that the DE
genes coexpressed with the TF genes in Module 1, particularly those at day 5, may play a broader role than those
in other modules during the hypertrophic process. We also checked the enriched functions of TFs themselves for each module at each time point. To identify
enriched functions of a TF in the network, we applied the GO-Slim enrichment analysis using all expressed genes
as the background but excluding those genes related to fundamental transcriptional molecular-level functions
(see Methods). For the TF genes in Module 1, the enriched functions, particularly for those up-regulated at day
3, included skeletal system, nervous system, and muscle organ development, segment specification, pattern spec-
ification process, and cell cycle (Fig. 4). However, only skeletal system, muscle organ, system development, and
cell cycle can be found at the later time points in the same module and the enriched functions of digestive tract
mesoderm development were found at day 14 only. Results In contrast, we could not find any enriched functions for the
down-regulated TF genes in Module 1 from day 3 to day 7. In addition, almost all enriched functions found for
up-regulated TF genes in Module 1 from day 3 to day 14 were also enriched for down-regulated TF genes at day
28 (Fig. 4), indicating that these enriched functions were up-regulated mostly at day 3 or at days 5, 7, and 14 but
were all down-regulated at day 28. The transition in enriched functions from day 14 to day 28 could be explained
by switching from up- to down-regulated TF genes in Module 1 (Fig. 3). For the up-regulated TF genes in Module 2, only the function of biosynthesis process was enriched at day 5 but
many important functions were enriched at day 28, including ectoderm, nervous system, muscle organ, embryo,
and mesoderm development (Fig. 4). For the down-regulated TF genes in Module 2, most enriched functions
were found at days 3 and 14 (Fig. 4). In contrast to Module 1, most of the up-regulated TF genes in Module 2 did
not have enriched functions until day 28. At day 28, many enriched functions for down-regulated TF genes in
Module 1 were also found for up-regulated TFs in Module 2, indicating that TF genes in Module 2 were recruited
to regulate these functions in the later stage of pressure overload. For TF genes in Module 3, we found no enriched function for the up-regulated TF genes at any time point,
while many functions for down-regulated TF genes were found at day 7 (Fig. 4). Th
b
l
l h
h
d TF
M d l
d
l
l
h The above results reveal that the coexpressed TF genes in Modules 1 and 2 successively regulate the important
functions associated with the cardiac hypertrophy. The TF genes in Module 1 probably responded to the pressure
overload stimulus at the early stage (day 3) and continuously regulated some developmental functions until day
14. Then, the TF genes in Module 2 took over most of the functions and had four extra enriched functions at day
28. Finally, the TF genes in Module 3 had a few enriched functions from days 7 to 28. MiRNAs may suppress the expression of TF genes at different stages. Results That is, most of the enriched functions at day 7 were derived from the DE genes up-regulated
at either day 3 or day 5 and those first up-regulated at day 7 did not seem to have strong functional preference. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 3 www.nature.com/scientificreports/ Thus, the DE genes that were up-regulated at an early time point (day 3 or 5) likely play a more specific role than
those upregulated at a later stage in the process of TAB-induced cardiac hypertrophy in mice. Three TF coexpression modules regulate the genes with enriched functions related to cardiac
hypertrophy. We used all DE TF genes and their expression profiles in TAB to construct a coexpression
network in which each node represents a DE TF gene and an edge between two nodes represents a positive
correlation (PCC ≥ 0.9) between the two DE TF genes. In the network, there were 206 DE TF genes each with at
least one edge and the total number of edges was 670 (Fig. 3A). The network could be partitioned by a modified
bridge-finding algorithm into three major modules, Modules 1, 2, and 3, which included 94, 79, and 33 TF genes,
respectively (Fig. 3A; see Methods). In addition, there were 8 DE TF genes that had no connection with any TF
gene in the first three modules; they were assigned to Module 4 and were ignored in the subsequent analysis. d h
d d
l
f
h
h
d l
d i
We integrated the up and down regulation information at each time point into the modules (Fig. 3B), and
found that Modules 1, 2 and 3 showed distinct gene up- and down-regulation patterns (numbers shown in Fig. 3C
and D and proportions shown in Suppl. Fig. S6). In Module 1, most of the TF genes were up-regulated from days
3 to 7 and half of them were down-regulated after day 7 (Suppl. Fig. S6A). In Module 2, most of the TF genes
were down-regulated at days 3 and 5 (Fig. 3D), but they began to be up-regulated after day 5 (Suppl. Fig. S6B). In Module 3, over half of the TF genes were down-regulated at day 7 (Suppl. Fig. S6C), while a few of the TF
genes were up-regulated at other time points (Fig. 3C). Results We defined that a DE
miRNA putatively suppresses the expression of a TF gene at a time point if the following three conditions are
satisfied: (1) at least one binding site of the DE miRNA is found in the 3′UTR of the TF gene, (2) the miRNA
is up-regulated at the time point, and (3) the TF gene is not up-regulated at that time point. According to this
definition, we found that 69 miRNAs might down-regulate the expression of 130 TF genes at any of the five time
points (Suppl. File S2). The numbers of the suppressing miRNAs and corresponding TF targets are 28, 37, 31, 22,
and 44, and 93, 79, 87, 68, and 92 at days 3, 5, 7, 14, and 28, respectively (Suppl. Fig. S8). Because a miRNA can
suppress multiple TF genes and a TF gene can be targeted by multiple miRNAs, the relationships of suppression
from miRNAs to TF genes can be many-to-many. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 4 www.nature.com/scientificreports/ Figure 3. A positive gene coexpression network for differentially expressed (DE) TF genes under the TAB
condition. (A) The four modules of TF genes in the network. (B) TF genes in Modules 1, 2 and 3 have different
patterns of differential expression at each time point. The red and green nodes, respectively, indicate the up- and
down-regulated TF genes at the time point. The line charts represent the numbers of (C) up-regulated and (D)
down-regulated DE TF genes in Modules 1, 2 and 3 at different time points. Figure 3. A positive gene coexpression network for differentially expressed (DE) TF genes under the TAB
condition. (A) The four modules of TF genes in the network. (B) TF genes in Modules 1, 2 and 3 have different
patterns of differential expression at each time point. The red and green nodes, respectively, indicate the up- and
down-regulated TF genes at the time point. The line charts represent the numbers of (C) up-regulated and (D)
down-regulated DE TF genes in Modules 1, 2 and 3 at different time points. We found that the up-down trend for the numbers of suppressing DE miRNAs was opposite to that for the
number of suppressed TF gene targets at Day3 and day 5, but the same after day 7 (Suppl. Fig. S8). Results Based on this
observation, we combined the analysis from the TF gene coexpression network of TF genes and miRNAs and
hypothesized that the functions related to cardiac hypertrophy were induced by the up-regulated TF genes in
Module 1 at days 3 and 5 but suppressed by some miRNAs after day 7. Runt related transcription factor 1 (Runx1),
for example, in Module 1 is a key regulator of heart post-myocardial infarction24 and was up-regulated from day
3 to day 14 and likely suppressed by some known cardiac miRNAs, such as miR-126–5p, miR-195, miR-208b, and SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 5 www.nature.com/scientificreports/ Figure 4. The enriched GO-Slim terms of TFs in the three modules at each time point. The major columns on
left represent the five time points from day 3 to day 28 and the three sub-columns within each major column
represent Modules 1, 2, and 3. The rows give the GO-Slim descriptions. The up and down arrows represent the
GO Slim in the row enriched (FDR<0 05) for up and down regulated DE TF genes of the modules at the time Figure 4. The enriched GO-Slim terms of TFs in the three modules at each time point. The major columns on
left represent the five time points from day 3 to day 28 and the three sub-columns within each major column
represent Modules 1, 2, and 3. The rows give the GO-Slim descriptions. The up and down arrows represent the
GO-Slim in the row enriched (FDR < 0.05) for up- and down-regulated DE TF genes of the modules at the time
point. miR-21 at day 28 (Suppl. File S2). As another example, Cyclin E1 (Ccne1), a regulator related to defective cardi-
ovascular development25, also in Module 1, was up-regulated at days 3, 7, and 14 and likely suppressed by miR-
26b and miR-107 at day 28. Moreover, Toll-like receptor 2 (Tlr2), a regulator involved in the signaling pathway of
cardiomyocyte dysfunction and inflammatory responses26, also in Module 1, was up-regulated at day 7 and then
likely suppressed by miR-208b at days 14 and 28. Gene Regulatory Network for Pressure Overload Cardiac Hypertrophy. Integrating our data with
the target pair information from several interactome databases (see Methods), we constructed the regulatory
relationships of DE genes by DE TF genes and DE miRNAs for pressure overload cardiac hypertrophy. Results The three
relationships considered in this network were: (1) the regulatory pair of TF gene and target gene, (2) the regula-
tory pair of miRNA and target gene, and (3) the coexpressed pair of TF gene and miRNA (see Methods). In the
last relationship, we did not consider the regulatory pair of TF gene and miRNA because only a few of the regula-
tory relationships have been identified so far. We identified 207 TF genes, 148 miRNAs, and 1,080 non-TF genes
with the regulatory or coexpressed relationships in TAB. For the target DE genes, we analyzed their enriched
functions and found 220 more enriched GO terms in addition to those for all DE genes (Suppl. File S3). Moreover,
we also found that the proportion of cardiovascular-associated (CV) genes among the target genes (25%) was sig-
nificantly higher than those among total DE genes (20%) and among all expressed genes (20%) (p < 0.01). These 6 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 www.nature.com/scientificreports/ Figure 5. The gene regulatory network in TAB. (A) Network for all TF genes (red nodes), non-TF genes (green
nodes), and miRNAs (purple nodes) and the edges of positive (orange) and negative (blue) regulations in TAB. (B) A schematic gene regulatory network for a TF gene, a miRNA, and a non-TF gene. (C) A sub-network
centered at the TF Egr2 gene to its direct targets, where genes with red name represent the cardiovascular-
associated (CV) genes. Figure 5. The gene regulatory network in TAB. (A) Network for all TF genes (red nodes), non-TF genes (green
nodes), and miRNAs (purple nodes) and the edges of positive (orange) and negative (blue) regulations in TAB. (B) A schematic gene regulatory network for a TF gene, a miRNA, and a non-TF gene. (C) A sub-network
centered at the TF Egr2 gene to its direct targets, where genes with red name represent the cardiovascular-
associated (CV) genes. esults suggest that the identified target DE genes in TAB and the associated regulators (TFs and miRNAs) likely
lay an important role for the induction of cardiac hypertrophy by pressure overload. In addition, we integrated these relationships together and constructed a regulatory/coexpressed network. In
the network, each node represents a gene, a TF gene, or a miRNA (Fig. 5A) and each edge represents one type of
the three relationships between two nodes (Fig. 5B). www.nature.com/scientificreports/ www.nature.com/scientificreports/ CV gene
TF Name
Number of edges
Outward (+, −)
Inward (+, −)
D3
D5
D7
D14
D28
1
Runx1
64
53 (43, 10)
11 (5, 6)
1
1
1
1
1
Il6
41
37 (29, 8)
4 (3, 1)
1
1
1
1
Egr2
34
32 (24, 8)
2 (2, 0)
1
1
1
1
1
Sox9
24
24 (19, 5)
0 (0, 0)
1
1
1
1
1
Tlx1
21
21 (7, 14)
0 (0, 0)
−1
−1
Pou2f2
82
80 (64, 16)
2 (1, 1)
1
1
1
Batf
37
34 (30, 4)
3 (1, 2)
1
1
1
Mxi1
19
18 (7, 11)
1 (0, 1)
−1
Sox10
15
15 (13, 2)
0 (0, 0)
1
Tgif1
20
14 (13, 1)
6 (2, 4)
1
1
1
Vdr
55
52 (43, 9)
3 (2, 1)
1
1
Irf7
36
34 (33, 1)
2 (2, 0)
1
1
Pou2af1
17
17 (11, 6)
0 (0, 0)
1
1
Rest
17
17 (8, 9)
0 (0, 0)
−1
1
Nfe2
14
13 (9, 4)
1 (0, 1)
1
E2f1
153
152 (127, 25)
1 (0, 1)
1
1
Egr1
128
124 (99, 25)
4 (3, 1)
−1
1
Fos
92
92 (80, 12)
0 (0, 0)
−1
Rfx4
19
18 (15, 3)
1 (1, 0)
−1
−1
1
Rel
19
17 (17, 0)
2 (0, 2)
−1
−1
1
Gata1
35
34 (30, 4)
1 (0, 1)
−1
Gli1
39
34 (16, 18)
5 (0, 5)
−1
Zfp354c
13
12 (8, 4)
1 (0, 1)
−1
1
Egr3
9
9 (8, 1)
0 (0, 0)
1
Prdm1
9
6 (5, 1)
3 (1, 2)
1
miRNA ID
Number of edges
Outward
Inward
D3
D5
D7
D14
D28
mmu-miR-26b
78
70
8
1
1
1
mmu-miR-23b
60
54
6
1
1
1
1
1
mmu-miR-98
54
44
10
1
1
1
1
1
mmu-let-7b/g/e
46
37
9
1
1
mmu-miR-146a/b
22
18
4
1
1
mmu-miR-130a
23
14
9
1
1
mmu-miR-3963
14
10
4
1
mmu-miR-125a-5p
14
6
8
1
1
mmu-miR-1224
9
7
2
−1
mmu-miR-208b
47
39
8
1
1
mmu-miR-126-5p
42
31
11
1
1
mmu-miR-130b
27
21
6
1
mmu-miR-497
58
48
10
1
mmu-miR-499
45
36
9
1
mmu-miR-152
34
29
5
1
Table 1. List of hubs in TAB-preferential regulatory network for each time point. www.nature.com/scientificreports/ (A) Top 5 TF genes (upp
table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point Table 1. List of hubs in TAB-preferential regulatory network for each time point. (A) Top 5 TF genes (upper
table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point. The values 1 and −1 in the five right most columns represent up- and down-regulated differential expression,
respectively, from day 3 to day 28. Table 1. List of hubs in TAB-preferential regulatory network for each time point. (A) Top 5 TF genes (upper
table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point. The values 1 and −1 in the five right most columns represent up- and down-regulated differential expression,
respectively, from day 3 to day 28. 41, 34, 24, and 21, respectively (Table 1A). Three of them, Runx1, Il6, and Sox9, have been reported as CV genes
in previous studies24, 27, 28. In addition, at the same time point three first emerged miRNAs with the three largest
numbers of connecting edges were miR-26b, miR-23b, and miR-98 (Table 1B), which all have been reported as
relevant miRNAs in cardiac hypertrophy29–31. Results For each pair of TF gene and target gene, the edge represents
the positive or negative regulation from the TF gene to the target gene. For each pair of miRNA and gene, the edge
represents the negative regulation from the miRNA to the target gene. For each pair of TF gene and miRNA, the
edges from miRNA to TF gene and from TF gene to miRNA represent the negative regulation and positive coex-
pression, respectively. Egr2, an example shown in Fig. 5C, was one of the key regulators in TAB and had 30 target
genes, including two TF genes, and was coexpressed with one miRNA. In addition, ~75% of the target genes were
positively coexpressed with Egr2, indicating that Egr2 is a positive regulator for most target genes. To identify important regulators at each time point, we calculated the numbers of inward and outward edges
and their sum for each regulator node. Then, the regulator nodes that first emerged at that time point were
selected and sorted by the numbers of connecting edges. Table 1A and B show the connection and merged infor-
mation for top 5 selected TF genes and top 3 selected miRNAs, respectively, at each time point. For example,
Runx1, Interleukin 6 (Il6), Early growth factor 2 (Egr2), Sex determining region y-box 9 (Sox9), and T-cell leukemia
homeobox 1 (Tlx1) were the top 5 TF genes that first emerged at day 3 and their total numbers of edges are 64, SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 7 www.nature.com/scientificreports/ In addition, many enriched GO groups were
also associated with the event of hypertrophic stimulus response22, such as detection of stimulus (GO:0051606),
response to stimulus (GO:0050896), sensory perception of chemical stimulus (GO:0007606), positive regula-
tion of response to external stimulus (GO:0032103) in BP category, receptor activity (GO:0004872), ion channel
activity (GO:0005216) in MF category and membrane part (GO:0044425), extracellular matrix (GO:0031012) in
CC category. For the event of intracellular signaling, the GO similar groups such as G-protein-coupled receptor
signaling pathway (GO:0007186) in the BP category, cytokine activity (GO:0005125), and molecular transducer
activity (GO:0060089) in the MF category were overrepresented. Moreover, other GO groups regarding the gene
regulation were enriched in our analysis, such as negative regulation of peptidase activity (GO:0010466), positive
regulation of behavior (GO:0048520), cell proliferation (GO:0008284), immune system process (GO:0002684),
and multicellular organismal process (GO:0051240) in BP category (Suppl. Table 1).i g
p
(
)
g
y (
pp
)
In term of specific genes as hypertrophic markers32, 33, some immediate-early genes, such as Fos and Egr1,
and fetal genes, such as Atrial natriuretic factor (Nppa), Beta-myosin heavy chain (Myh7), and Skeletal alpha actin
(Acta1) were also differentially expressed. However, many of these genes were not up-regulated or down-regulated
at all time points. For example, Myh7 was up-regulated at all time points except day 14, whereas Egr1, a TF, was
down-regulated only at day 14. Thus, our data suggest that cardiac samples should be taken at several different
time points over the time course in order, to have a reliable view of the gene expression profile over the time
course.h The dynamic change of individual gene revealed in this study suggests critical time point of each gene play-
ing its role to affect the progression of cardiac hypertrophy (Suppl. File. S1). For example, Fkbp1b modulates
the calcium release from sarcoplasmic reticulum in cardiomyocyte and disruption of Fkbp1b results in cardiac
hypertrophy in male mice34. In our results, during the developing stage, Fkbp1b was downregulated only before
the hypertrophic growth of myocardium (day 3) and this suggests that downregulation of Fkbp1b at day 3 may
be important to trigger the hypertrophic growth of heart. In contrast, expression pattern of Egr1 was upregulated
and reached maximal level in the early stage (day 5) and downregulated at day 14. www.nature.com/scientificreports/ coexpression network was constructed. Based on these results, we made the following observations that may
answer questions related to the gene regulation in cardiac hypertrophy.i q
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First, the PCCs for filtered non-TF genes, TF genes, and miRNAs between TAB and sham decreased from day
3, reached the lowest at day 5, and then returned to the same level at days 7 and 14 (Fig. 1). The global expression
change was likely caused by many genes and miRNAs simultaneously in response to the pressure overload stimuli
in the early stage, consistent with the previous study of pressure overload induced cardiac hypertrophy in mice16. Second, for miRNAs a globally significant transition occurred at day 28 (Fig. 1), indicating that miRNAs may
play a regulatory role in cardiac hypertrophy at day 28. Third, the number of changes between suppressing DE
miRNAs and that of suppressed DE TF gene targets showed the same trend only after day 7. We speculated that
many DE TF genes were regulated by DE miRNAs in the later stages (Suppl. Fig. S8). Fourth, many CV TF genes
in Module 1 were up-regulated at the early stages but down-regulated by miRNAs later (Suppl. File S2). Fifth,
many functions related to cardiac hypertrophy were enriched in up-regulated DE TF genes in the early stages but
enriched in down-regulated DE TF genes in the later stages (Fig. 4). From the last three observations, we may
speculate that these functions were probably suppressed by DE miRNAs. Therefore, we hypothesize that TFs reg-
ulate genes and miRNAs in responding to the pressure overload stimuli in the early stages, and then miRNAs may
regulate TF genes in a feedback way for maintaining the tissue homeostasis in the hypertrophic process. g
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In term of enriched GO functions for the DE genes, we found that the GO groups were mostly consistent with
the general diagram of events found in the process of cardiomyocyte hypertrophy22, including hypertrophic stim-
ulus response, intracellular signaling, and change in gene expression. www.nature.com/scientificreports/ Our finding suggests that Egr1
participates in developing stage of cardiac hypertrophy but may not be required for the compensatory stage of
hypertrophy. This may be reflected by the reduced cardiac hypertrophy in the Egr1 knockout mice35. In addition,
we found expression of Gli1 was upregulated only at the late stage of cardiac hypertrophy (day 28). Gli1 is a
marker of perivascular mesenchymal stem cells and contributes to injury-induced organ fibrosis36. Removal of
Gli1 + cells reduces the pressure overload-induced cardiac hypertrophy and cardiac fibrosis36. The late induction
of Gli1 may reflect organ damage accumulated after long-term chronic pressure stress and also a hint of initiation
of decompensation. Overall, our time domain-based quantification results can compensate the functional infor-
mation derived from genetic modified mice studies. gi
Based on the targeting and coexpression relationships, we constructed a TF-miRNA-gene regulation and
coexpression network and identified the hubs as potential candidates of essential regulators for cardiac hyper-
trophy (Table 1). Among the 25 TF candidates, 13 (~52%) of them are CV genes, which is significantly higher
than the CV gene proportion in all expressed TF genes (22%), indicating that these detected TF genes are likely
related to cardiac hypertrophy (Table 1A). For example, Egr2, not annotated as a CV gene yet, was differentially
expressed at the beginning of TAB-induced cardiac hypertrophy and ~42% of its targets are CV genes, two of
which, Fibroblast growth factor 8 (Fgf8) and Noggin (Nog), have been reported to negatively regulate cardiac mus-
cle tissue development37, 38. As Egr1 and Egr3, two paralogous genes of Egr2, are both CV genes, and Egr2 is likely
a CV gene and an essential regulator for TAB-induced cardiac hypertrophy. Discussion In this study, we analyzed the murine heart transcriptome data obtained at days 3, 5, 7, 14, and 28 under two
conditions: with and without pressure overload. The expression levels were calculated for all expressed genes and
miRNAs under the two conditions at the five time points and differentially expressed genes and miRNAs were
identified. In addition, the expression profiles of the DE TF genes in TAB were used to infer their coexpression
modules and predict potential functions. According to the targeting and coexpression information, the potential
targets of the miRNAs and TF gene targets were identified and, finally, a TF gene-miRNA-gene regulation and 8 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 www.nature.com/scientificreports/ www.nature.com/scientificreports/ p
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Fluorescent targets were prepared from 2.5 µg total RNA samples using miRNA ULSTM Labeling Kit
(Kreatech Diagnostics. USA) and then were hybridized to the Mouse & Rat miRNA OneArray® with Phalanx
hybridization buffer using OneArray® Hybridization Chamber. After 16 hrs hybridization, non-specific binding
targets were washed away. The slides were scanned using a DNA Microarray Scanner (Model 4000B, Molecular
Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed by GenePix 4.1 soft-
ware (Molecular Devices). The microarray data have been submitted to the National Center for Biotechnology Information Gene
Expression Omnibus database under accession number GSE99460. Quantitative Real-time RT-PCR. The first-strand cDNA was synthesized from 1 μg of total RNA using the
SuperScript III Reverse-Transcriptase Kit (Invitrogen). Real-time PCR reactions were performed in trip-
licate in 96-well plates with use of an ABI 7500 Real-Time PCR System instrument (Applied Biosystems). cDNA was amplified by the SYBR green PCR method (Kapa Biosystems). The relative expressions of Egr1,
Egr2 and cMyc genes were quantified by the comparative cycle threshold (Ct) method (∆∆Ct), with GAPDH
as an endogenous control and normalized to day 3 sham. Sequences for primers were for mouse egr1, sense,
5′-TACGAGCACCTGACCACAGAGT-3′ and antisense, 5′-GCTGGGATAACTTGTCTCCACC-3′; egr2,
sense, 5′-GTTGTGCGAGGAGCAAATGA-3′ and antisense, 5′-GCGAAGCTACTCGGATACGG -3′; cmyc,
sense, 5′-AGCAGCGACTCTGAAGAAGAG-3′ and antisense, 5′-GAGACGTGGCACCTCTTGAG-3′; and for
GAPDH, sense, 5′-CTTCACCACCATGGAGAAGG-3′ and antisense, 5′-GGCATGGACTGTGGTCATGAG-3′. cDNA and miRNA microarray data processing and normalization. For each cDNA array, the inten-
sities were firstly normalized by median scaling normalization method, then taken the average of repeated data
from the same sample. The whole data for a probe were removed if the intensity values were negative or less than
one in any of the five time points. The remaining probe number was 20,021. The quantile approach was applied
for the between-sample normalization. For each time point and condition data set, the intensity values were first
sorted from the highest to the lowest. Second, for each condition the medium values of all intensity values at the
same order positions were calculated. Finally, the normalized intensity values of each data set were re-assigned by
the medium values of each corresponding sorted order position. If a gene had multiple probe sets, only that with
the totally maximum absolute fold changes among all time points was selected to represent the expression profile
of this gene. The final gene number for the analysis was 16,152. www.nature.com/scientificreports/ www.nature.com/scientificreports/ ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes
of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes
of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes
of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. Whole Genome OneArray® and miRNA OneArray®. Total RNA Isolation. Total RNA was
extracted using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The concentration and purity of the RNA was measured by NanoDrop 1000 spectrophotometer (Thermo Fisher
Scientific). Purity was checked by the ratio of the OD260/OD280 and OD260/OD230. The quality of total RNA
was accessed using Agilent 2100 Bioanalyzer (Aglient Technologies, Santa Clara, CA, USA). Mouse OneArray®. The Mouse Whole Genome OneArray® v2 (Phalanx Biotech Group, Taiwan) contains
27,307 DNA oligonucleotide probes, and each probe is a 60-mer designed in the sense direction. Among the
probes, 26,423 probes correspond to the annotated genes in RefSeq v51 and Ensembl v65 database and the other
884 probes are used for control. The detailed descriptions of the gene array list are available at http://www.pha-
lanx.com.tw/products/MOA.php. Fluorescent RNA targets were prepared from 1 µg total RNA samples using OneArray® Amino Allyl aRNA
Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare). They were then hybridized to
the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-specific binding targets were washed away. The slides were scanned using a DNA
microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 Fluorescent intensities of each spot were
analyzed by GenePix 4.1 software (Molecular Devices). Mouse & Rat miRNA OneArray®. Mouse & Rat miRNA OneArray® v3 (Phalanx Biotech Group, Taiwan) con-
tains triplicate 1086 unique miRNA probes from Mouse (miRBase Release 17) and 676 unique miRNA probes
from Rat (miRBase Release 17). In addition, it also contains 144 experimental control probes. The detailed
descriptions of the gene array list are available at http://www.phalanx.com.tw/products/MRmiOA_Probe.php. Materials and Methods Animal model of cardiac hypertrophy and experimental design. Eight-week-old adult male mice
(C57BL/6 J) weighing 20–25 g were anaesthetized (vaporized 1% isoflurane) and subjected to pressure overload
by transverse aortic banding (TAB) according to the method described previously18, 19. Animals were kept under
specific pathogen-free conditions, and all procedures performed were approved by the Institutional Animal
Care and Use Committee (IACUC) of Academia Sinica, Taiwan. All experimental procedures were carried out
in accordance with approved guidelines of the IACUC. The RNAs of cardiac tissues were taken from the left SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 9 www.nature.com/scientificreports/ The species Mus musculus
was selected and the false discovery rate (FDR) threshold was set to 0.05. The functional analysis tool used for the
TFs themselves in the network was PANTHER against the background set of all expressed genes with the FDR
threshold of 0.05 by the Benjamini-Hochberg procedure. Partition for the constructed TF coexpression network. An iterated bisection clustering method was
applied to divide a connected network into multiple partitions step-by-step. First, all the bridges in the network
were identified by a bridge-finding algorithm40. A bridge is an edge that when it is removed from a connected
network, the network is divided into two separate networks. Second, the balancing values for the bridges with
the size (number of nodes in the network) of the larger partition were calculated. Third, the bridge with smallest
balancing value was selected as the cutting edge to divide the network into two partitions. Then the largest one
from all partitions was chosen and divided further by repeating the method until no partition with size greater
than 10 can be obtained, which is too few to do the functional enrichment test. Target gene prediction for TF and miRNA. The TF-target interaction data were integrated from two
different sets: one predicted by Ernst et al.41, which had 468,319 interactions, and the other by Gerstein et al.42,
which had 538,949 interactions. The original data of these two sets were both predicted in human. Using the ort-
holog mapping, both human data sets had been transferred as the mouse data set already41, 42. The two transferred
mouse datasets were combined together. The miRNA-target interaction data was integrated from one experimen-
tal, miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/), and two predicted datasets, TargetScanMouse Release 6.2
(http://www.targetscan.org/mmu_61/) and miRanda August 2010 release (http://www.microrna.org/microrna/). In miRTarBase Release 4.5, the number of miRNA-target interaction pairs for human was 38,113, where the
numbers of miRNAs and target genes were 587 and 12,194, respectively. In contrast, the interaction number
for mouse was only 9,378 where the numbers of miRNAs and target genes were 217 and 4,443, respectively. Using a similar procedure, the human data were converted to the mouse data by the ortholog mapping approach. If the miRNA and targets were both conserved in mouse, the pairs were also applied to the mouse analysis. In total, 48,466 miRNA-target pairs were collected from this data set. www.nature.com/scientificreports/ The Scatter Plots between TAB and sham gene
expression levels at different time points were shown in Suppl. Fig. S2.li pf
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For the miRNA array data, the miRNAs with flags <0 within repeated probes and all chips were filtered out
first. Then, the intensity values from repeated probes within one chip were combined by median. Then the com-
bined values were normalized by a quantile normalized method within technical replicate. The processed data
were provided by Phalanx Biotech Group, Taiwan. The number of remaining miRNAs was 928. The procedure for
between-sample normalization is the same as that for cDNA array data39. TF and cardiovascular-associated gene information. The mouse TFs, transcription co-factors, and
chromatin remodeling factors were collected from AnimalTFDB (http://www.bioguo.org/AnimalTFDB/) includ-
ing 1,457 TFs of 71 families, 107 chromatin remodeling factors, and 279 transcription co-factors. Ignoring those
without gene symbols, the final list included 1,740 TFs, transcription co-factors, and chromatin remodeling fac-
tors in total. The miRNA information was downloaded from miRBase (http://www.mirbase.org/) and the version
was release 17. The cardiovascular GO Annotation Initiative gene list (comprising 4,054 genes) was assembled by SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 10 www.nature.com/scientificreports/ merging 3 existing cardiovascular-associated (CV) gene lists (http://www.ebi.ac.uk/GOA/CVI) and downloaded
from (ftp://ftp.ebi.ac.uk/pub/databases/). merging 3 existing cardiovascular-associated (CV) gene lists (http://www.ebi.ac.uk/GOA/CVI) and downloaded
rom (ftp://ftp.ebi.ac.uk/pub/databases/). Identification of differentially expressed (DE) genes and miRNAs. For each time point, the
fold-change of a gene was calculated by the log2 ratio of the intensity values measured from TAB-operated hearts
over that measured from sham hearts. Then, the average and standard deviation of the total fold-change ratios for
each time point were calculated. A differentially expressed (DE) gene was defined that its fold change was posi-
tively higher or negatively lower than two times of the standard deviation in any of the five time points. The same
procedure was also applied to the miRNA array data. Correlation, statistical test, and functional enrichment analysis. The correlations of two intensity
expression profiles were measured by Pearson correlation coefficient. The functional analysis tool used for the DE
genes and genes coexpressed with DE TF genes in the network were GOrilla (http://cbl-gorilla.cs.technion.ac.il/)
and PANTHER (http://www.pantherdb.org) that can identify enriched Gene Ontology (GO) and GO-Slim terms
in ranked lists of genes against the background set of all expressed genes in this study. www.nature.com/scientificreports/ In the miRanda data set, 246,504 mouse
miRNA-gene interactions had been predicted and were directly downloaded from the microcosm website (http://
www.ebi.ac.uk/enright-srv/microcosm/) with p-value < 0.01, including 568 miRNAs and 19,183 target genes. In
the TargetScanMouse dataset, both the conserved and non-conserved target site predictions were downloaded
and the conserved predictions had 774 miRNAs and 11,828 genes and the non-conserved ones had 779 miRNAs
and 18,249 genes. Finally, these three datasets were combined together and only the pairs of DE miRNAs and DE
target genes were selected. TF-miRNA-gene regulatory and coexpression network construction. The TF-miRNA-gene net-
work was constructed by considering the following three relationships: (1) the regulatory pair of TF gene and tar-
get gene, (2) the regulatory pair of miRNA and target gene, and (3) the coexpressed pair of TF gene and miRNA. For the first relationship, if a DE gene not only was coexpressed, either positively or negatively, with a DE TF gene
in TAB but also had one or more of the DE TF gene predicted binding sites in the promoter region, they were
defined as a regulatory pair of TF gene and target gene. For the second relationship, a regulatory pair of miRNA
and target gene was defined as a DE gene that was not only negatively coexpressed with the DE miRNA in TAB
but also a predicted target of that miRNA. For the third relationship, the coexpressed relationship of TF gene and
miRNA, rather than the regulatory relationship, was considered because only a few of the TF-miRNA interac-
tions were then available. The coexpressed pair of TF gene and miRNA was defined if a DE miRNA was positively
coexpressed with a TF gene only in TAB. All networks were visualized by Cytoscape (http://www.cytoscape.org/). 3. Xin, M., Olson, E. N. & Bassel-Duby, R. Mending broken hearts: cardiac development as a basis for adult heart regeneration and
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15. Sheehy, S. P., Huang, S. & Parker, K. K. Author Contributions C.-C.C. and A.C.-C.S. directed the project and designed the study. L.L., Y.-T.C. and C.-C.C. performed
experiments. Y.-M.C., A.C.-C.S. and C.-C.C. analyzed the data. Y.-M.C., Y.-W.C., W.-H.L., A.C.-C.S. and C.-C.C. wrote the manuscript. Acknowledgements g
We thank Chih-Hao Chang, Han-Chu Hsu, and Shih-Ying Wu for excellent technical assistance. The work was
supported by the Ministry of Science and Technology, Taiwan (102-2320-B-001-012-MY3 and 105-2320-B-001-
020 -MY3 to C.-C.C. and 103-2221-E-001-025-MY2 and 105-2221-E-001-026-MY3 to A.C.-C.S.). SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 12 www.nature.com/scientificreports/ SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 Additional Information Supplementary information accompanies this paper at doi:10.1038/s41598-017-07981-4h Competing Interests: The authors declare that they have no competing interests. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and
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License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
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copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2017 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 13 |
https://openalex.org/W2619736762 | https://hal.inria.fr/hal-01527495v3/document | English | null | Neural style transfer | null | 2,017 | cc-by-sa | 12,987 | To cite this version: Amir Semmo, Tobias Isenberg, Jürgen Döllner. Neural Style Transfer: A Paradigm Shift for Image-
based Artistic Rendering?. NPAR 2017 - Proceedings of the International Symposium on Non-
Photorealistic Animation and Rendering (NPAR as part of Expressive), ACM, Jul 2017, Los Angleles,
United States. pp.5:1-5:13, 10.1145/3092919.3092920. hal-01527495v3 This is the authors’ version of the work. It is posted here for your personal use. Not
for redistribution. The defnitive version will be published in Proceedings of Non-
Photorealistic Animation and Rendering (NPAR ’17).
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NPAR’17, Los Angeles, CA, USA
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DOI: 10.1145/3092919.3092920 ACM Reference format: ACM Reference format:
Amir Semmo, Tobias Isenberg, and Jürgen Döllner. 2017. Neural Style Trans-
fer: A Paradigm Shift for Image-based Artistic Rendering? In Proceedings of
Expressive, Los Angeles, CA, USA, July 28-29, 2017 (NPAR’17), 13 pages. DOI: 10.1145/3092919.3092920 Neural Style Transfer:
A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer:
A Paradigm Shif for Image-based Artistic Rendering? Amir Semmo
Hasso-Plattner-Institut,
Faculty of Digital Engineering,
University of Potsdam, Germany
amir.semmo@hpi.uni-potsdam.de
Tobias Isenberg
Inria & Université Paris-Saclay
France
tobias.isenberg@inria.fr
Jürgen Döllner
Hasso-Plattner-Institut,
Faculty of Digital Engineering,
University of Potsdam, Germany
doellner@hpi.uni-potsdam.de
Input
‘Mosaic’
‘Udnie’
‘La Muse’ / Oil Paint
‘The Scream’ / Watercolor
Neural Style Transfer
Neural Style Transfer with Filtering
Figure 1: Outputs of a feed-forward NST using CNNs for image processing (Johnson et al. 2016a,b). The potentials and impact
of NST on IB-AR and its combinations with paradigms such as image fltering (here: oil paint, watercolor) are discussed in this
paper. “Brooklyn Bridge” by Curtis MacNewton is licensed under CC BY-SA 2.0;1 derivatives implicate style variants. Amir Semmo
Hasso-Plattner-Institut,
Faculty of Digital Engineering,
University of Potsdam, Germany
amir.semmo@hpi.uni-potsdam.de Jürgen Döllner
Hasso-Plattner-Institut,
Faculty of Digital Engineering,
University of Potsdam, Germany
doellner@hpi.uni-potsdam.de Jürgen Döllner
Hasso-Plattner-Institut,
Faculty of Digital Engineering,
University of Potsdam, Germany
doellner@hpi.uni-potsdam.de Tobias Isenberg
Inria & Université Paris-Saclay
France
tobias.isenberg@inria.fr Tobias Isenberg
Inria & Université Paris-Saclay
France
tobias.isenberg@inria.fr Neural Style Transfer with Filtering ‘Udnie’ Input ‘The Scream’ / Watercolor ‘La Muse’ / Oil Paint
Neural Style Transfer with Filtering ‘Mosaic’ Neural Style Transfer ‘Udnie’ ‘Mosaic’ ‘La Muse’ / Oil Paint ‘Udnie’ ‘La Muse’ / Oil Paint Input ‘The Scream’ / Watercolor Input Figure 1: Outputs of a feed-forward NST using CNNs for image processing (Johnson et al. 2016a,b). The potentials and impact
of NST on IB-AR and its combinations with paradigms such as image fltering (here: oil paint, watercolor) are discussed in this
paper. “Brooklyn Bridge” by Curtis MacNewton is licensed under CC BY-SA 2.0;1 derivatives implicate style variants. • Computing methodologies →Non-photorealistic render-
ing; Image processing; In this meta paper we discuss image-based artistic rendering (IB-AR)
based on neural style transfer (NST) and argue, while NST may
represent a paradigm shift for IB-AR, that it also has to evolve as
an interactive tool that considers the design aspects and mecha-
nisms of artwork production. IB-AR received signifcant attention
in the past decades for visual communication, covering a plethora
of techniques to mimic the appeal of artistic media. Example-based
rendering represents one the most promising paradigms in IB-AR to
(semi-)automatically simulate artistic media with high fdelity, but
so far has been limited because it relies on pre-defned image pairs
for training or informs only low-level image features for texture
transfers. Advancements in deep learning showed to alleviate these
limitations by matching content and style statistics via activations
of neural network layers, thus making a generalized style trans-
fer practicable. We categorize style transfers within the taxonomy
of IB-AR, then propose a semiotic structure to derive a technical
research agenda for NSTs with respect to the grand challenges of
NPAR. We fnally discuss the potentials of NSTs, thereby identifying
applications such as casual creativity and art production. • Computing methodologies →Non-photorealistic render-
ing; Image processing; 1CC BY-SA 2.0 license: http://creativecommons.org/licenses/by-sa/2.0 KEYWORDS style transfer, stylization, convolutional neural networks, image-
based artistic rendering, image processing, semiotics HAL Id: hal-01527495
https://inria.hal.science/hal-01527495v3
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INTRODUCTION Non-photorealistic rendering (NPR) constitutes a highly active re-
search domain of computer graphics that deals with the expres-
sion, recognition, and communication of complex image contents
by means of information abstraction and highlighting (DeCarlo
and Santella 2002; Gooch 2010; Hertzmann 2010; Lansdown and
Schofeld 1995). In particular, image-based artistic rendering (IB-AR)
enjoys a growing popularity in mobile expressive rendering (Dev
2013; Winnemöller 2013) to simulate the appeal of traditional artis-
tic styles and media for visual communication (Kyprianidis et al. 2013; Rosin and Collomosse 2013) such as pencil, pen-and-ink, oil
paint, and watercolor. Classical IB-AR techniques typically model
the design aspects that are involved with these artistic styles, i. e., to
direct the smoothing and contour highlighting of image fltering, NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Semmo et al. Style
Content
Texture Transfer / Risser et al. (2017)
Style
Content
Color Transfer / Gatys et al. (2016b)
Style
Content
Portrait Stylization / Selim et al. (2016)
Frame i+1
Frame i
Frame i+2
Frame i+3
Video Stylization / Johnson et al. (2016a; 2016b)
Casual Creativity / Prisma (iOS)
Content / Style Mask
Casual Creativity / likemo.net
Figure 2: Overview of NST techniques and applications. Previous works used implementations of NSTs to perform general-
ized color and texture transfers, stylize videos, and provide means for casual creativity in mobile expressive rendering. Im-
ages © Risser et al. (2017), from Gatys et al. (2016b) © IEEE, from Selim et al. (2016) © ACM, all used with permission. Style
Content
Portrait Stylization / Selim et al. (2016) Portrait Stylization / Selim et al. (2016) Content / Style Mask
Casual Creativity / likemo.net Frame i+1
Frame i
Frame i+2
Frame i+3
Video Stylization / Johnson et al. (2016a; 2016b) Casual Creativity / Prisma (iOS) Casual Creativity / Prisma (iOS) Video Stylization / Johnson et al. (2016a; 2016b) Casual Creativity / likemo.net Figure 2: Overview of NST techniques and applications. Previous works used implementations of NSTs to perform general-
ized color and texture transfers, stylize videos, and provide means for casual creativity in mobile expressive rendering. Im-
ages © Risser et al. (2017), from Gatys et al. (2016b) © IEEE, from Selim et al. (2016) © ACM, all used with permission. In this paper we discuss the potentials and challenges of NST for IB-
AR. 1
INTRODUCTION In the following section, we frst provide a conceptual overview
for (neural) style transfer and show how the design process dif-
fers from classical IB-AR paradigms (Section 2). Next, we provide
a semiotic structure for IB-AR that combines design aspects and
mechanisms of artwork production with well-established design
principles of NPAR (Section 3). We then use this structure to cat-
egorize current (neural) style-transfer techniques (Section 4) and
derive a technical research agenda for NST (Section 5) including
potential mutual inclusions with other IB-AR paradigms such as
image fltering (Figure 1). With this research agenda we shed light
on how NSTs may contribute to deal with the grand challenges
of NPAR put forth by Salesin (2002) and revisited by Gooch et
al. (2010), and how they can be evolved as interactive tools that
consider mechanisms of artwork production. Finally, we identify
potential future applications such as casual creativity (Section 6). the approximation of image contents via rendering primitives (e. g.,
brush strokes, stipples), or an image segmentation. A more gener-
alized approach has been introduced by example-based rendering
(EBR), which employs machine learning or statistical models to em-
ulate characteristics of artistic styles from visual examples (Kypri-
anidis et al. 2013). Previous techniques in EBR, however, typically
require analogous style and content pairs for training (Hertzmann
et al. 2001) or only inform low-level image features for texture
transfers, thus limiting its application and creative control over
the design aspects. Advancements in deep learning and convolu-
tional neural networks (CNNs) demonstrated that these technical
limitations can be alleviated as follows: (1) Deep CNNs are able to accurately classify high-level im-
age contents across generalized data sets (Simonyan and
Zisserman 2015). (2) Layers of pre-trained deep CNNs can be activated to match
content and style statistics, and thus perform a neural
style transfer (NST) between arbitrary images (Gatys et al. 2016b) (Figure 1). 2
ARTISTIC STYLE TRANSFER WITHIN THE
TAXONOMY OF IB-AR TECHNIQUES Style Transfer using Neural Networks: Techniques that
employ neural networks to separate and recombine the
content and style of arbitrary inputs. Typically, loss func-
tions are minimized iteratively to balance the components
of style and content in the output (Gatys et al. 2016b), or
train feed-forward neural networks for linear image trans-
formation (Johnson et al. 2016a,b). III. Style Transfer using Neural Networks: Techniques that
employ neural networks to separate and recombine the
content and style of arbitrary inputs. Typically, loss func-
tions are minimized iteratively to balance the components
of style and content in the output (Gatys et al. 2016b), or
train feed-forward neural networks for linear image trans-
formation (Johnson et al. 2016a,b). (1) Heuristics-based Algorithms: Paradigms that are based
on rendering functions, which are implemented by a do-
main expert who explicitly models individual artistic styles
and its correspondent design aspects or mechanisms. This
group basically comprises stroke-based rendering, region-
based techniques, image processing and fltering, and may
also account for physically-based simulations. We believe this classifcation helps to organize EBR techniques
by their technical foundation and underpins the maturation from
application-specifc (e. g., color transfers) towards generalized style
transfers. In the following section, we defne design aspects and
mechanisms important for implementing these three concepts. We believe this classifcation helps to organize EBR techniques
by their technical foundation and underpins the maturation from
application-specifc (e. g., color transfers) towards generalized style
transfers. In the following section, we defne design aspects and
mechanisms important for implementing these three concepts. (2) Style Transfer Algorithms: Example-based rendering
which is directed to learn or reproduce artistic styles from
visual examples (ground-truth data sets). This type often
comprises statistical models and optimization schemes to
balance aspects of content and style in the stylized output. 2
ARTISTIC STYLE TRANSFER WITHIN THE
TAXONOMY OF IB-AR TECHNIQUES To this end, we argue that deep learning denotes a key technique
in the chronology of IB-AR (Kyprianidis et al. 2013), as it makes—
for the frst time—a generalized style transfer practicable. First
applications demonstrate this process using the example of color
and texture transfers as well as casual creativity systems and ser-
vices (Figure 2). To provide a sophisticated paradigm shift for IB-AR,
however, we believe that NSTs need to mature from color and tex-
ture transfers to interactive tools that consider the design aspects
and mechanisms involved in artwork production, i. e., to ease the
visual expression of artists, non-artists (i. e., general public), and
scientists (Gooch et al. 2010; Isenberg 2016; Salesin 2002). IB-AR is related to the processes of visual abstraction that are in-
volved in the creation of general artworks (Hertzmann 2010; Ma
2002) and used to express uncertainty, communicate abstract ideas,
and evoke the imagination (Gooch et al. 2010) by addressing the ra-
tional, emotional, and cognitive qualities of the human mind (Halper
et al. 2003; Hertzmann 2010). For an efective visual abstraction, the
separation of content from style is thus considered to be a key factor
to allow us to distinguish between the mechanisms used for captur-
ing the essence of an image, on the one side, and the design aspects
that drive the aesthetic appeal to stimulate human senses (Gooch
et al. 2010; Salesin 2002), on the other side. To this end, research in Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA ... Neural Style Transfer
Content Image
Output Image
Loss Network (DNN)
Loss Functions
Minimization
λ
Style Image
... Image Statistics-/Analogies-based Style Transfer
Input Image
Output Image
Matching Pipeline
Optimization
Functions
Content Image
Style Image
... Heuristics-based Algorithms
Artistic Styles
Input Image
Output Image
Rendering Pipeline
Artworks
Rendering
Functions
Training Data
Processing Pipeline
Processing Functions
Image Data
Texture-Transfer-Only Data/Functions
Manual Modeling Effort
Figure 3: Overview of style transfer concepts, which difer in the way artistic styles are modeled or transferred: heuristics-
based algorithms (left) and style transfers based on image statistics or analogies (middle) require explicit modeling or training
phases prior to application, whereas NSTs (right) combine both aspects in a single phase. 2
ARTISTIC STYLE TRANSFER WITHIN THE
TAXONOMY OF IB-AR TECHNIQUES Loss Functions Texture-Transfer-Only Data/Functions
Manual Modeling Effort Image Data Texture-Transfer-Only Data/Functions
Manual Modeling Effort Processing Pipeline Figure 3: Overview of style transfer concepts, which difer in the way artistic styles are modeled or transferred: heuristics-
based algorithms (left) and style transfers based on image statistics or analogies (middle) require explicit modeling or training
phases prior to application, whereas NSTs (right) combine both aspects in a single phase. the feld of IB-AR has been devoted to deduce the design aspects of
an artistic style that are involved in artwork production: color transfers that equalize the mean and variance be-
tween content and style images (Neumann and Neumann
2005; Reinhard et al. 2001). Defnition “Artistic Style”: The constant form—and some-
times the constant elements, qualities, and expression—in Defnition “Artistic Style”: The constant form—and some-
times the constant elements, qualities, and expression—in Defnition “Artistic Style”: The constant form—and some-
times the constant elements, qualities, and expression—in
the art of an individual or a group. II. Style Transfer using Image Analogies: Techniques that
use image pairs for training—a source image and an artistic
depiction of this image—i. e., to learn an analogous trans-
formation such that content images can be transformed
into an artistic rendering of similar visual style (Hertzmann
et al. 2001). II. Style Transfer using Image Analogies: Techniques that
use image pairs for training—a source image and an artistic
depiction of this image—i. e., to learn an analogous trans-
formation such that content images can be transformed
into an artistic rendering of similar visual style (Hertzmann
et al. 2001). the art of an individual or a group. the art of an individual or a group. — Meyer Schapiro (Schapiro 1994) — Meyer Schapiro (Schapiro 1994) IB-AR implementations typically require programmers to model
the design space as well as the defning and distinguishing charac-
teristics of an artistic style. Here, we see two general approaches
which align with Kyprianidis et al.’s (2013) taxonomy as follows: III. Style Transfer using Neural Networks: Techniques that
employ neural networks to separate and recombine the
content and style of arbitrary inputs. Typically, loss func-
tions are minimized iteratively to balance the components
of style and content in the output (Gatys et al. 2016b), or
train feed-forward neural networks for linear image trans-
formation (Johnson et al. 2016a,b). III. 3
A SEMIOTIC STRUCTURE FOR ARTISTIC
STYLE TRANSFER Prominent examples of heuristics-based algorithms are the stroke-
based rendering approach of Hertzmann (1998), the cartoon pipeline
of Winnemöller et al. (2006), and the watercolor system of Bousseau
et al. (2006). For style transfer algorithms, by contrast, the litera-
ture primarily distinguishes between EBR techniques that transfer
color or texture (Kyprianidis et al. 2013). However—with the matu-
ration of machine learning—we believe that this strict separation
is no longer practicable because color and texture represent only
two out of many variables to defne the composition of artistic
styles, and deep learning enables NSTs to abstract from applica-
tions (e. g., color/texture transfer). To this end, we conjecture that
it is worthwile to provide a process-oriented taxonomy for EBR
that refects how artistic style transfers are modeled or technically
implemented. Given artistic works as ground-truth data, we ar-
gue that three concepts may distinguish current and future EBR
techniques (Figure 3): Semiotics deals with the study of symbols and how they commu-
nicate image contents or information in a meaningful way (Bertin
2010). In artwork production, elements of design are considered to
be fundamental aspects of pictorial semiotics (Rudner 1951), whose
mutual impact defne the “composition” of an artwork, and thus
its artistic style. Therefore, we believe that the transfer of proven
design aspects and mechanisms of artwork production to modern
media and imaging technologies, and the development of new artis-
tic styles are key challenges for current and future research. In
IB-AR theory (Hertzmann 2010), a semiotic structure that considers
these design aspects and the mechanisms of interactive NPAR has
not been formulated yet. We believe, however, that such a structure
is essential to provide developers of NPAR techniques with the con-
ceptual means to help them compose and extend artistic styles as
well as evolve (neural) style transfers as interactive tools that ease
the visual expression of artists, non-artists and scientists for illus-
trative visualization (Gooch et al. 2010; Isenberg 2016; Salesin 2002). We thus formulate a semiotic structure that is based on graphic I. Style Transfer using Image Statistics: Techniques that
balance content and style of two separate inputs using sta-
tistical models. Prominent examples are histogram-based I. Style Transfer using Image Statistics: Techniques that
balance content and style of two separate inputs using sta-
tistical models. Prominent examples are histogram-based NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. 3
A SEMIOTIC STRUCTURE FOR ARTISTIC
STYLE TRANSFER (2005)
×
×
Pouli & Reinhard (2011)
×
×
×
Reinhard et al. (2001)
×
×
Wu et al. (2013)
×
×
×
Xiao & Ma (2009)
×
×
×
Yang et al. (2017)
×
×
×
Image Statistics
Ashikhmin (2003)
×
×
×
×
Bénard et al. (2013)
×
×
×
×
×
×
×
×
×
×
×
Berger et al. (2013)
×
×
×
×
Efros & Freeman (2001)
×
×
Fiser et al. (2016)
×
×
×
×
×
×
Hashimoto et al. (2003)
×
×
×
×
Hertzmann (2001)
×
×
Hertzmann et al. (2002)
×
×
×
×
Lee et al. (2011)
×
×
×
×
Image Analogies
Wang et al. (2013)
×
×
×
Zhao & Zhu (2011)
×
×
×
×
Anderson et al. (2016)
×
×
×
×
Champandard (2016)
×
×
×
×
×
Chen & Schmidt (2016)
×
×
Dumoulin et al. (2017)
×
×
Gatys et al. (2016a)
×
×
×
Gatys et al. (2016b)
×
×
×
Gatys et al. (2016c; 2017)
×
×
×
×
×
×
Gupta et al. (2017)
×
×
×
×
Huang & Belongie (2017)
×
×
×
Iizuka et al. (2016)
×
×
×
Johnson et al. (2016a)
×
×
×
Li & Wand (2016)
×
×
Liu et al. (2017)
×
×
×
×
×
Risser et al. (2017)
×
×
×
×
×
Ruder et al. (2016)
×
×
×
×
Selim et al. (2016)
×
×
×
×
×
×
Taigman et al. (2016)
×
×
Ulyanov et al. (2016a)
×
×
Neural Networks
Ulyanov et al. (2017a)
×
×
×
×
Ulyanov et al. (2016b)
×
× 1. Modeling Aspects: They deal with encoding real-world
phenomena as color maps, and complementary information
as feature maps (e. g., results of an image segmentation,
saliency analysis, optical fow estimation) and geometry
maps (e. g., depth). 1. Modeling Aspects: They deal with encoding real-world
phenomena as color maps, and complementary information
as feature maps (e. g., results of an image segmentation,
saliency analysis, optical fow estimation) and geometry
maps (e. g., depth). 2. Filtering Aspects: They are used to select and apply dif-
ferent confgurations of composition variables according
to image location, color, or feature. Filtering aspects should
provide efective control to globally and locally adjust the
level of abstraction. Examples are the luminance-based
placement of stipples (Martín et al. 3
A SEMIOTIC STRUCTURE FOR ARTISTIC
STYLE TRANSFER Input Images
Reality /
Virtuality
Output Image
Modeling
1. Modeling Aspects
Color Maps
Feature Maps
Geometry Maps
Perceives
Location
Color
Feature
2. Filtering Aspects
Implements Techniques
Parameterizes Techniques
Composition Variables
Engineer / Domain Expert
Consumer / Artist
5. Design Mechanisms
Space / Texture
Transparency
Orientation
Shading
Shadows
Crispness
Resolution
4. Graphical Variables
Form
Shape
Size
Color
3. Graphical Elements
Point
Line
Area
2D Element
System / Design Instance
6. Perceptional Aspects
Flatness
Motion Coherence
Temporal Continuity
Pictorial Cues
Configures / Controls
Figure 4: Semiotic structure comprising graphical core variables and mechanisms that may be considered for style transfers. Engineer / Domain Expert Reality /
Virtuality igure 4: Semiotic structure comprising graphical core variables and mechanisms that may be consi comprising graphical core variables and mechanisms that may be considered for style transfers. Figure 4: Semiotic structure comprising graphical core variables and mechanisms that may be considered for style transfers. Table 1: Overview of image-based artistic style transfer tech-
niques and how they relate to semiotic aspects. Current
NST techniques apparently lack to model graphical ele-
ments/variables and provide interactive (creative) control. semiology principles of Bertin (2010) and MacEachren et al. (2012)
that provide a theoretical foundation to visualization (Figure 4). The visual variables described by Bertin (2010) and MacEachren
et al. (2012), however, cannot fully express the unique requirements
of interactive media and systems (e. g., animation, video, interac-
tive parameterizations). We thus extend the classifcation by the
concepts of fltering and perception to consider interactivity, level
of abstraction, and coherence/continuity issues of NPAR as well. This way, user involvement can be considered as a key mechanism
for maintaining an iterative feedback loop between a system—as
design instance implementing NPAR techniques—and the user’s
requirements—as consumer/artist. In particular, it is directed to
interactively adjust the semiotic structure that defnes aspects of
modeling, fltering, composition and perception (Figure 4): Publication
Color Maps
Feature Maps
Geometry Maps
Location-based Filtering
Color-based Filtering
Feature-based Filtering
Point / Line / Area
Color / Brightness
Form / Shape / Size
Space / Texture
Transparency
Orientation
Shading / Shadows
Crispness / Resolution
Coherence / Continuity
Pictorial Cues
User Interaction
Arbelot et al. (2016)
×
×
×
×
×
×
×
Chang et al. (2015)
×
×
×
×
×
Kim et al. (2009)
×
×
×
×
×
×
×
×
Maciejewski et al. (2008)
×
×
×
×
×
×
×
×
Martín et al. 3
A SEMIOTIC STRUCTURE FOR ARTISTIC
STYLE TRANSFER (2011)
×
×
×
×
×
×
×
×
×
Neumann Broth. (2005)
×
×
Pouli & Reinhard (2011)
×
×
×
Reinhard et al. (2001)
×
×
Wu et al. (2013)
×
×
×
Xiao & Ma (2009)
×
×
×
Yang et al. (2017)
×
×
×
Image Statistics
Ashikhmin (2003)
×
×
×
×
Bénard et al. (2013)
×
×
×
×
×
×
×
×
×
×
×
Berger et al. (2013)
×
×
×
×
Efros & Freeman (2001)
×
×
Fiser et al. (2016)
×
×
×
×
×
×
Hashimoto et al. (2003)
×
×
×
×
Hertzmann (2001)
×
×
Hertzmann et al. (2002)
×
×
×
×
Lee et al. (2011)
×
×
×
×
Image Analogies
Wang et al. (2013)
×
×
×
Zhao & Zhu (2011)
×
×
×
×
Anderson et al. (2016)
×
×
×
×
Champandard (2016)
×
×
×
×
×
Chen & Schmidt (2016)
×
×
Dumoulin et al. (2017)
×
×
Gatys et al. (2016a)
×
×
×
Gatys et al. (2016b)
×
×
×
Gatys et al. (2016c; 2017)
×
×
×
×
×
×
Gupta et al. (2017)
×
×
×
×
Huang & Belongie (2017)
×
×
×
Iizuka et al. (2016)
×
×
×
Johnson et al. (2016a)
×
×
×
Li & Wand (2016)
×
×
Liu et al. (2017)
×
×
×
×
×
Risser et al. (2017)
×
×
×
×
×
Ruder et al. (2016)
×
×
×
×
Selim et al. (2016)
×
×
×
×
×
×
Taigman et al. (2016)
×
×
Ulyanov et al. (2016a)
×
×
Neural Networks
Ulyanov et al. (2017a)
×
×
×
×
Ulyanov et al. (2016b)
×
× Publication
Color Maps
Feature Maps
Geometry Maps
Location-based Filtering
Color-based Filtering
Feature-based Filtering
Point / Line / Area
Color / Brightness
Form / Shape / Size
Space / Texture
Transparency
Orientation
Shading / Shadows
Crispness / Resolution
Coherence / Continuity
Pictorial Cues
User Interaction
Arbelot et al. (2016)
×
×
×
×
×
×
×
Chang et al. (2015)
×
×
×
×
×
Kim et al. (2009)
×
×
×
×
×
×
×
×
Maciejewski et al. (2008)
×
×
×
×
×
×
×
×
Martín et al. (2011)
×
×
×
×
×
×
×
×
×
Neumann Broth. 4.1
Style Transfer using Image Statistics color blending via overdraw or layering, the orientation of
graphical elements, the shading and lighting conditions,
and the crispness/resolution of image features. Previous
works deal with mechanisms for stylized shadows (DeCoro
et al. 2007), the orientation and layering of curved brush
strokes (Hertzmann 1998), and low-pass image flters. color blending via overdraw or layering, the orientation of
graphical elements, the shading and lighting conditions,
and the crispness/resolution of image features. Previous
works deal with mechanisms for stylized shadows (DeCoro
et al. 2007), the orientation and layering of curved brush
strokes (Hertzmann 1998), and low-pass image flters. Most techniques using image statistics are designed to perform
color transfers. Here we can only mention the most representative
works and refer to Faridul et al.’s (2014) survey for a comprehensive
overview. The majority of techniques equalizes the mean and vari-
ance of a style and content image to control color distributions via
luminance-based (Reinhard et al. 2001) or HSL-based (Neumann and
Neumann 2005) histograms. Extensions integrate feature maps to
consider local information as well, such as image segmentation (Wu
et al. 2013; Xiao and Ma 2009), edge-aware texture descriptors (Arbe-
lot et al. 2016), and semantics (Yang et al. 2017) to colorize grayscale
images. With interactive methods it is also possible to maintain
control over a set of colors that is involved in palette-based color
transfers (Chang et al. 2015; Pouli and Reinhard 2011). 6. Perceptional Aspects: IB-AR typically aims to reproduce
a hand-drawn look, where “distracting fickering and slid-
ing artifacts” for animated scenes (e. g., virtual environ-
ments, video) should be minimized (Bénard et al. 2011). Bénard et al. (2011) propose this challenge to be a concur-
rent fulfllment of three goals: fatness, motion coherence,
and temporal continuity. In addition, we conjecture that
pictorial cues are important perceptional aspects because
artists often carefully consider linear perspective, occlu-
sion, and texture gradients to infer depth in their artworks. Another classical application for image statistics can be found in
image stippling (Martín et al. 2017). Here, patterns are learned and
applied through example using statistical texture measures (Kim
et al. 2009; Maciejewski et al. 2008), modeling aspects such as the
location of points (stipples), texture, shading, and resolution, which
should depend on the spatial size of the output image. Martín et
al. 4.1
Style Transfer using Image Statistics (2011) evolve these methods towards a “scale-dependent, example-
based stippling technique that supports both low-level stipple place-
ment and high-level interaction with the stipple illustration.” These
methods are prime examples for how style transfers can be im-
plemented on a primitive level, considering graphical elements
explicitly rather than texture patches. The mutual impact of these aspects defne the individual artistic
style and composition, and thus should be considered when design-
ing and implementing style transfers. In particular, we argue that
color and texture are only two semiotic aspects most techniques cur-
rently serve. By contrast, a “successful” modeling approach should
consider the distinctive design aspects and mechanisms involved
in a particular artistic style, i. e., with respect to the rendering func-
tions, optimization functions for image statistics and analogies, or
loss functions for neural networks (Section 2). 2The overview gives a non-exhaustive general picture of how semiotics are considered
in current research, we expect it to be extended with future research. 3
A SEMIOTIC STRUCTURE FOR ARTISTIC
STYLE TRANSFER 2015), the location-
dependent placement of contour lines (Cole et al. 2008),
and feature-guided image fltering using orientation infor-
mation (Kyprianidis and Döllner 2008). 3. Graphical Elements: These elements comprise rendering
primitives such as points, lines, areas, and generalized 2D
elements. They may also defne rendering paths or loca-
tions for texturing, e. g., stippling, contour-lining, and the
decoration of image segments. 4. Graphical Variables: They refer to the illusion of physical
mass and density (form), image regions with well-defned
boundaries (shape), the size of graphical elements, and color
including brightness as phenomena of light and human vi-
sual perception. Prominent examples refer to rendering
with reduced color palettes and at multiple scales (Kypri-
anidis et al. 2013). 5. Design Mechanisms: They deal with the surface charac-
ter and relationships among image features with respect to
position and direction (space/texture), transparency to infer Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Conv1_1
Conv4_1
Content Image
Style Image
Conv2_1
10 -4
10 -4
10 -5
10 -3
10 -2
Conv3_1
Conv2_1
Figure 5: Adjusting the level of abstraction: (top) using diferent relative weightings between content/style reconstruction,
(bottom) matching the style representation with layer subsets of the VGG-Network. Images from Gatys et al. (2016b), © IEEE,
used with permission. Style image by Wassily Kandinsky is in the public domain (source: Google Art Project). 10 -3 Content Image 10 -2 g
Style Image C
2 1 Conv1 1 Conv4_1 Conv3_1 Conv2_1 Conv4_1 Conv1_1 Style Image Figure 5: Adjusting the level of abstraction: (top) using diferent relative weightings between content/style reconstruction,
(bottom) matching the style representation with layer subsets of the VGG-Network. Images from Gatys et al. (2016b), © IEEE,
used with permission. Style image by Wassily Kandinsky is in the public domain (source: Google Art Project). 4.3
Style Transfer using Neural Networks To discuss this subfeld, we draw on Gatys et al. (2016b) defnition
of NSTs. Given a style image, a content image and a loss network,
e. g., VVG-16 (Simonyan and Zisserman 2015), that is used to defne
several loss functions to measure the diference between the output
image and a target image, one can compute an output image by
minimizing a weighted combination of the loss functions. Gatys et
al. (2016b) initially defne perceptual loss functions that control fea-
ture and style reconstructions to balance the components of content
and style, and control spatial smoothness by regularizing the total
variation, then solve the optimization problem using L-BFGS (Fig-
ure 5). Besides texture transfers, this approach can be employed
to perform sophisticated color transfers as well, e. g., to colorize
grayscale images (Iizuka et al. 2016). Because this generalized style
transfer employs back-propagation and combines learning and ap-
plication in a single phase, we denote it as an iterative approach
and distinguish it from the approach that separates learning from
application to train a feed-forward neural network. Feed-forward Approaches. The solving of NSTs optimization prob-
lems is computationally extensive. Some approaches thus provide
approximations by computing the weights of a feed-forward neural
network. Here, test images sets, e. g., ImageNet (Krizhevsky et al. 2012) or MS-COCO (Lin et al. 2014), are often used in a training
phase performed once per artistic style, after which the obtained
generative convolutional networks are used for linear image trans-
formation (Johnson et al. 2016a,b; Ulyanov et al. 2016a, 2017a,b). Johnson et al. (2016a; 2016b) and Ulyanov et al. (2016a) showed
that these networks can be three orders of magnitude faster than
the iterative approach. The output quality of these approaches can
be further improved by employing network layers for (adaptive)
instance normalization (Huang and Belongie 2017; Ulyanov et al. 2016b) that align the mean and variance of features of the con-
tent and style images. Conceptual limitations of these approaches,
however, lie in the limited level of detail: style characteristics are
generalized and not balanced for a unique style/content image
pair (Figure 7). Alternative approaches either employ simpler loss
functions with only local matching constraints, e. g., using a single
layer of a pre-trained loss network (Chen and Schmidt 2016), or
learn multiple styles or generative networks at once (Dumoulin
et al. 2017; Zhang and Dana 2017) to improve versatility. Iterative Approaches. 4.2
Style Transfer using Image Analogies Most style transfer techniques defned by image analogies are based
on texture transfers. Its basic idea is to copy image patches from
a style image to a content image in a way that locally shares and
minimizes pixel diferences in the content image, thereby using
a smoothness constraint to provide similarity with adjacent tex-
tures (Efros and Freeman 2001). Hertzmann (2001) defnes this as an
optimization problem by learning the analogous transformation of
a style/ground-truth image pair (A,A′) and applying it to a content
image B to obtain a stylized output B′ such that A : A′ :: B : B′. In this section we now provide an overview2 of existing techniques
with respect to the three concepts of style transfer and show how
they consider aspects of the semiotic structure (Figure 4). We pro-
vide a summary of this discussion in Table 1. NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Color Control
Size Control
Input with Feature Map
Location-based Style Control
Figure 6: Adjustments of loss functions for NST to control
graphical variables of the semiotic structure. Images © Gatys
et al. (2016c), used with permission. Location-based Style Control Input with Feature Map Ashikhmin (2003) provides conditions for how to integrate user-
defned feature maps to adjust parameter values of the texture trans-
fer. The approach can also be used to learn stroke placements for
contour-lining (Hertzmann et al. 2002) in domains such as portrait
sketches using templates (Zhao and Zhu 2011) and modeling image
features at multiple scales for level of abstraction rendering (Berger
et al. 2013). Further extensions use edge and orientation information
encoded in feature maps to control the placement of texture patches
(Lee et al. 2011) and individual brush strokes (Wang et al. 2013),
learn multiple styles and stroke patterns for portrait sketching and
painting (Berger et al. 2013; Zhao and Zhu 2011), and estimate mo-
tion using fow felds to stabilize temporal coherence (Hashimoto
et al. 2003). Bénard et al. (2013) propose a sophisticated system for
artists that performs style transfers for animations using orienta-
tion, velocity, and geometry information of 3D models to direct the
transfer with shading and lighting conditions, and to ensure tem-
poral and style continuity. In addition, they support overdraw and
partial transparency using a layering approach explicitly defned
by the artist. 4.3
Style Transfer using Neural Networks Extensions of Gatys et al.’s (2016b) work
primarily defne additional loss functions to control the output’s
composition. MRFs loss functions, for instance, can be used as a local
constraint to provide a more accurate texture patch matching and
blending (Li and Wand 2016), histogram losses may produce outputs
that statistically match style images more accurately (Risser et al. 2017), and a depth loss function to consider the spatial distribution
of image features (Liu et al. 2017). Further, a temporal loss function
based on optical fow can be used to stabilize temporal coherence
when applied on a per-frame basis to video (Anderson et al. 2016;
Gupta et al. 2017; Ruder et al. 2016; Selim et al. 2016). A few works
controlled perceptual factors locally by considering feature maps
using semantics-based image segmentation, such as to subdivide the
optimization problem of NST to local image regions (Champandard
2016) or facial regions of portrait images (Selim et al. 2016) to 4.2
Style Transfer using Image Analogies Most of these works, however, typically consider only
luminance- or color-guidance texture transfers, yet other informa-
tion may be considered as well such as illumination as shown by
Fišer et al. (2016) for stylized 3D models. Input with Feature Map Location-based Style Control Size Control Color Control Size Control Color Control Figure 6: Adjustments of loss functions for NST to control
graphical variables of the semiotic structure. Images © Gatys
et al. (2016c), used with permission. provide semantically more accurate transfers. Some enhancements
also considered composition variables of the semiotic structure such
as color, size, and location-based fltering by introducing control
measures (Gatys et al. 2016a,c, 2017) (Figure 6). We see these works
as a starting point to evolve NSTs as interactive tools for IB-AR that
facilitate creative expression, which we discuss below. 5
A TECHNICAL RESEARCH AGENDA FOR
NEURAL STYLE TRANSFER NST is a relatively new feld of research but has already shown
promising results for generalized style transfers. We believe its
future directions can be defned in the context of some of the grand
challenges of NPAR (Gooch et al. 2010; Isenberg 2016; Salesin 2002), Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Input Image (Content)
Style Image
deepart.io
Pikazo
Ulyanov et al. (2017b) / BN
Ulyanov et al. (2017b) / IN
Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward approaches (BN: batch nor-
malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. Style Image Style Image Ulyanov et al. (2017b) / IN deepart.io Input Image (Content) Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward approaches (BN: batch nor-
malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward
malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. of its analogy to patch-based texturing, divisionism can be
modeled quite accurately by current loss functions. i. e., its combination with other IB-AR paradigms for providing
algorithmic aesthetics, improving the fdelity in reproducing and
extending artistic styles towards new forms of art, and its parama-
terization to evolve as interactive tools that “support full design
cycle” (Salesin 2002) and ease visualization tasks. With these chal-
lenges and semiotics-oriented overview of Section 4 in mind, we
thus propose the following technical research agenda. i. e., its combination with other IB-AR paradigms for providing
algorithmic aesthetics, improving the fdelity in reproducing and
extending artistic styles towards new forms of art, and its parama-
terization to evolve as interactive tools that “support full design
cycle” (Salesin 2002) and ease visualization tasks. With these chal-
lenges and semiotics-oriented overview of Section 4 in mind, we
thus propose the following technical research agenda. • Cubism depicts subjects using simplifed shapes and forms
for composition, which are often portrayed using multiple
perspectives. Here, NST techniques would need to infer
geometric transformations and match geometric represen-
tations, e. g., as practiced by Mital et al. (2013), in corre-
spondence with the color similarity. • Pop Art typically composes images by thick outlines, bold
solid colors and Ben-Day dots. Proposal 1: Semiotics-based Loss Functions Current NST techniques primarily depend on color statistics for
style transfer, but model color as a mutual inclusion and efect
of multiple composition variables. However, we believe that loss
functions need to be defned for individual composition variables
and controlled fltering-wise by providing modeling information
that, e. g., encode how the size, shape, orientation, transparency,
shading, and shadows are aligned with the contents of a style image. For instance, stroke-based rendering models the image composi-
tion by placing, orienting, and layering individual brush strokes as
graphical elements (Kyprianidis et al. 2013). Typically, techniques
estimate image fow (Wang et al. 2004; Yan et al. 2008; Zeng et al. 2009) or derive local surface properties (Sloan et al. 2001) to guide
brush strokes with the orientation of image features or the shading
and lighting conditions (Fišer et al. 2016). Together with texture
layering, e. g., of painterly art maps or dictionaries (Yan et al. 2008;
Zeng et al. 2009), they provide better quality in preserving fne
texture details and modeling style characteristics induced by form,
shape, and orientation. For the latter, we believe a similar loss used
for temporal consistency (Gupta et al. 2017; Ruder et al. 2016)—but
based on image orientation information—could help guide the tex-
ture transfer. There is also demand to explicitly model semiotic
aspects that consider feature semantics. Here, Figure 8 exemplifes
some limitations that NSTs currently face for three artistic styles: The examples of cubism and pop art demonstrate that the coupling
of individual semiotic aspects with the semantics of content and
style images requires sophisticated rule-based algorithms. Eventu-
ally, this would lead to couple feature-level engineering with the
architecture engineering approach of deep learning. 5
A TECHNICAL RESEARCH AGENDA FOR
NEURAL STYLE TRANSFER Here, current NST tech-
niques face multiple limitations in reproducing shape, pre-
serving the semantic composition, and style characteristics
such as the regularity and color inversion of halftoning. Proposal 2: Combination with IB-AR Paradigms Local efects and phenomena of traditional artistic media such
as oilpaint, pencil, or watercolor at high-fdelity and resolution
are still hard to reproduce by NSTs. Here, we believe that NSTs
may be used as one of multiple processing stages in IB-AR, and
combined with the knowledge and algorithms of other paradigms. NSTs would thus not operate at the lowest level of detail, but as a
frst stage that introduces higher-level abstractions—to be followed
by a low-level, established technique to simulate drawing media
and their interplay with substrates. For instance, specialized line
drawing algorithms can be used to detect and stylize (salient) edges,
e. g., via diference-of-Gaussians (Winnemöller et al. 2012), edge-
preserving fltering for noise reduction (Kyprianidis et al. 2013), and
the constraints of stroke-based rendering to control the placement
of graphical elements, e. g, based on luminance to direct (tonal)
art maps for pencil rendering (Lee et al. 2006; Praun et al. 2001)
or structure grids for feature-guided stippling (Son et al. 2011) to • Divisionism represents images by regularly aligned ren-
dering primitives, e. g., brush strokes that optically com-
pose image features when viewed from distance. Because • Divisionism represents images by regularly aligned ren-
dering primitives, e. g., brush strokes that optically com-
pose image features when viewed from distance. Because NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Content Image
Style Image / Divisionism
Neural Style Transfer
Style Image / Cubism
Neural Style Transfer
Style Image / Pop Art
Neural Style Transfer
Figure 8: Limitations of current NSTs for simulating artistic styles. Style images of Robert Delaunay and Juan Gris are in the
public domain (source: Wikimedia Commons). Content image from Son et al. (2011) © Elsevier Inc, used with permission. Style Image / Pop Art
Neural Style Transfer Neural Style Transfer Style Image / Divisionism Neural Style Transfer Style Image / Divisionism Style Image / Cubism Neural Style Transfer Style Image / Cubism Style Image / Pop Art Neural Style Transfer Style Image / Pop Art Content Image Content Image Figure 8: Limitations of current NSTs for simulating artistic styles. Style images of Robert Delaunay and Juan Gris are in the
public domain (source: Wikimedia Commons). Content image from Son et al. (2011) © Elsevier Inc, used with permission. Content Image
Style Image [Randy Glass]
Neural Style Transfer
Son et al. Proposal 2: Combination with IB-AR Paradigms (2011)
Style Image [Igor Lukyanov]
Neural Style Transfer
Praun et al. (2001) / Lee et al. (2006)
Figure 9: Comparison of NSTs with heuristics-based algorithms for stippling and hatching. Content image and stippling
from Son et al. (2011) © Elsevier Inc, style images © Randy Glass and © Igor Lukyanov, all used with permission. Style Image [Igor Lukyanov] Neural Style Transfer Style Image [Igor Lukyanov] Neural Style Transfer Style Image [Randy Glass] Content Image
Style Image [Randy Glass]
Neural Style Transfer
Son et al. (2011)
Style Image [Igor Lukyanov]
Neural St
Figure 9: Comparison of NSTs with heuristics-based algorithms for stippling and hatching. C
from Son et al. (2011) © Elsevier Inc, style images © Randy Glass and © Igor Lukyanov, all used wi Content Image Praun et al. (2001) / Lee et al. (2006) Proposal 4: Providing Interactivity avoid the artifacts from pure NSTs shown in Figure 9. In Figure 10
we show results of a case study, where image fltering is employed
in a post-processing stage to NST to simulate local efects such
as edge darkening, pigment density variation, and wet-in-wet of
watercolors quite accurately (Bousseau et al. 2006; Wang et al. 2014),
whereas fow-based Gaussian fltering with Phong shading is used
to flter low-level noise and create smooth continuous oilpaint-like
texture efects (Hertzmann 2002; Semmo et al. 2016b) In both cases
we used the abstract style of Pablo Picasso’s “La Muse” to generate
an efect of higher-level abstraction, before adding mentioned flters
to simulate the respective low-level, local paint characteristics. Recently, Isenberg (2016) argued that EBR approaches have the
potential to enable users to provide “both higher-level interaction
and low-level control”—suggesting that this allows us to create
both interaction environments for artists who need a wide range
of low-level to high-level control and for non-artists whose inter-
action needs are likely easier satisfed with high-level interactions
such as the application of flters. Many traditional EBR approaches,
however, have relied on a close relationship between input style
and input context, e. g., for hatching (Gerl and Isenberg 2013). NSTs
have the potential to address this very problem: styles are more
easy to capture and thus the interactive application of stye becomes
easier. So far, however, NST are typically treated like a “black box”,
supporting only the high-level application of a captured style. To
enable the interaction spectrum that Isenberg (2016) calls for, it
would be necessary to integrate more local control. Artists need
to be able to afect the result on a semantic level: controlling how
larger regions are treated, change groups of marks, and even adjust
a single mark. One approach could be to provide loss functions
that operate on primitive-level and single design aspects as well,
e. g., graphical elements such as brush strokes in a style image. For
example, Figure 9 demonstrates how a purely global NST approach
fails in several regions, and local control such as the change of an
underlying directional feld, e. g., as practiced by (Salisbury et al. 1994), seems to be missing. Proposal 5: Supporting Visualization Tasks With respect to aesthetic evaluation, Salesin (2002) and Gooch
et al. (2010) raised the issue of a “Turing Test” that determines if
CG imagery can be indistinguishable from imagery produced by
humans. While the utility of such a test is being debated (Hall and
Lehmann 2013), some authors have included respective questions in
their evaluations (Gatys et al. 2016b; Isenberg et al. 2006). Gatys et al. for instance, evaluated their NST technique (2016b) in a preliminary
choice experiment, asking participants to fnd the hand-painted
images in a set of 10 hand-painted/NST image pairs. The average of
their 45,000 participants answered 6.1 image pairs correctly.3 With
the further consideration of semiotic aspects, in particular fltering
that includes semantics to resolve incoherences in color transfers,
it would be great to gather more information such as response time
and eye fxations to determine apparent locations or aspects of style
incoherence—information that may be injected into the learning
phase for improving a style transfer. Semiotics are inherently linked with the theory of (information)
visualization (Bertin 2010). In particular, style transfers have been
commonly used in illustrative visualization (Rautek et al. 2008), e. g.,
for the stylization of lines to depict fow (Everts et al. 2015), to make
phenomena—hidden in complex data sets—visible to the human
mind. However, efective visualization must also “enable analysis
of the supplied information, while easing the cognitive burden of
a user” (Gooch et al. 2010). NSTs based on deep CNNs emulate
functionalities of the visual cortex by solving tasks through hierar-
chical processing (DiCarlo et al. 2012), but need to be performed
in a context-dependent manner, e. g., with respect to a user’s task
and data domain, for efective visualization. Here, we imagine the
development of toolboxes or palettes of illustration styles that can
be interactively applied by professional illustrators, in a way that
considers an interaction spectrum from low-level to high-level con-
trols (Isenberg 2016). For example, a palette for computer-supported
hatching and stippling could be provided that alleviates some of
the tediousness of manual processes, but that includes support for
higher-level illustration processes, e. g., (Martín et al. 2011), where
NSTs could suggest regions to be fltered or regions to be contrast-
adjusted. The layers of deep CNNs that capture multiple levels of
abstraction could be interactively used for this purpose to direct
the interactive visualization/illustration process. Proposal 3: New Forms of Styles Gooch et al. (Gooch et al. 2010) provided an overview of NPAR re-
search through Heinlein’s maturation model, and argue that NPAR
has left the frst stage—emulating and imitating artistic styles—,
evolved towards the second stage by optimizing the performance of
the (used) technology, and is about to move towards the last stage,
where the technology becomes seamless and almost transparent. In
this respect, we believe that NST provides new opportunities for the
frst two stages, but needs to “incorporate elements such as interac-
tion, collaboration, human perception and cognition” (Gooch et al. 2010) to approach the third stage. In particular, here we see two
potential use cases for NST. First, modifying learned artistic styles
by providing mechanisms to specify transfer or loss functions that
change particular design aspects or variables. Second, performing a
style transfer by taking rule-based algorithms into account, i. e., to
learn styles not only from style images but also a set of descriptions
how an artistic style should look like, which makes new forms of
styles—that have never been seen before—practicable. Moreover, it is important to consider the input from several style
images, which is technically demonstrated by Johnson et al. (2016a;
2016b) for blending multiple styles. This could be extended to either
learn a particular technique/style or even an artist’s design prin-
ciples more reliably, or it could be used to combine two diferent NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer
Neural Style Transfer with Post-process Watercolor Rendering
Neural Style Transfer with Post-process Oilpaint Filtering
Content Image
Figure 10: Post-process image fltering to reduce low-level noise and inject paint characteristics. NST results are combined
with watercolor rendering (Bousseau et al. 2006; Wang et al. 2014) and oilpaint fltering (Semmo et al. 2016b). Content image
by Frank Köhntopp is in the public domain. Figure 10: Post-process image fltering to reduce low-level noise and inject paint characteristics. NST results are combined
with watercolor rendering (Bousseau et al. 2006; Wang et al. 2014) and oilpaint fltering (Semmo et al. 2016b). Content image
by Frank Köhntopp is in the public domain. for portrait images (Selim et al. 2016)), and data-domain specifc
design mechanisms such as generalization (MacEachren 1995). styles in the same target image. Proposal 3: New Forms of Styles For example for the latter, illustra-
tions that combine diferent depiction styles to steer attention and
create focus and context view would be an important application
domain. Such an approach, however, would need local control or
a semantic/semiotic processing of the content image by the NST
algorithm, e. g., as is partially practiced by Gatys et al. (2016c; 2017)
using feature maps, and interactive performance for immediate vi-
sual feedback, but which is currently a strong limitation of iterative
NST techniques. 3According to Leon Gatys in his talk at CVPR 2016 on “Image Style Transfer Using
Convolutional Neural Networks” (Gatys et al. 2016b). Proposal 6: Evaluation The evaluation of aesthetics and practical benefts for illustration
or visualization tasks remains an important issue in IB-AR (Gooch
2010; Hall and Lehmann 2013; Hertzmann 2010; Isenberg 2013). For
efective comparison of NST techniques, we believe there is demand
for a standardized benchmark image set such as the general NPAR
set provided by Mould and Rosin (2016). 5Tate IK Prize 2016. http://www.tate.org.uk/about/projects/ik-prize-2016. Last fol-
lowed: 04/09/2017.
6Adobe
Artistic
Eye.
http://blogs.adobe.com/conversations/2017/03/
de-youngsters-photos-get-the-look-of-masterpieces.html. Last followed: 04/09/2017. 4Stephen Merity. 2016. In deep learning, architecture engineering is the new feature
engineering. http://smerity.com/articles/2016/architectures_are_the_new_feature_
engineering.html. Last followed: 04/09/2017. Proposal 5: Supporting Visualization Tasks Finally, we believe
that, with the generalized application of NSTs, more complex artis-
tic styles of several visualization domains could be served, such
as medical imaging or cartography, but which requires NSTs to
consider the semantics of style and content images (e. g., as shown With respect to task efciency, studies are required to determine
if NSTs only copy low-level style aspects or if they also maintain
higher-level semantics of image contents. These studies could also
be used to determine to what degree NSTs introduce abstraction,
whether the degree of abstraction can be intentionally controlled,
and how it can be seamlessly interpolated for an interactive appli-
cation as discussed above. In particular, the meaningful interaction
with NSTs as tools for artists or scientists (e. g., with respect to
illustrative visualization) requires investigation. NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Painting from ‘Loving Vincent’
Content
Style transfer from deepart.io
Style
Figure 11: Comparison between emulating an artistic style
via painting (oil on canvas) and a NST. Results from “Loving
Vincent” © BreakThru Films, used with permission. Style
image by Vincent van Gogh is in the public domain. Style transfer from deepart.io
Style Painting from ‘Loving Vincent’
Content 6
APPLICATIONS The shift from feature engineering towards architecture engineer-
ing4 of deep learning enables IB-AR to abstract from input data,
and thus increase the general applicability in highly dynamic envi-
ronments. Here, we see the following potentials for using NSTs. 7
CONCLUSION Deep learning has opened new possibilities for IB-AR to make a gen-
eralized style transfer practicable. On the one hand, NSTs provide
new potentials for using IB-AR in context-sensitive and creative
application domains, such as casual creativity apps for mobile ex-
pressive rendering and production tools for feature flms. On the
other hand, NSTs currently provide only “black box” solutions from
a HCI point-of-view: research (so far) has mainly focused on tuning
hyperparameters of deep neural networks. To this end, we propose
a semiotic structure to provide developers of NST techniques with
the conceptual means of artworks production to help them compose
and extend artistic styles, as well as consider design aspects and
mechanisms for evolving NSTs as interactive tools. In particular, we
hope that this structure helps researchers to identify requirements
for semiotics-based loss functions, combine NSTs with the knowl-
edge of other IB-AR paradigms, promote completely new artistic
styles, and assist applications in illustrative visualization. Casual Creativity NSTs have particularly enriched casual creativity applications (Win-
nemöller 2013) in ubiquitous environments such as mobile comput-
ing. This domain has largely been devoted to image fltering and
processing to date, providing only constrained efects (Dev 2013). Prominent examples are the web service deepart.io and the iOS
app Prisma—attracting 60 million users in three weeks—, which
also started to establish their own social media communities for
sharing and commenting on stylized outputs. We believe, how-
ever, that these apps have to evolve from “black box” solutions
towards user-centric tools (Winnemöller 2013) to further promote
visual expression. Here, a metaphor for on-screen parameter paint-
ing (Semmo et al. 2016a) may be used to tune hyperparameters of
neural networks, while hiding the computational complexity. Style transfer from deepart.io Painting from ‘Loving Vincent’ Painting from ‘Loving Vincent’ Figure 11: Comparison between emulating an artistic style
via painting (oil on canvas) and a NST. Results from “Loving
Vincent” © BreakThru Films, used with permission. Style
image by Vincent van Gogh is in the public domain. Art Production Machine learning has gathered particular interest as an interactive
component of exhibition and art installations, e. g., Tate Modern’s IK
Prize 2016 winner Recognition5 uses pattern recognition to compare
art to photojournalism. For instance, Adobe’s Artistic Eye6 uses
NSTs to enable children transform their self-portraits into artistic
renditions in the style of a museum’s exhibits, while Becattini et
al. (2016) combined NSTs with art explorations, allowing users to
scan exhibits and transfer their style to user-defned images. Salesin (2002) had envisioned the support of artists to be a major
goal of NPAR, i. e., developing tools that make their life easier but
that do not constrain their capabilities in visual expression (Isen-
berg 2016). We discussed in Section 5 that this requires NSTs to
evolve as interactive tools. One example is the system by Fišer et
al. (2016) in which artists are able to draw over a printed stencil,
while their individual style is transferred in real-time onto 3D mod-
els, dealing with proper light propagation and auto-completion. Another example is the system for watercolor rendering with art-
directed control of Montesdeoca et al. (2016; 2017), where the efects
shown in Figure 10 (among others) can be controlled via on-screen
painting. Here, a long-term goal would be to integrate NSTs in
the production pipeline of feature flms, e. g., as evaluated by Joshi
et al. (2017) for Come Swim, reaching a quality level to assist the
laborious production of fully painted animated flms such as Loving
Vincent (Mackiewicz and Melendez 2016) (Figure 11), e. g., with
respect to temporal coherence and the placement of graphical ele-
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https://openalex.org/W4234804721 | https://www.qeios.com/read/6PM4KG/pdf | English | null | Body Weight Gain Reason Not Done | Definitions | 2,020 | cc-by | 60 | Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Body Weight Gain Reason Not Done National Cancer Institute National Cancer Institute Qeios ID: 6PM4KG · https://doi.org/10.32388/6PM4KG Source National Cancer Institute. Body Weight Gain Reason Not Done. NCI Thesaurus. Code
C119770. The explanation given as to why body weight gain was not assessed. Qeios ID: 6PM4KG · https://doi.org/10.32388/6PM4KG 1/1 |
https://openalex.org/W2100730679 | https://europepmc.org/articles/pmc3694491?pdf=render | English | null | Retinal Layers Changes in Human Preclinical and Early Clinical Diabetic Retinopathy Support Early Retinal Neuronal and Müller Cells Alterations | Journal of diabetes research | 2,013 | cc-by | 6,628 | Hindawi Publishing Corporation
Journal of Diabetes Research
Volume 2013, Article ID 905058, 8 pages
http://dx.doi.org/10.1155/2013/905058 Hindawi Publishing Corporation
Journal of Diabetes Research
Volume 2013, Article ID 905058, 8 pages
http://dx.doi.org/10.1155/2013/905058 Hindawi Publishing Corporation
Journal of Diabetes Research
Volume 2013, Article ID 905058, 8 pages
http://dx.doi.org/10.1155/2013/905058 Stela Vujosevic1 and Edoardo Midena1,2 1 Department of Ophthalmology, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
2 Fondazione G. B. Bietti, Via Livenza 3, 00198 Roma, Italy 1 Department of Ophthalmology, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
2 Fondazione G. B. Bietti, Via Livenza 3, 00198 Roma, Italy Correspondence should be addressed to Edoardo Midena; edoardo.midena@unipd.it Received 8 March 2013; Revised 17 May 2013; Accepted 20 May 2013 Academic Editor: Ahmed M. Abu El-Asrar Copyright © 2013 S. Vujosevic and E. Midena. This is an open access article distributed under the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly
cited. Purpose. To evaluate the changes in thickness of individual inner and outer macular and peripapillary retinal layers in diabetes. Methods. 124 subjects (124 eyes) were enrolled: 74 diabetics and 50 controls. Macular edema, proliferative diabetic retinopathy
(DR), any intraocular treatment and refractive error > 6 diopters were the main exclusion criteria. Full ophthalmic examination,
stereoscopic fundus photography, and spectral domain-OCT were performed. After automatic retinal segmentation (layering) in
5 layers, the thickness of each layer was calculated, and values compared among groups. Results. Thirty patients had no DR, 44
patients had non proliferative DR. A significant increase of inner plexiform and nuclear layers was found in DR eyes versus controls
(𝑃< 0.001). A significant decrease (𝑃< 0.01) of retinal nerve fiber layer (RNFL) and at specific sites of retinal ganglion cell layer
(𝑃= 0.02) was documented in the macula. In the peripapillary area there were no differences between diabetics and controls. Conclusions. Decreased RNFL thickness and increased INL/OPL thickness in diabetics without DR or with initial DR suggest early
alterations in the inner retina. On the contrary, the outer retina seems not to be affected at early stages of DM. Automatic intraretinal
layering by SD-OCT may be a useful tool to diagnose and monitor early intraretinal changes in DR. 1. Introduction according to which neurodegeneration precedes the vas-
cular one is confirmed by some electrophysiological and
psychophysical studies, which show that the alterations are
present even before the microvascular damage becomes
ophthalmoscopically or angiographically visible. Such retinal
function alterations mainly consist in contrast sensitivity loss,
altered color perception, and failure of retinal recovery time
[5, 6]. Moreover, it has been observed that in diabetic mice
the oscillatory potentials of the electroretinogram (ERG)
have increased peak latencies and/or reduced amplitudes,
suggesting a compromised inner retinal function secondary
to neuronal transmission alterations or to the combined loss
of amacrine and ganglion cells [7]. Diabetic retinopathy (DR) is the first cause of visual impair-
ment and blindness in the adult working-age population
[1]. For a long period of time, DR has been considered
primarily a retinal microvascular disorder caused by the
direct effects of hyperglycemia and by the metabolic path-
ways it activates [2]. Nevertheless, some recent studies have
demonstrated that retinal neurodegeneration (the result of
a negative balance between neurotoxic and neuroprotective
factors) is present even before the development of clinically
detectable microvascular damage. Retinal neurodegeneration
may therefore represent an early event in the pathophysiol-
ogy of DR and may anticipate the onset of microvascular
changes [2–4]. The term neurodegeneration used in this
paper encompasses pathologic phenomena affecting both the
pure neuronal component and the glial one. The hypothesis During the course of DR, apoptotic cells have been
observed in all retinal layers, suggesting the involvement
of different types of neurons [8]. Numerous studies have
evidenced that diabetes, through the alteration of different 2 Journal of Diabetes Research Journal of Diabetes Research 2.1.2. Fundus Photography. Color stereoscopic fundus pho-
tographs (7 ETDRS fields) were taken after an adequate
dilatation by a trained photographer using the same TOP-
CON TRC 50IA 35 degree fundus camera (TOPCON, Tokyo,
Japan). Diabetic retinopathy was graded as no DR and as
nonproliferative DR mild or moderate DR (NPDR) by two
independent graders experienced in grading DR. metabolic pathways, induces functional deficits and even the
loss of different types of retinal cells which cover from the
inner to the outer retinal cells: ganglion cells, bipolar cells,
amacrine cells, horizontal cells, and eventually photorecep-
tors [9]. Different authors reported a decrease in retinal thickness
in diabetic eyes with or without clinical signs of DR com-
pared to normal subjects [10–13]. Biallosterski et al. 1. Introduction found
a significant reduction in pericentral macular thickness in
53 diabetic patients with mild nonproliferative DR [10]. Van
Dijk et al. have demonstrated by spectral domain optical
coherence tomography (SD-OCT) a decrease in the inner
retinal thickness in the macula in diabetics with mild DR,
suggesting that this phenomenon might be firstly due to
ganglion cells loss in the pericentral areas and secondly to
retinal nerve fiber layer (RNFL) thinning in the peripheral
macula [14, 15].h 2.1.3. Spectral Domain OCT. All eyes were examined with
spectral domain optical coherence tomography (SD-OCT,
RS-3000, NIDEK, Gamagori, Japan). This instrument has
a light source of 880 nm wavelength. Each eye was exam-
ined, after pupillary dilation, both in the macula and the
peripapillary area. The following scanning protocols were
used: “Macula Map” in the macula and “Disc Circle” in the
peripapillary area.h y
The Macula Map scan pattern evaluates 6 × 6 mm area
centered on the fovea with 64 horizontal B-scan lines, each
consisting of 1024 A-scans per line. For each SD-OCT linear
scan, an automatic algorithm has individuated 5 different
retinal layers based on the different shades of gray corre-
sponding to the reflectivity indexes of each layer, which
include from inside to outside the following: inner limiting
membrane + nerve fiber layer (ILM + RNFL); ganglion cell
layer + inner plexiform layer (GCL + IPL); inner nuclear
layer + outer plexiform layer (INL + OPL); outer nuclear
layer + external limiting membrane (ONL + ELM); and
inner segment/outer segment photoreceptor layer + retinal
pigment epithelium (IS/OS + RPE). Retinal thickness was
automatically calculated in the 9 ETDRS areas (consisting in
a central circular zone with a 1-mm diameter, representing
the foveal area and inner and outer rings of 3 and 6 mm
diameter, resp.). The inner and the outer rings are divided
into four quadrants: superior, nasal, inferior, and temporal. Mean retinal thickness and mean thickness of each of the
five retinal layers in each of the nine ETDRS subfields were
recorded (Figures 1(a) and 1(b)). The main purpose of this study was to identify in vivo, by
SD-OCT, the changes in thickness of selected retinal layers
both in the macula and the peripapillary area in diabetic
patients without DR or with early stages of DR (mild and
moderate nonproliferative DR) versus normal subjects. 2. Material and Methods One hundred twenty-four subjects (74 diabetic patients and
50 normal subjects) were included in this study. One eye
of each subject was used for the spectral domain optical
coherence tomography (SD-OCT) analysis. The exclusion
criteria were as follows: proliferative DR, macular edema, any
type of previous retinal treatment (macular laser photocoagu-
lation, vitrectomy, intravitreal steroids, and/or antiangiogenic
drugs), any intraocular surgery, refractive error > 6D, previ-
ous diagnosis of glaucoma, ocular hypertension, uveitis, other
retinal diseases, neurodegenerative disease (e.g., Alzheimer’s,
Parkinson’s, and dementia), and significant media opacities
that precluded fundus examination or imaging. A written consent form was obtained from all patients as
well as the approval from our institutional ethics committee. The study was conducted in accordance with the tenets of the
Declaration of Helsinki. In the peripapillary area, a circle scan centered on the
optic disc (3.46 mm diameter, “Disc Circle” option) was used. Peripapillary retinal thickness was automatically measured by
the instrument in the temporal, superior, nasal, and inferior
quadrants (Figure 1(c)). Each subject underwent a complete ophthalmic examina-
tion, with determination of best corrected visual acuity, ante-
rior segment examination, Goldman applanation tonometry,
indirect ophthalmoscopy, and 90D lens biomicroscopy. Then,
SD-OCT and fundus photography were obtained. If any instrument error in the automatic segmentation of
retinal layers was documented, the manual correction con-
sisted in the repositioning into proper place of the incorrectly
placed points (using high magnification images), in order to
redefine the retinal profile. Each grader was blinded to clinical
data of all examined eyes. 2.1. Study Procedures 2.1.4. Statistics. Age, spherical equivalent, IOP, and visual
acuity were compared among groups by means of analysis
of variance (ANOVA); The mean values of retinal layers’
thickness in each group, both in macula and peripapillary
area, were confronted using the repeated measures analysis
of variances (ANOVA-RM). In cases of significant results
(𝑃< 0.05), the ANOVA-RM was followed by the Bonferroni
multiple comparisons post hoc test. All statistical analyses 2.1.1. Visual Acuity. Best corrected distance visual acuity
(BCVA) for each eye was measured by a trained examiner
using standard Early Treatment Diabetic Retinopathy Study
(ETDRS) protocol at 4-meter distance with a modified
ETDRS distance chart transilluminated with a chart illumi-
nator (Precision Vision) [16]. Visual acuity was scored as the
total number of letters read correctly and converted to the
logarithm of the minimum angle of resolution (logMar). 2.1.1. Visual Acuity. Best corrected distance visual acuity
(BCVA) for each eye was measured by a trained examiner
using standard Early Treatment Diabetic Retinopathy Study
(ETDRS) protocol at 4-meter distance with a modified
ETDRS distance chart transilluminated with a chart illumi-
nator (Precision Vision) [16]. Visual acuity was scored as the
total number of letters read correctly and converted to the
logarithm of the minimum angle of resolution (logMar). 2.1.4. Statistics. Age, spherical equivalent, IOP, and visual
acuity were compared among groups by means of analysis
of variance (ANOVA); The mean values of retinal layers’
thickness in each group, both in macula and peripapillary
area, were confronted using the repeated measures analysis
of variances (ANOVA-RM). In cases of significant results
(𝑃< 0.05), the ANOVA-RM was followed by the Bonferroni
multiple comparisons post hoc test. All statistical analyses 3 3 Journal of Diabetes Research (b)
ILM
NFL/GCL
IPL-INL
OPL-ONL
IS/OS
RPE-BM
RNFL
GCL
IPL
INL
OPL
ONL
IS/OS
RPE
ELM
(a)
(c)
90∘
Figure 1: Spectral domain OCT automatic segmentation of retinal layers in the macula ((a) and (b)) and in the peripapillary area (c). In the
macula the segmentation is performed on the linear scan (b) and in the peripapillary area on the circular scan around the optic disc (c). were performed with SAS 9.2 for Windows, SAS (Cary, NC,
USA). were performed with SAS 9.2 for Windows, SAS (Cary, NC,
USA). were performed with SAS 9.2 for Windows, SAS (Cary, NC,
USA). and inferior inner quadrant (IIM, 𝑃= 0.01) in no DR group
versus controls. RNFL thickness was significantly decreased
in the SOM (𝑃< 0.0001), NOM (𝑃= 0.0003), IOM (𝑃=
0.001), TOM (𝑃= 0.01), and SIM (𝑃= 0.003), in the NPDR
group versus controls (Figure 2(a)).i 2.1. Study Procedures Six
lines determine 5 retinal layers which from inside out are as follows: inner limiting membrane + nerve fibre layer (ILM + RNFL); ganglion cell
layer + inner plexiform layer (GCL + IPL); inner nuclear layer + outer plexiform layer (INL + OPL); outer nuclear layer + external limiting
membrane (ONL + ELM); and inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE) (a). (b)
(c)
90∘ ILM
NFL/GCL
IPL-INL
OPL-ONL
IS/OS
RPE-BM
RNFL
GCL
IPL
INL
OPL
ONL
IS/OS
RPE
ELM
(a) 90∘ (b) (a) (c) Figure 1: Spectral domain OCT automatic segmentation of retinal layers in the macula ((a) and (b)) and in the peripapillary area (c). In the
macula the segmentation is performed on the linear scan (b) and in the peripapillary area on the circular scan around the optic disc (c). Six
lines determine 5 retinal layers which from inside out are as follows: inner limiting membrane + nerve fibre layer (ILM + RNFL); ganglion cell
layer + inner plexiform layer (GCL + IPL); inner nuclear layer + outer plexiform layer (INL + OPL); outer nuclear layer + external limiting
membrane (ONL + ELM); and inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE) (a). Table 1: Demographic characteristics of the patients. Control
Diabetic
Grade of DR
No DR
NPDR
Patients, number
50
74
30
44
Mean age, yrs (SD)
55.8 (13.0)
56.4 (12.7)
56.1 (12.8)
55.9 (12.6)
Mean diabetes duration, yrs (SD)
—
5.9 (4.1)
18.6 (10.3)
Mean HbA1c % (SD)
—
8.1 (1.4)
7.8 (0.8)
8.2 (1.5)
Visual acuity, logMAR (SD)
0.003 (0.020)
0.011 (0.039)
0.024 (0.066)
IOP, mmHg (SD)
15.3 (1.9)
16.1 (3.4)
16.8 (3.2)
SE, (SD)
−0.04 (1.5)
0.46 (1.1)
0.42 (1.0)
SD: standard deviation; No DR: diabetic patients without retinopathy; NPDR: non proliferative diabetic retinopathy; IOP: intraocular pressure; SE: spherical
equivalent. Table 1: Demographic characteristics of the patients. 3. Results In the macula, ILM + RNFL thickness was significantly
decreased in the superior outer quadrant (SOM, 𝑃< 0.0001),
inferior outer quadrant (IOM, 𝑃< 0.0001), temporal outer
quadrant (TOM, 𝑃= 0.01), nasal outer quadrant (NOM,
𝑃= 0.0003), superior inner quadrant (SIM, 𝑃= 0.0003), INL/OPL thickness was significantly increased in the
central OCT subfield (CSF, 𝑃= 0.004), SIM (𝑃= 0.003),
NIM (𝑃= 0.04), TIM (𝑃= 0.0018), SOM (𝑃= 0.002), IOM
(𝑃= 0.04), and TOM (𝑃= 0.001) in the NPDR group versus
controls (Figure 2(c)).hf There was no difference in the ONL/ELM and IS/OS –
RPE thickness between diabetics with and without DR and
controls (Figures 2(d) and 2(e)).i In the peripapillary area, retinal thickness was signifi-
cantly decreased with increasing age (𝑃= 0.0021) and in 4 Journal of Diabetes Research 30
40
50
60
70
80
90
100
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
Control
No DR
NPDR
30
40
50
60
70
80
90
100
110
Control (C)
No DR (ND)
NPDR (DR)
20
30
40
50
60
70
80
Control (C)
No DR (ND)
NPDR (DR)
(𝜇)
(𝜇)
(𝜇)
(b)
(d)
(e)
∗= P < 0.05
Inner ring
Outer ring
Inner ring
Outer ring
Inner ring
Outer ring
GCL + IPL
ONL + ELM
IS/OS + RPE
control), diabetics without retinopathy (no DR), and dia
by spectral domain OCT in 9 ETDRS areas in the macu
l layer + inner plexiform layer (GCL + IPL); (c) inner nu
miting membrane (ONL + ELM); and (e) inner segment/
) indicates statistically significant values; CSF: central su
quadrant; IIM: inferior inner quadrant; TIM: temporal
uadrant; IOM: inferior outer quadrant; TOM: temporal 30
40
50
60
70
80
90
100
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
(𝜇)
Inner ring
Outer ring
GCL + IPL 30
40
50
60
70
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
Control
No DR
NPDR
30
40
50
60
70
80
90
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
0
10
20
30
40
50
60
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
30
40
50
60
70
80
90
100
110
Control (C)
No DR (ND)
NPDR (DR)
20
30
40
50
60
70
80
Control (C)
No DR (ND)
NPDR (DR)
(𝜇)
(𝜇)
(𝜇)
(𝜇)
(𝜇)
(a)
(c)
(b)
(d)
(e)
∗= P < 0.05
∗= P < 0.05
∗= P < 0.05
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-ND
C-ND
Inner ring
Inner ring
Outer ring
Outer ring
Inner ring
Outer ring
Inner ring
Outer ring
Inner ring
Outer ring
ILM + RNFL
INL + OPL
C-DR
C-DR C-DR C-DR C-DR C-DR
C-DR
ND-DR
ONL + ELM
IS/OS + RPE
Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics
with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. 3. Results (a)
Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear
layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer
segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield
thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner
quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer
quadrant. 3. Results 30
40
50
60
70
80
90
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
0
10
20
30
40
50
60
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
(𝜇)
(𝜇)
(a)
(c)
∗= P < 0.05
∗= P < 0.05
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-ND
C-ND
Inner ring
Outer ring
Inner ring
Outer ring
ILM + RNFL
INL + OPL
C-DR
C-DR C-DR C-DR C-DR C-DR
C-DR
ND-DR 30
40
50
60
70
80
90
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
0
10
20
30
40
50
60
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
Control (C)
No DR (ND)
NPDR (DR)
(𝜇)
(𝜇)
(a)
(c)
∗= P < 0.05
∗= P < 0.05
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
∗
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-ND
C-ND
Inner ring
Outer ring
Inner ring
Outer ring
ILM + RNFL
INL + OPL
C-DR
C-DR C-DR C-DR C-DR C-DR
C-DR
ND-DR 0
10
20
30
40
50
60
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
(𝜇)
∗= P < 0.05
∗
∗
∗
∗
∗
∗
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-DR
C-ND
C-ND
C-ND
Inner ring
Outer ring
ILM + RNFL CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
30
40
50
60
70
80
90
100
110
(𝜇)
(b)
∗= P < 0.05
Inner ring
Outer ring
ONL + ELM 30
40
50
60
70
80
90
CSF
SIM
NIM
IIM
TIM SOM NOM IOM TOM
(𝜇)
∗= P < 0.05
∗
∗
∗
∗
∗
∗
∗
Inner ring
Outer ring
INL + OPL
C-DR
C-DR C-DR C-DR C-DR C-DR
C-DR
ND-DR CSF
SIM NIM
IIM
TIM SOM NOM IOM TOM
20
30
40
50
60
70
80
(𝜇)
Inner ring
Outer ring
IS/OS + RPE (c) (e) Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics
with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. 3. Results GCL/IPL thickness was not statistically significantly dif-
ferent between diabetics and controls, although there was a
trend toward decreasing thickness in no DR group versus
controls in the inner and outer rings’ quadrants. GCL/IPL
thickness was significantly decreased only in the NOM and
SOM (𝑃= 0.02, for both) in diabetics with no DR versus
NPDR group (Figure 2(b)).i Of 124 enrolled subjects 74 were diabetics, (49 males and
25 females). Of 50 normal subjects, 21 were males and 29
females. Mean age of diabetics was 56.4 ± 12.7 years (range:
31–83 years); mean age of controls was 55.8 ± 13 years (range:
25–80 years). Thirty eyes were graded as no DR and 44 eyes as
nonproliferative DR (NPDR). Eighteen patients (24.32%) had
type 1 DM and 56 (75.68%) had type 2 DM. Mean HbA1c was
8.1% (range: 5.3%–11%). There was no significant difference in
age (ANOVA, 𝑃= 0.98), spherical equivalent (ANOVA, 𝑃=
0.12), IOP (ANOVA, 𝑃= 0.4), and visual acuity (ANOVA,
𝑃= 0.5) among controls, no DR, and NPDR groups (Table 1). 3. Results (a)
Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear
layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer
segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield
thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner
quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer
quadrant. Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics
with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. (a)
Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear
layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer
segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield
thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner
quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer
quadrant. 3. Results Journal of Diabetes Research 5 60
70
80
90
100
110
120
130
140
ILM + RNFL
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(a)
0
10
20
30
40
50
60
70
80
GCL + IPL
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(b)
0
10
20
30
40
50
60
70
80
INL + OPL
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(c)
0
10
20
30
40
50
60
70
80
ONL + ELM
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(d)
20
30
40
50
60
70
80
90
100
IS/OS + RPE
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(e)
igure 3: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics
with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 4 peripapillary areas (temporal,
uperior, nasal, and inferior). (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer
GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM);
nd (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). There is no significant difference in
he retinal layer thickness among the controls, no DR, and NPDR groups. 3. Results 0
10
20
30
40
50
60
70
80
GCL + IPL
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇) 60
70
80
90
100
110
120
130
140
ILM + RNFL
Temporal
Superior
Nasal
Inferior
(𝜇) (b)
20
30
40
50
60
70
80
90
100
IS/OS + RPE
Control
Temporal
Superior
Nasal
Inferior
(𝜇) (a)
0
10
20
30
40
50
60
70
80
INL + OPL
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(c) (a)
0
10
20
30
40
50
60
70
80
INL + OPL
Temporal
Superior
Nasal
Inferior
(𝜇) 0
10
20
30
40
50
60
70
80
ONL + ELM
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(d) (b)
20
30
40
50
60
70
80
90
100
IS/OS + RPE
Control
No DR
NPDR
Temporal
Superior
Nasal
Inferior
(𝜇)
(e) (c) (e) (d) Figure 3: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics
with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 4 peripapillary areas (temporal,
superior, nasal, and inferior). (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer
(GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM);
and (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). There is no significant difference in
the retinal layer thickness among the controls, no DR, and NPDR groups. males versus females (𝑃= 0.0004) in both controls and
diabetics.if explained by progressive ganglion cells and astrocytes loss
induced by diabetes. It may depend on a direct toxicity of
hyperglycemia or on M¨uller cells dysfunction, which are
unable to maintain an adequate osmotic equilibrium between
the intra- and the extracellular matrices with consequent
apoptosis of neuronal cells and progressive axonal degen-
eration [2, 9, 17–20]. Different authors have reported the
thinning of RNFL and, in some cases, of the GCL + IPL
complex, suggesting that retinal neurodegeneration is an
early event in diabetes mellitus, representing a preclinical
stage of DR [15, 21, 22]. In fact, the decrease of RNFL thickness
in the superior macular region in diabetics without DR or
with minimal signs of DR has been documented in vivo [23–
26]. Lonneville et al. 3. Results have demonstrated that RNFL thickness
decreases with poor metabolic control in diabetics with or ILM + RNFL thickness was significantly different in 4
quadrants, thicker in the superior and inner quadrants, and
thinner in the nasal and temporal quadrants. There was
no significant difference in the ILM + RNFL, GCL/IPL,
INL/OPL, ONL/ELM, and IS/OS −RPE thickness between
controls and diabetics (Figure 3). 4. Discussion Moreover, as inner and outer retinas appear
differently affected, it seems crucial to have the possibility to
evaluate the different retinal layers separately. (c) Figure 4: Spectral domain OCT linear scans in the macula of (a)
normal subject, (b) diabetic patient without retinopathy, and (c)
diabetic patient with mild nonproliferative diabetic retinopathy. The
arrows indicate a progressive thinning of the retinal nerve fiber layer
in diabetics (without and with retinopathy) versus normal subjects. without clinically detectable DR [27]. In this study, we did
not find significant difference in RNFL thickness between
diabetics without DR and with NPDR. This is probably due
to the fact that all our patients were at early stages of DR
and had quite good metabolic control. In this study we did
not find statistically significant difference in the thickness of
GCL/IPL between diabetics and controls, although there was
a trend of decreasing GCL/IPL thickness in diabetics without
DR versus controls in the pericentral macula. This may be due
to the small differences in the specific layer thickness, thus
suggesting a more numerous study population.h f
In conclusion, the thinning of the inner neural retina in
diabetic patients without clinically detectable retinopathy and
with mild and moderate nonproliferative retinopathy without
macular edema is confirmed in vivo using SD-OCT. Retinal
thinning is mainly due to the selective thinning of inner
retinal layers in the central retina, strongly suggesting an early
neuronal loss in DR. The neuronal loss is accompanied (or
induced) by M¨uller cells activation, with increasing thickness
in the INL. Automatic intraretinal layering by SD-OCT may
be a useful tool to diagnose and monitor early intraretinal
changes in diabetic retinopathy. gg
g
y p p
The INL and the OPL showed increased thickness in
diabetic patients with NPDR versus controls in this study. The INL is mainly formed by the nuclei of bipolar and M¨uller
cells and by the association of horizontal and amacrine cells. Different experimental studies have reported an activation of
M¨uller cells with consequent hypertrophy in the earlier stages
of diabetic retinopathy [28–32]. No histopathologic studies
have reported changes in OPL thickness in the early stages of
diabetes mellitus. Therefore, the INL/OPL thickening would
be mostly due to the changes in INL thickness. INL thicken-
ing, never previously reported in vivo, may represent a sign
of M¨uller cells activation which is represented by significant
hypertrophy of these cells. 4. Discussion In this study we report a decrease in RNFL thickness in
the macula of diabetic eyes even without any clinical sign
of retinopathy (Figure 4). Reduced RNFL thickness may be Journal of Diabetes Research 6 (a)
(b)
(c)
Figure 4: Spectral domain OCT linear scans in the macula of (a)
normal subject, (b) diabetic patient without retinopathy, and (c)
diabetic patient with mild nonproliferative diabetic retinopathy. The
arrows indicate a progressive thinning of the retinal nerve fiber layer
in diabetics (without and with retinopathy) versus normal subjects. (a) microvascular lesions, although it is still not known which
one of these two events appears first [39, 40]. M¨uller cells
become hyperplastic in DM, with an increasing number
of nuclei, as histopathologically demonstrated. In fact, the
number of cell nuclei is increased in the INL and reaches a
multiplication factor of 1.6 times, at 20 weeks of DM [28].hif (a) There was not a significant difference in ONL/ELM
thickness between diabetics without DR and normal subjects. In diabetics with retinopathy the ONL/ELM was reduced just
in the superior macular quadrants. The photoreceptor/RPE
layer was not different in thickness between diabetics and
normal subjects. Therefore, it seems that outer retina is not
significantly influenced by diabetes at least in the early stages
of disease whereas the inner retina is precociously affected (b) (b) (c) il
of disease, whereas the inner retina is precociously affected. In the peripapillary area, although RNFL thickness was
reduced in diabetics versus controls, it did not reach statistical
and clinical significance, probably due to the fact that in
this area small changes are more difficult to be clinically
detected because of the high density of retinal nerve fibers
[41]. The automatic segmentation of SD-OCT used in this
study, although not able to identify any single retinal layer,
but rather layers by couple, can be easily used in both the
macula and the peripapillary region for the inner and outer
retinal thickness analysis in normal subjects and in diabetic
eyes. Its use in a more advanced cases of diabetic retinopathy,
mostly in macular edema, needs to be further validated. A
detection of retina layer thickness changes in diabetic patients
without retinopathy or at early stages of retinopathy may
also help in the early diagnosis of retinal tissue loss in DM
and to better elucidate the pathophysiology of this severe
chronic disease. This study was supported by grant from the 7th Framework
Programme (EUROCONDOR. FP7-278040). This study was supported by grant from the 7th Framework
Programme (EUROCONDOR. FP7-278040). 4. Discussion M¨uller cells are particularly sus-
ceptible to hyperglycemia and are recognized as key elements
in the onset and the progression of retinal damage induced by
hyperglycemia [33]. Diabetes induces hypertrophy (swelling)
of M¨uller cells with a limited impact on the apoptotic cascade
[34, 35]. Metabolic and morphological alterations of M¨uller
cells induce secondary progressive neuronal loss, due to
the crucial role of M¨uller cells in mediating relationship
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Experimental Ophthalmology, vol. 245, no. 5, pp. 627–636, 2007. [37] H. W. Van Dijk, F. D. Verbraak, P. H. B. Kok et al., “Early
neurodegeneration in the retina of type 2 diabetic patients,”
Investigative Ophthalmology & Visual Science, vol. 53, pp. 2715–
2719, 2012. [38] T. W. Gardner, D. A. Antonetti, A. J. Barber, K. F. LaNoue, and
S. W. Levison, “Diabetic retinopathy: more than meets the eye,”
Survey of Ophthalmology, vol. 47, no. 2, pp. S253–S262, 2002. [39] E. Carrasco, C. Hern´andez, A. Miralles, P. Huguet, J. Farr´es,
and R. Sim´o, “Lower somatostatin expression is an early
event in diabetic retinopathy and is associated with retinal
neurodegeneration,” Diabetes Care, vol. 30, no. 11, pp. 2902–
2908, 2007. [40] E. Carrasco, C. Hern´andez, I. de Torres, J. Farr´es, and R. Sim´o, “Lowered cortistatin expression is an early event in the
human diabetic retina and is associated with apoptosis and glial
activation,” Molecular Vision, vol. 14, pp. 1496–1502, 2008. [41] B. Fortune, H. Yang, N. G. Strouthidis et al., “The effect of
acute intraocular pressure elevation on peripapillary retinal
thickness, retinal nerve fiber layer thickness, and retardance,”
Investigative Ophthalmology and Visual Science, vol. 50, no. 10,
pp. 4719–4726, 2009. |
https://openalex.org/W2136938899 | https://figshare.com/articles/journal_contribution/Supplementary_Figure_Legends_from_PI3_-Kinase_Inhibition_Forestalls_the_Onset_of_MEK1_2_Inhibitor_Resistance_in_i_BRAF_i_-Mutated_Melanoma/22530428/1/files/39993551.pdf | English | null | PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in <i>BRAF</i>-Mutated Melanoma | Cancer discovery | 2,015 | cc-by | 741 | SUPPLEMENTARY FIGURE LEGENDS Figure S1: BP2C mouse melanoma-derived cells are sensitive to PI3Kα-selective
inhibition Figure S1: BP2C mouse melanoma-derived cells are sensitive to PI3Kα-selective
inhibition (A) BP2C melanoma cells were cultured in the presence of the indicated concentrations of
BYL719 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining
was quantified as described above. Values are normalized to DMSO control and error bars
represent SEM. (B) BP2C melanoma cells were cultured in the presence of the indicated concentrations of
BYL719 with cells counted every 24 hours for a total period of 72 hours. Cell counts are
indicated as change in cell number relative to the number of cells at the initiation of drug
treatment and error bars represent SEM. (C) Lysates of BP2C melanoma cells cells treated for 6 hours with DMSO, LGX818 (100nM),
BYL719 (5μM) or the combination of both agents were analyzed by immunoblotting. (D) Mice bearing BRAFV600E/PIK3CAH1047R melanoma were dosed with a single dose of BYL719
(50mg/kg) and sacrificed at the indicated times post dose. Lysates of melanomas that had been
snap frozen in liquid nitrogen were analyzed by immunoblotting. Figure S3: PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on
BRAFV600E/ PTENNull melanoma-derived cells Figure S2: BRAFV600E/PTENNull melanoma-derived cells are sensitive to PI3Kβ-sparing
PI3’ kinase inhibition (A) M233 or M249 melanoma cells were cultured in the presence of the indicated
concentrations of KIN193 or GSK771 for 72 hours before being fixed and stained with Crystal
Violet. Crystal Violet staining was quantified as described above. Values indicated are
normalized to DMSO control and error bars represent SEM. (B) Lysates of 1205Lu, WM793, M233, M249, B10C, or BPC melanoma cells treated for 24
hours with the indicated concentrations of KIN193 or GSK771 were analyzed by
immunoblotting. (C) M233 or M249 melanoma cells were cultured in the presence of the indicated
concentrations of GDC-0032 (blue) or GDC-0941 (pink) for 72 hours prior to fixation and
staining with Crystal Violet. Crystal Violet staining was quantified as described above. Values
indicated are normalized to DMSO control and error bars represent SEM. (D) Lysates of 1205Lu, WM793, M233 or M249 melanoma cells treated for 24 hours with DMSO
or GDC-0941 or GDC-0032 (with drug treatment applied from 10μM to 31.25 nM in two-fold
dilution series as indicated) were analyzed by immunoblotting. (E) Lysates of 1205Lu melanoma cells treated for treated for 24 hours with DMSO, GDC-0032
(0032), BYL719 (BYL), IPI145 (IPI) or BYL719+IPI145 (BYL+IPI) (all at 5μM) were analyzed by
immunoblotting. Figure S3: PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on
BRAFV600E/ PTENNull melanoma-derived cells (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM),
GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM),
GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM),
GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (B) B10C, M233 or M249 melanoma cells were cultured in the presence of GDC-0032 (5μM),
GDC-0973 (1μM) or GDC-0973 plus GDC-0032 with cells fixed and stained with Crystal Violet
every 24 hours for of 72 hours. Crystal Violet staining was quantified as described above. Error
bars represent SEM. Asterisks indicate significant difference between combination drug
treatment and single agent drug treatment (2-way ANOVA, p<0.0001). Figure S4: BRAFV600E/PTENWT melanoma cells are sensitive to PI3Kβ-sparing PI3’-kinase
inhibition, and PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on
BRAFV600E/ PTENWT melanoma cells (A) SK-MEL-239 melanoma cells were cultured in the presence of the indicated concentrations
of KIN193 or GSK771 for 72 hours before being fixed and stained with Crystal Violet. Crystal
Violet staining was quantified as described above. Values indicated are normalized to DMSO
control and error bars represent SEM. (B) Lysates of SK-MEL-239 melanoma cells treated for 24 hours with the indicated
concentrations of KIN193 or GSK771 were analyzed by immunoblotting. (C) SK-MEL-239 melanoma cells were cultured in the presence of the indicated concentrations
of GDC-0941 or GDC-0032 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining was quantified as described above. Values indicated are normalized to
DMSO control and error bars represent SEM. (D) Lysates of SK-MEL-239 melanoma cells treated for 6 hours with GDC-0973 (1μM), GDC-
0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. |
https://openalex.org/W2955038587 | https://europepmc.org/articles/pmc6681330?pdf=render | English | null | Expression of miR159 Is Altered in Tomato Plants Undergoing Drought Stress | Plants | 2,019 | cc-by | 8,943 | Received: 27 May 2019; Accepted: 27 June 2019; Published: 2 July 2019 Abstract: In a scenario of global climate change, water scarcity is a major threat for agriculture, severely
limiting crop yields. Therefore, alternatives are urgently needed for improving plant adaptation
to drought stress. Among them, gene expression reprogramming by microRNAs (miRNAs) might
offer a biotechnologically sound strategy. Drought-responsive miRNAs have been reported in many
plant species, and some of them are known to participate in complex regulatory networks via
their regulation of transcription factors involved in water stress signaling. We explored the role
of miR159 in the response of Solanum lycopersicum Mill. plants to drought stress by analyzing the
expression of sly-miR159 and its target SlMYB transcription factor genes in tomato plants of cv. Ailsa Craig grown in deprived water conditions or in response to mechanical damage caused by
the Colorado potato beetle, a devastating insect pest of Solanaceae plants. Results showed that
sly-miR159 regulatory function in the tomato plants response to distinct stresses might be mediated
by differential stress-specific MYB transcription factor targeting. sly-miR159 targeting of SlMYB33
transcription factor transcript correlated with accumulation of the osmoprotective compounds proline
and putrescine, which promote drought tolerance. This highlights the potential role of sly-miR159 in
tomato plants’ adaptation to water deficit conditions. Expression of miR159 Is Altered in Tomato Plants
Undergoing Drought Stress María José López-Galiano 1, Inmaculada García-Robles 1
, Ana I. González-Hernández 2
Gemma Camañes 2
, Begonya Vicedo 2, M. Dolores Real 1 and Carolina Rausell 1,* Gemma Camañes
, Begonya Vicedo , M. Dolores Real
and Carolina Rausell
1
Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain
2
Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I,
12071 Castellón, Spain
*
C
d
li
ll@
T l
34 96 354 3397 *
Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 *
Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 *
Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 Plants 2019, 8, 201; doi:10.3390/plants8070201 plants plants 1. Introduction Climate change due to increasing concentration of CO2 in the atmosphere is leading to rising
temperatures, altered rainfall patterns, and more frequent and severe drought episodes [1], which
negatively impact crop production. Therefore, gaining knowledge about how plants regulate
their adaptation to stress is critical to find ways to enhance plant performance in eventually
drier environments. To cope with drought, plants activate a complex cascade of events at the cellular level that include
extensive metabolic and gene transcriptional reprogramming to protect cells from osmotic stress, and
limit water loss. The response of plants to drought stress involves genes related to diverse functional
categories such as genes encoding proteins participating in the direct protection of essential proteins and
membranes (osmoprotectants, free radical scavengers, etc.), genes encoding membrane transporters
and ion channels that promote water uptake, and genes encoding stress related regulatory proteins such
as kinases and transcription factors belonging to the V-myb myeloblastosis viral oncogene homolog
(MYB), basic-helix-loop-helix (bHLH), basic region/leucine zipper (bZIP), NAM, ATAF1/2, and CUC
(NAC), and APETALA2/ethylene-responsive element binding protein (AP2/EREBP) families [2]. Plants 2019, 8, 201; doi:10.3390/plants8070201 www.mdpi.com/journal/plants Plants 2019, 8, 201 2 of 11 The phytohormone Abscisic acid (ABA) coordinates the plant’s response to reduced
water availability by modulating the expression of some of the drought responsive genes [3]. Interestingly, microRNAs (miRNAs) have been recently reported to mediate drought tolerance by
post-transcriptionally regulating drought-responsive genes, some of which are known to be controlled
by ABA signaling pathways [4]. An example of such intricate regulatory network is provided by
miR159, which in Arabidopsis germinating seeds, has been reported to be induced by ABA and drought
treatments, and promote transcript cleavage of the ABA positive regulators MYB33 and MYB101
transcription factors, thereby playing a key role in ABA response [5]. The miR159 family is highly conserved among monocot and dicot plants, but in plants undergoing
drought, miR159’s relative abundance varies in a tissue- and species-specific manner. For instance,
miR159 was reported to be up-regulated by drought stress in Arabidopsis [6], and maize [7], but
down-regulated in cotton [8], and potato [9], whereas in barley and alfalfa, miR159 was down-regulated
in roots and up-regulated in leaves in response to drought stress [10,11]. Pegler et al. 1. Introduction [12] proposed that
the differential miRNA abundance across species following drought or salt stress exposure might be in
part due to differential distribution of regulatory transcription factor binding sites within the putative
promoter region of the miRNA gene, which encodes the highly conserved, stress-responsive miRNA. To expand our knowledge on the miR159 regulatory network involved in tomato plants’ response
to drought stress, in the present work we analyzed the expression of miR159 and its predicted target
genes in tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig undergoing drought stress, in
which we previously reported that ABA hormone is accumulated after water deprivation [13]. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress To assess miR159 expression in tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig
following a seven-day water deprivation, we analyzed sly-miR159 (GenBank: 102464332) transcript
levels by RT-qPCR in control tomato plants and plants undergoing drought stress. Results showed
significantly reduced expression of sly-miR159 in response to stress (Figure 1A). However, in recent
high-throughput sequencing studies performed by Liu et al. [14,15], miR159 was not found among the
miRNAs differentially expressed after 10 days of drought stress in a sensitive and a tolerant tomato
cultivar. This apparent discrepancy with our results might be due to the differential experimental
conditions or techniques used to measure miRNA expression, but is most probably due to the fact that
the tomato cultivars were different, since it has been reported that miRNAs respond to environmental
stresses in a genotype-dependent manner [16]. As in plants, most miRNAs negatively regulate their
target genes, we hypothesized that sly-miR159 gene targets that are upregulated in tomato plants
grown in water-limited conditions in our experimental conditions may play beneficial roles in the
adaptive responses to drought stress. In Arabidopsis, a clade of seven closely related GAMYB-like genes (MYB33, MYB101, MYB65, MYB81,
MYB97, MYB104, and MYB120) share a conserved putative miR159-binding site [17]. The GAMYB-like
genes encode a highly conserved family of R2R3-type MYB domain transcription factors that are
regulated by Gibberellic acid (GA) and ABA and participate in the GA signaling pathway [18]. Recent studies in potato plants highlight the involvement of miR159 and its targets GAMYB-like
genes in the response of this species to water stress [9]. Using psRNATarget software [19] we
identified the following putative GAMYB-like transcription factor genes that are sly-miR159 targets in
tomato: SlMYB33 (Solyc01g009070.2.1), SlMYB65 (Solyc06g073640.2.1), SlMYB104 (Solyc11g072060.1.1),
SlMYB97 (Solyc10g019260.1.1), and SlMYB120 (Solyc01g090530.1.1). Figure 1B shows the nucleotide
sequence of the sly-miR159-binding sites in the tomato SlMYB transcripts identified, which strongly
resemble those found in AtMYB transcripts targeted by miR159 in Arabidopsis [20]. 3 of 11
express Plants 2019, 8, 201
water stres
[22] Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato pla
undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato pla
and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-bind
sites in tomato GAMYB-like transcripts. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress (A) RT-qPCR analysis of sly-miR159 expression in control tomato pla
and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-bind
sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-c
red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green lett
(C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes express
in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and (
data shown are the mean of three independent experiments ± standard error (SE). Asterisk indica
that differences between means of control and undergoing drought stress tomato plants w
statistically significant (Student’s t-test, p < 0.05). Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants
undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants
and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-binding
sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-case
red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green letters. (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in
control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and (C), data
shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that
differences between means of control and undergoing drought stress tomato plants were statistically
significant (Student’s t-test, p < 0.05). To further assess the involvement of sly-miR159 in the regulation of SlMYB33 gene express
under drought stress, we aimed at analyzing SlMYB33 cleavage fragments. We designed two p
of primers to amplify SlMYB33 mRNA fragments in small RNA samples isolated from total RNA
Li et al. [21] identified 127 MYB genes in the tomato genome and classified the corresponding
proteins into 18 subgroups based on domain similarity and phylogenetic topology, and suggested
that conserved motifs outside the MYB domain might reflect their functional conservation. SlMYB33,
SlMYB65, and SlMYB104 proteins cluster in subgroup 12, in which the three of them are the only
ones (out of the thirteen subgroup members) sharing the conserved motifs 14 and 15 outside the MYB
domain. SlMYB97 and SlMYB120 proteins constitute subgroup 15, which is composed only by these
two MYB proteins that have no conserved motifs outside the MYB domain. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress Nucleotides in the cleavage site are underlined, lower-c
red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green lett
(C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes express
in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and
data shown are the mean of three independent experiments ± standard error (SE). Asterisk indica
that differences between means of control and undergoing drought stress tomato plants w
statistically significant (Student’s t-test, p < 0.05). B
sly-miR159
AUCUCGAGGGAAGUUAGGUUU-5’
SlMYB33
UGGAGCUCCCUUCAcUCCAAA-3’
SlMYB65
UcGAGCUCCCUUCAcUCCAAA-3’
SlMYB104
UGGAGCUCCCUUCuuUCCAAA-3’
SlMYB97
UGGAGCUCCaUUCGAUCCAAA-3’
SlMYB120
UGGAGCUCCaUUCGAUCCAAA-3’
0.0E+00
2.0E-06
4.0E-06
6.0E-06
8.0E-06
1.0E-05
1.2E-05
SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120
Relative number of molecules (N0)
Control
Drought
C
*
0
1.2x10-5
1.0x10-5
8.0x10-6
6.0x10-6
4.0x10-6
2.0x10-6
0
0
0.5
1
1.5
2
2.5
sly-miR159 relative number of molecules (N0)
A
*
2.5
2.0
1.5
1.0
0.5
0
Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants
undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants
and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-binding
sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-case
red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green letters. (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in
control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and (C), data
shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that
differences between means of control and undergoing drought stress tomato plants were statistically
significant (Student’s t-test, p < 0.05). B
sly-miR159
AUCUCGAGGGAAGUUAGGUUU-5’
SlMYB33
UGGAGCUCCCUUCAcUCCAAA-3’
SlMYB65
UcGAGCUCCCUUCAcUCCAAA-3’
SlMYB104
UGGAGCUCCCUUCuuUCCAAA-3’
SlMYB97
UGGAGCUCCaUUCGAUCCAAA-3’
SlMYB120
UGGAGCUCCaUUCGAUCCAAA-3’
0.0E+00
2.0E-06
4.0E-06
6.0E-06
8.0E-06
1.0E-05
1.2E-05
SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120
Relative number of molecules (N0)
Control
Drought
C
*
0
1.2x10-5
1.0x10-5
8.0x10-6
6.0x10-6
4.0x10-6
2.0x10-6
0 B 0
0.5
1
1.5
2
2.5
sly-miR159 relative number of molecules (N0)
A
*
2.5
2.0
1.5
1.0
0.5
0 A 0.0E+00
2.0E-06
4.0E-06
6.0E-06
8.0E-06
1.0E-05
1.2E-05
SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120
Relative number of molecules (N0)
Control
Drought
C
*
0
1.2x10-5
1.0x10-5
8.0x10-6
6.0x10-6
4.0x10-6
2.0x10-6
0 C SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato pla
undergoing drought stress. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly-
iR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows
dicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region,
d primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B)
T-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants
llowing 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene
pression was used as normalization control. For each sample, three biological replicates were
ooled and analyzed. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of
sly-miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and
arrows indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding
region, and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding
region. (B) RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato
plants following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene
expression was used as normalization control. For each sample, three biological replicates were pooled
and analyzed. Interestingly, Qin et al. [23] proposed that MYB33 transcription factor may enhance drought
erance by means of promoting osmotic pressure balance reconstruction and reactive oxidative
ecies (ROS) scavenging, since ectopic over-expression of wheat MYB33 gene in Arabidopsis induced
e expression of AtP5CS and AtZAT12 genes involved in proline synthesis and ascorbate peroxidase
nthesis, respectively. Accordingly, we observed an induction of SlP5CS gene expression and a
markable increase in proline levels relative to other amino acids in tomato plants grown in water-
ortage conditions compared to irrigated control plants (Figure 3A,B), suggesting that sly-miR159
ght participate in the tomato plants’ adaptive response to drought stress via induction of SlMYB33
nscription factor gene expression. Nevertheless, further research is needed to demonstrate
hether the sly-miR159-SlMYB33 pathway is necessary for drought tolerance in the tomato cultivar
lsa Craig. T
l [24]
d
b li
di
i
b
l
i
d
li
Interestingly, Qin et al. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress We analyzed the expression of sly-miR159 MYB predicted targets in control tomato plants and
plants undergoing drought stress by RT-qPCR (Figure 1C). Only SlMYB33 gene showed statistically
significant induction in water-stressed tomato plants, exhibiting an opposite pattern of expression
relative to that of sly-miR159, which suggests that this MYB gene may be regulated by sly-miR159 in
tomato plants in response to drought stress. In line with this hypothesis, in potato plants in which the
CBP80 gene encoding a protein involved in RNA processing was silenced, improved tolerance to water
stress was correlated with decreased levels of miR159 and enhanced MYB33 gene expression [22]. To further assess the involvement of sly-miR159 in the regulation of SlMYB33 gene expression
under drought stress, we aimed at analyzing SlMYB33 cleavage fragments. We designed two pairs of
primers to amplify SlMYB33 mRNA fragments in small RNA samples isolated from total RNA of control
tomato plants and tomato plants following a seven-day water deprivation (Materials and Methods,
Section 4.3). Figure 2A shows the annealing positions of both pairs of PCR primers. The primer pair 4 of 11
nd Plants 2019, 8, 201
l
l OFw and ORv anneals to sequences within a SlMYB33 mRNA region downstream of the predicted
sly-miR159-binding site, yielding a 199 bp SlMYB33 amplification product. The primer pair FFw and
FRv anneals to sequences flanking the putative cleavage site in the predicted sly-miR159-binding region,
yielding a 200 bp SlMYB33 amplification product only when the SlMYB33 mRNA is not cleaved at
the sly-miR159 cleavage site. Therefore, we hypothesized that if sly-miR159 is not involved in the
regulation of SlMYB33 gene expression of the same amplification patterns of control vs. drought,
then small RNA samples with both primer pairs would be expected. Figure 2B shows the results
obtained in the RT-PCR amplifications using the two pairs of primers. Lower amounts of amplification
products were obtained using primers OFw and ORv in tomato plants grown under water scarcity
compared to control plants. In contrast, higher amount of PCR amplified product was observed in
drought-stressed tomato plants than in control tomato plants using primers FFw and FRv. Collectively,
these results support targeted cleavage of SlMYB33 transcripts by sly-miR159 that might participate in
the transcriptional regulation of the tomato plants’ response to drought stress. ethods, Section 4.3). Figure 2A shows the annealing positions of both pairs of PCR primers. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress The
mer pair OFw and ORv anneals to sequences within a SlMYB33 mRNA region downstream of the
edicted sly-miR159-binding site, yielding a 199 bp SlMYB33 amplification product. The primer pair
w and FRv anneals to sequences flanking the putative cleavage site in the predicted sly-miR159-
nding region, yielding a 200 bp SlMYB33 amplification product only when the SlMYB33 mRNA is
t cleaved at the sly-miR159 cleavage site. Therefore, we hypothesized that if sly-miR159 is not
volved in the regulation of SlMYB33 gene expression of the same amplification patterns of control
drought, then small RNA samples with both primer pairs would be expected. Figure 2B shows
e results obtained in the RT-PCR amplifications using the two pairs of primers. Lower amounts of
mplification products were obtained using primers OFw and ORv in tomato plants grown under water
arcity compared to control plants. In contrast, higher amount of PCR amplified product was
served in drought-stressed tomato plants than in control tomato plants using primers FFw and FRv. llectively, these results support targeted cleavage of SlMYB33 transcripts by sly-miR159 that might
rticipate in the transcriptional regulation of the tomato plants’ response to drought stress. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly-
miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows
indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region,
and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B)
RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants
following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene
expression was used as normalization control. For each sample, three biological replicates were
pooled and analyzed. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of
sly-miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and
arrows indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding
region, and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding
region. (B) RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato
plants following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene
expression was used as normalization control. For each sample, three biological replicates were pooled
and analyzed. gure 2. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress [23] proposed that MYB33 transcription factor may enhance drought
tolerance by means of promoting osmotic pressure balance reconstruction and reactive oxidative
species (ROS) scavenging, since ectopic over-expression of wheat MYB33 gene in Arabidopsis induced
the expression of AtP5CS and AtZAT12 genes involved in proline synthesis and ascorbate peroxidase
synthesis, respectively. Accordingly, we observed an induction of SlP5CS gene expression and
a remarkable increase in proline levels relative to other amino acids in tomato plants grown
in water-shortage conditions compared to irrigated control plants (Figure 3A,B), suggesting that
sly-miR159 might participate in the tomato plants’ adaptive response to drought stress via induction of
SlMYB33 transcription factor gene expression. Nevertheless, further research is needed to demonstrate
whether the sly-miR159-SlMYB33 pathway is necessary for drought tolerance in the tomato cultivar
Ailsa Craig. Tonon et al. [24] proposed a strong metabolic coordination between polyamines and proline
thways in response to osmotic stresses. Therefore, we analyzed polyamine levels in tomato plants
dergoing drought stress and non-stressed control plants (Figure 3C), and results showed increased
cumulation of putrescine a polyamine reported to have a role in protecting plants during water
Tonon et al. [24] proposed a strong metabolic coordination between polyamines and proline
pathways in response to osmotic stresses. Therefore, we analyzed polyamine levels in tomato
plants undergoing drought stress and non-stressed control plants (Figure 3C), and results showed 5 of 11 Plants 2019, 8, 201 increased accumulation of putrescine, a polyamine reported to have a role in protecting plants during
water-deficient conditions, as well as oxidative stress [25]. In wheat, Pál et al. [26] recently described
that ABA pre-treatments induced the expression of P5CS gene and enhanced the accumulation of
putrescine. Authors suggested that the connection between polyamine metabolism and ABA signaling
may control the regulation and maintenance of polyamine and proline levels under osmotic stress
conditions in wheat seedlings. , ,
deficient conditions, as well as oxidative stress [25]. In wheat, Pál et al. [26] recently described that
ABA pre-treatments induced the expression of P5CS gene and enhanced the accumulation of
putrescine. Authors suggested that the connection between polyamine metabolism and ABA
signaling may control the regulation and maintenance of polyamine and proline levels under osmotic
stress conditions in wheat seedlings. Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
undergoing drought stress. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and
tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water
1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato
plants were statistically significant (Student’s t-test, p < 0.05). C
0
5
10
15
20
25
30
35
40
45
50
Put
Spd
Spn
Polyamines (μg/g)
Control
Drought
*
-20
0
20
40
60
80
100
120
140
160
180
200
Ala Asp Glu Gln His
Lys Met Phe Pro Ser Thr Trp Tyr Val
Amino acids (μg/g)
Control
Drought
B
*
*
*
*
0.0E+00
5.0E-05
1.0E-04
1.5E-04
2.0E-04
2.5E-04
SlP5CS relative number of molecules (N0)
A
*
2.5x10-4
2.0x10-4
1.5x10-4
1.0x10-4
5.0x10-5
0
Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and
tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines
levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves
were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates
that differences between means of control and undergoing drought stress tomato plants were statistically
significant (Student’s t-test, p < 0.05). -20
0
20
40
60
80
100
120
140
160
180
200
Ala Asp Glu Gln His
Lys Met Phe Pro Ser Thr Trp Tyr Val
Amino acids (μg/g)
Control
Drought
B
*
*
*
* 0.0E+00
5.0E-05
1.0E-04
1.5E-04
2.0E-04
2.5E-04
SlP5CS relative number of molecules (N0)
A
*
2.5x10-4
2.0x10-4
1.5x10-4
1.0x10-4
5.0x10-5
0 B Control
Drought A 0
5
10
15
20
25
30
35
40
45
50
Put
Spd
Spn
Polyamines (μg/g)
Control
Drought
* C Control
Drought Figure 3. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and
tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water
1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato
plants were statistically significant (Student’s t-test, p < 0.05). Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and
tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines
levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves
were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates
that differences between means of control and undergoing drought stress tomato plants were statistically
significant (Student’s t-test, p < 0.05). 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33
2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 f
y
p
f
g
g f
To ascertain whether SlMYB33 targeting by sly-miR159 is stress-specific, we analyzed the
expression of sly-miR159 and its predicted MYB target genes in tomato plants attacked by the
coleopteran insect pest Colorado potato beetle (CPB), in which we previously reported that, as
opposed to tomato plants undergoing drought stress, ABA was not accumulated [13]. In the present
work, neither SlP5CS gene expression were induced, nor were increased proline and putrescine levels
observed in infested tomato plants compared to tomato control plants (Figure 4), corroborating that
To ascertain whether SlMYB33 targeting by sly-miR159 is stress-specific, we analyzed the
expression of sly-miR159 and its predicted MYB target genes in tomato plants attacked by the
coleopteran insect pest Colorado potato beetle (CPB), in which we previously reported that, as opposed
to tomato plants undergoing drought stress, ABA was not accumulated [13]. In the present work,
neither SlP5CS gene expression were induced, nor were increased proline and putrescine levels
observed in infested tomato plants compared to tomato control plants (Figure 4), corroborating that
the plants’ response to this biotic stress is different from the plant response to water stress. Plants 2019, 8, 201
Plants 2019, 8, x FOR 6 of 11
6 of 11 he plants’ response to this biotic stress is different from the plant response to water stress. Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control
tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino
acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato
leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels
are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the
mean of three independent experiments ± standard error (SE). Asterisk indicates that differences
between means of control and undergoing drought stress tomato plants were statistically significant
(Student´s t-test, p < 0.05). 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33
2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 0
10
20
30
40
50
60
Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val
Amino acids (μg/g)
Control
CPB infestation
*
*
*
*
*
*
*
B
C
0
5
10
15
20
25
30
35
40
45
50
Put
Spd
Spn
Polyamines (μg/g)
Control
CPB infestation
A
0.0E+00
5.0E-05
1.0E-04
1.5E-04
2.0E-04
2.5E-04
3.0E-04
SlP5CS relative number of molecules (N0)
0
3.0x10-4
2.5x10-4
2.0x10-4
1.5x10-4
1.0x10-4
5.0x10-5
0
Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested
by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato
plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato
leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels
are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato leaves were
collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed
in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three
independent experiments ± standard error (SE). Asterisk indicates that differences between means
of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test,
p < 0.05). otic stress is different from the plant response to water stress. 0
10
20
30
40
50
60
Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val
Amino acids (μg/g)
Control
CPB infestation
*
*
*
*
*
*
*
B the plants response to this b
A
0.0E+00
5.0E-05
1.0E-04
1.5E-04
2.0E-04
2.5E-04
3.0E-04
SlP5CS relative number of molecules (N0)
0
3.0x10-4
2.5x10-4
2.0x10-4
1.5x10-4
1.0x10-4
5.0x10-5
0 B B A A C p
y
p
C
0
5
10
15
20
25
30
35
40
45
50
Put
Spd
Spn
Polyamines (μg/g)
Control
CPB infestation Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants
infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control
tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino
acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33
2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 Tomato
leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels
are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the
mean of three independent experiments ± standard error (SE). Asterisk indicates that differences
between means of control and undergoing drought stress tomato plants were statistically significant
(Student´s t-test, p < 0.05). Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested
by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato
plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato
leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels
are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato leaves were
collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed
in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three
independent experiments ± standard error (SE). Asterisk indicates that differences between means
of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test,
p < 0.05). Intriguingly, as it was observed in plants deprived of water, in infested tomato plants, sly-
miR159 was significantly down-regulated compared to non-infested control plants (Figure 5A). However, in plants attacked by CPB, among sly-miR159 putative MYB targets, only the SlMYB104
transcript factor gene was significantly up-regulated (Figure 5B), suggesting that sly-miR159 might
be regulating this specific MYB transcription factor in response to CPB damage. Intriguingly, as it was observed in plants deprived of water, in infested tomato plants, sly-miR159
was significantly down-regulated compared to non-infested control plants (Figure 5A). However, in
plants attacked by CPB, among sly-miR159 putative MYB targets, only the SlMYB104 transcript factor
gene was significantly up-regulated (Figure 5B), suggesting that sly-miR159 might be regulating this
specific MYB transcription factor in response to CPB damage. 7 of 11
7 of Plants 2019, 8, 201
l A
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
sly-miR159 relative number of molecules (N0)
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0
* Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants
infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and
tomato plants infested by CPB larvae. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33
2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104,
SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB
larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments
± standard error (SE). Asterisk indicates that differences between means of control tomato plants and
tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). B
0.0E+00
2.0E-07
4.0E-07
6.0E-07
8.0E-07
1.0E-06
1.2E-06
1.4E-06
1.6E-06
SlMYB33
SlMYB65
SlMYB104
SlMYB97
SlMYB120
Relative number of molecules (N0)
Control
CPB infestation
*
0
1.6 x10-6
1.4 x10-6
1.2 x10-6
1.0 x10-6
8.0 x10-7
6.0 x10-7
4.0 x10-7
2.0 x10-7
0
A
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
sly-miR159 relative number of molecules (N0)
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0
*
Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants
infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants
and tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104,
SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB
larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments ±
standard error (SE). Asterisk indicates that differences between means of control tomato plants and
tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). B
0.0E+00
2.0E-07
4.0E-07
6.0E-07
8.0E-07
1.0E-06
1.2E-06
1.4E-06
1.6E-06
SlMYB33
SlMYB65
SlMYB104
SlMYB97
SlMYB120
Relative number of molecules (N0)
Control
CPB infestation
*
0
1.6 x10-6
1.4 x10-6
1.2 x10-6
1.0 x10-6
8.0 x10-7
6.0 x10-7
4.0 x10-7
2.0 x10-7
0 A B Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plant
infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants an
tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104
SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CP
larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiment
± standard error (SE). Asterisk indicates that differences between means of control tomato plants an
tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). Figure 5. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33
2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants
infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants
and tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104,
SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB
larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments ±
standard error (SE). Asterisk indicates that differences between means of control tomato plants and
tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). In contrast, correlating with the lack of proline and putrescine accumulation, no variation w
detected in SlMYB33 transcription factor gene expression. This suggests that the specificity of th
stress response regulated by sly-miR159 might, at least in part, rely on the distinct MYB transcriptio
factor transcript that the sly-miR159 sRNA specifically regulates under each stress condition. It h
been proposed that additional factors other than complementarity and cleavage, such as targ
accessibility and secondary structure, RNA binding proteins, and target site context may modula
silencing efficiency [27], which might lie at the root of the stress specific miR159 regulation of MY
transcription factors, and deserve further research. In contrast, correlating with the lack of proline and putrescine accumulation, no variation was
detected in SlMYB33 transcription factor gene expression. This suggests that the specificity of the stress
response regulated by sly-miR159 might, at least in part, rely on the distinct MYB transcription factor
transcript that the sly-miR159 sRNA specifically regulates under each stress condition. It has been
proposed that additional factors other than complementarity and cleavage, such as target accessibility
and secondary structure, RNA binding proteins, and target site context may modulate silencing
efficiency [27], which might lie at the root of the stress specific miR159 regulation of MYB transcription
factors, and deserve further research. 3. Conclusio
3. Conclusions Overall, the results obtained in this work show the potential involvement of sly-miR159 in th
tomato plants’ response to different stresses through stress-specific MYB transcription facto
targeting. Under drought-stress, sly-miR159 targeting of SlMYB33 correlates with induction
SlP5CS gene expression and accumulation of the osmoprotective compounds proline and putrescin
pointing to the possible participation of this miR in the regulation of drought stress toleranc
Understanding the regulatory network underlying drought stress response may provide ne
biotechnological approaches to generate plants better adapted to dry environments. Our resul
support that in addition to using SlMYB33 transcription factor as a biotechnological target fo
metabolic engineering by ectopic expression, SlMYB33 gene expression reprogramming by sl
miR159 might develop into a useful system to improve plant drought tolerance in tomato plants
Overall, the results obtained in this work show the potential involvement of sly-miR159 in the
tomato plants’ response to different stresses through stress-specific MYB transcription factor targeting. Under drought-stress, sly-miR159 targeting of SlMYB33 correlates with induction of SlP5CS gene
expression and accumulation of the osmoprotective compounds proline and putrescine, pointing to
the possible participation of this miR in the regulation of drought stress tolerance. Understanding the
regulatory network underlying drought stress response may provide new biotechnological approaches
to generate plants better adapted to dry environments. Our results support that in addition to
using SlMYB33 transcription factor as a biotechnological target for metabolic engineering by ectopic
expression, SlMYB33 gene expression reprogramming by sly-miR159 might develop into a useful
system to improve plant drought tolerance in tomato plants. 4.2. Total RNA Isolation and RT-qPCR Analysis Total RNA was isolated from leaves of control tomato plants and plants undergoing drought stress
or CPB infestation using RiboPure Kit (Ambion, Cat. No. AM1924), following the manufacturer’s
protocol. TURBO DNA-free kit (Ambion, Cat. No. AM1907) was used to remove contaminating
genomic DNA from RNA preparations and RNA quality was evaluated by 1% agarose gel
electrophoresis and quantified spectrophotometrically (NanoDrop 2000, Thermo Scientific, Waltham,
MA, USA). RT-qPCR amplification was performed using SYBR Premix Ex Taq II (Takara). For sly-miR159 amplification 1 µg of RNA was polyadenylated in a final volume of 10 µL,
including 1 µL of 10x poly(A) polymerase buffer, 1 mM of ATP, and 1 unit of poly(A) polymerase
(New England Biolabs, Ipswich, MA, USA), and incubated at 37 ◦C for 15 min and then at 65 ◦C for
20 min. Polyadenylated RNA was reverse transcribed to complementary DNA (cDNA) using the
Universal RT-primer (Integrated DNA Technologies, Coralville, IA, USA) described in Balcells et al. [29]
(5′-CAGGTCCAGTTTTTTTTTTTTTTTVN-3′, where V is A, C, and G, and N is A, C, G, and T). Reverse
transcription reaction was performed using PrimeScript™RT reagent Kit (Takara) in a final volume of
10 µL, including 2 µL of 5X PrimeScript™Buffer, 0.5 µL of PrimeScript™RT Enzyme Mix I, and 1 µM
of Universal RT-primer, and it was incubated at 37 ◦C for 15 min followed by enzyme inactivation at 85
◦C for 5 s. Forward and reverse primers for miRNA RT-qPCR amplification were designed according
to Balcells et al. [29] (Table 1). Table 1. Primers used to analyze by RT-qPCR sly-miR159, SlMYB, and SlP5CS gene expression in
tomato plants. Gene
Forward Primer (5′-3′)
Reverse Primer (5′-3′)
Product Size (bp)
sly-miR159
CGCAGTTTGGATTGAAGGGAG
CAGGTCCAGTTTTTTTTTTTTTTTTAGAG
50
SlMYB33
TATGGGCATCCAGTCTCTCC
TGGGACTGGAAAAGATCGTC
199
SlMYB65
TCTGCTGCATCGGTGTTTAG
TCTGGCCTGGGACAGATAAG
164
SlMYB104
TTTCGGAATTGTTTGGAAGC
TGAAGAAGTTGCCGACAATG
110
SlMYB97
CATGTCCCCTTGGAAGATTTAG
CTAGTGGCAAAGCAAAGTCATC
181
SlMYB120
CACATTCCAGTCCAAACCAAC
CCTAGGTCGGAAGCACTGAG
116
SlP5CS
TGCTCAACAGGCCGGATATG
AAAGTGTGACCAAGGGGCTC
126
U6 snRNA
GGGGACATCCGATAAAATTGGAAC
TGGACCATTTCTCGATTTGTGC
88
RPS18
GGGCATTCGTATTTCATAGTCAGAG
CGGTTCTTGATTAATGAAAACATCCT
105 Table 1. Primers used to analyze by RT-qPCR sly-miR159, SlMYB, and SlP5CS gene expression in
tomato plants. For SlMYB33, SlMYB65, SlMYB104, SlMYB97, SlMYB120, and SlP5CS transcript amplification, the
PrimeScript™RT reagent kit (Takara) was used for cDNA synthesis according to the manufacturer’s
protocol using 50 ng/µL oligo(dT) (Promega), and 2.5 µM random hexamers (Applied Biosystems). Ten ng cDNA, and gene specific forward (F) and reverse (R) primers (Table 1), designed with
PRIMER3PLUS software [30], were used. 4.1. Plants 4.1. Plants
Thirty-day-old tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig (four-week-old) we
grown from germinated seeds in a growth chamber under the following environmental condition
16/8 h light/night cycle 26/18 °C day/night temperature cycle and 60% relative humidity (RH) Seed
Thirty-day-old tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig (four-week-old) were
grown from germinated seeds in a growth chamber under the following environmental conditions:
16/8 h light/night cycle, 26/18 ◦C day/night temperature cycle, and 60% relative humidity (RH). Seeds Plants 2019, 8, 201 8 of 11 were irrigated twice a week with distilled water during the first week, and with Hoagland solution
thereafter [28]. For drought stress experiments, thirty-day-old tomato plants were deprived of water for 7 days,
and leaf tissue from 3rd and 4th leaves was collected, frozen in liquid nitrogen, and stored at −80 ◦C. Leaf tissue from 3rd and 4th leaves of irrigated plants was also collected as control. For Colorado potato beetle (CPB) infestation, 15 CPB larvae of different developmental stages were
placed on the 3rd and 4th leaves of thirty-day-old tomato plants. When necessary, non-cooperative
larvae (molting or not eating) were removed and substituted. Leaf tissue left after 3 h of CPB feeding
and that of the non-infested control plants were harvested, frozen in liquid nitrogen, and stored at
−80 ◦C. 4.2. Total RNA Isolation and RT-qPCR Analysis A StepOnePlus Real-Time PCR system (Applied Biosystems) was used, under the conditions
recommended by the manufacturer, and the cycling parameters were: Initial polymerase activation
step at 95 ◦C for 30 s, 40 cycles of denaturation at 95 ◦C for 5 s, annealing, and elongation at 60 ◦C 9 of 11 Plants 2019, 8, 201 for 30 s. For each sample, three biological replicates (with 3 technical replicates each) were analyzed. Relative-fold calculations were made using RPS18 (ribosomal protein S18, GeneBank: 3950409) gene
to normalize gene expression, and U6 snRNA gene (GenBank: X51447.1) to normalize sly-miR159
expression (Table 1). LingReg software [31] was employed for the analysis of RT-qPCR experiments
and data were analyzed by Student’s t-test for statistically significant differences (p < 0.05). Each biological sample from the 3rd and 4th leaves of plants undergoing drought stress and their
corresponding controls consisted of a pool of total RNA from 25 plants. Biological samples in CPB
infestation experiments and their corresponding controls also consisted of a pool of total RNA from
25 plants. 4.3. Small RNA Isolation and RT-PCR Analysis The small RNA fraction in total RNA samples of control tomato plants and tomato plants following
7-day water deprivation was isolated using Nucleospin® miRNA (Macherey-Nagel, Bethlehem, PA,
USA) following the manufacturer’s instructions. For SlMYB33 small mRNA amplification, the PrimeScript™RT reagent kit (Takara, Shiga, Japan)
was used for cDNA synthesis according to the manufacturer’s protocol using 50 ng/µL oligo(dT)
(Promega, Madison, WI, USA) and 2.5 µM random hexamers (Applied Biosystems, Waltham, MA,
USA), 10 ng cDNA, and gene specific forward (F) and reverse (R) primers (Table 2), designed with
PRIMER3PLUS software [30]. RPS18 (ribosomal protein S18, GeneBank: 3950409) was used as a
reference gene. Table 2. Primers used to analyze SlMYB33 small transcript fragments by RT-PCR in tomato plants
annealing to a region outside the predicted sly-miR159 binding site in SlMYB33 mRNA (OFw, ORv) or
flanking the putative cleavage site within the predicted sly-miR159 binding site in SlMYB33 mRNA
(FFw, FRv). Table 2. Primers used to analyze SlMYB33 small transcript fragments by RT-PCR in tomato plants
annealing to a region outside the predicted sly-miR159 binding site in SlMYB33 mRNA (OFw, ORv) or
flanking the putative cleavage site within the predicted sly-miR159 binding site in SlMYB33 mRNA
(FFw, FRv). Primer Pair
Forward Primer (5′-3′)
Reverse Primer (5′-3′)
Product Size (bp)
OFw, ORv
TATGGGCATCCAGTCTCTCC
TGGGACTGGAAAAGATCGTC
199
FFw, FRv
ATGACGGTTCTTTGCTTGCT
CTGTCTGGTTTTGGAGTGAAGG
200
RPS18FW, RPS18RV
GGGCATTCGTATTTCATAGTCAGAG
CGGTTCTTGATTAATGAAAACATCCT
105 The cycling parameters were as follows: Initial polymerase activation step at 95 ◦C for 30 s,
40 cycles of denaturation at 95 ◦C for 5 s, annealing, and elongation at 60 ◦C for 30 s. For each sample,
three biological replicates were pooled and analyzed. Five microliters of the reaction volume were
separated in a 3% agarose gel. 4.4. Amino Acids and Polyamines Quantification Leaves were recollected after stress condition and frozen in liquid N2, ground, and lyoph q
2 g
y p
For amino acids analysis, dry tissue (0.1 g) was homogenized with 800 µL of extraction solution:
400 µL of distilled water, 200 µL of chloroform, and 200 µL of methanol per sample. Moreover, a
mixture of internal standards was added prior to extraction (100 ng of Phe 13C915N and 100 ng of
Thr 13C415N). Samples were filtered, and a final concentration of 1 mM perfluoroheptanoic acid as
ion-pairing reagent was added to each sample. A 20 µL aliquot was injected into a high-performance
liquid chromatography system (HPLC) with an XSelect HSS C18 column (5 µm 2.1 × 100 mm) which
was interfaced with a triple quadrupole mass spectrometer (TQD, Waters, Manchester, UK). Polyamine analysis was conducted according to the method described by Sánchez-López et al. [32],
using as internal standards a mixture of [13C4]-putrescine and 1,7-diamineheptane. To analyze each
condition, ten independent biological replicates per sample were generated and three independent
experiments were conducted. 10 of 11 Plants 2019, 8, 201 10 of 11 Author Contributions: Conceptualization, I.G.-R., M.D.R. and C.R.; Funding acquisition, I.G.-R., G.C., B.V.,
M.D.R. and C.R.; investigation, M.J.L.-G., I.G.-R., A.I.G.-H. and G.C.; writing—original draft, M.D.R. and C.R.;
writing—review and editing, M.J.L.-G., I.G.-R., G.C. and B.V. Funding:
This
work
was
supported
by
“MINECO”
and
“FEDER”
(AGL2013-49023-C3-1,2,3-R;
AGL2017-85987-C3-1,2-R). M.J. López-Galiano was awarded with a University of Valencia Ph. D. fellowship. Acknowledgments: We thank the Genomics, Proteomics and Greenhouse Facilities from the SCSIE of the
University of Valencia and the SCIC from the University Jaume I. Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the
study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to
publish the results. References . Swann, A.L.S. Plants and drought in a changing climate. Curr. Clim. Chang. Rep. 2018, 4, 192–201. [Cross 1. Swann, A.L.S. Plants and drought in a changing climate. Curr. Clim. Chang. Rep. 2018, 4, 192–201. [CrossRef]
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article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
https://openalex.org/W4229041434 | https://www.frontiersin.org/articles/10.3389/fcvm.2022.849688/pdf | English | null | Machine Learning for Prediction of Outcomes in Cardiogenic Shock | Frontiers in cardiovascular medicine | 2,022 | cc-by | 7,830 | ORIGINAL RESEARCH
published: 06 May 2022
doi: 10.3389/fcvm.2022.849688 ORIGINAL RESEARCH
published: 06 May 2022
doi: 10.3389/fcvm.2022.849688 Machine Learning for Prediction of
Outcomes in Cardiogenic Shock
Fangning Rong †, Huaqiang Xiang †, Lu Qian, Yangjing Xue, Kangting Ji* and Ripen Yin*
Department of Cardiology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University,
Wenzhou, China Objective: The management of cardiogenic shock (CS) in the elderly remains a major
clinical challenge. Existing clinical prediction models have not performed well in assessing
the prognosis of elderly patients with CS. This study aims to build a predictive model,
which could better predict the 30-day mortality of elderly patients with CS. Keywords: cardiogenic shock, intensive care unit, machine learning, CoxBoost, predictive model Edited by:
Francois Roubille,
Université de Montpellier, France †These authors have contributed
equally to this work Specialty section:
This article was submitted to
Heart Failure and Transplantation,
a section of the journal
Frontiers in Cardiovascular Medicine
Received: 06 January 2022
Accepted: 07 March 2022
Published: 06 May 2022 Specialty section:
This article was submitted to
Heart Failure and Transplantation,
a section of the journal
Frontiers in Cardiovascular Medicine
Received: 06 January 2022 Received: 06 January 2022
Accepted: 07 March 2022
Published: 06 May 2022 Edited by:
Francois Roubille,
Université de Montpellier, France
Reviewed by:
Ole Kristian Lerche Helgestad,
Odense University Hospital, Denmark
Haobo Li,
China-Japan Friendship
Hospital, China
Dion Stub,
The Alfred Hospital, Australia
Zhongheng Zhang,
Sir Run Run Shaw Hospital, China
*Correspondence:
Kangting Ji
jikt@wmu.edu.cn
Ripen Yin
15948657@qq.com
†These authors have contributed
equally to this work Edited by:
Francois Roubille,
Université de Montpellier, France
Reviewed by:
Ole Kristian Lerche Helgestad,
Odense University Hospital, Denmark
Haobo Li,
China-Japan Friendship
Hospital, China
Dion Stub,
The Alfred Hospital, Australia
Zhongheng Zhang,
Sir Run Run Shaw Hospital, China
*Correspondence:
Kangting Ji
jikt@wmu.edu.cn
Ripen Yin
15948657@qq.com
†These authors have contributed
equally to this work Edited by:
Francois Roubille,
Université de Montpellier, France Edited by:
Francois Roubille,
Université de Montpellier, France Methods:
We extracted data from the Medical Information Mart for Intensive
Care III version 1.4 (MIMIC-III) as the training set and the data of validation sets
were collected from the Second Affiliated Hospital and Yuying Children’s Hospital of
Wenzhou Medical University. Three models, including the cox regression model, the
Least Absolute Shrinkage and Selection Operator (LASSO) regression model, and the
CoxBoost model, were established using the training set. Through the comparison
of area under the receiver operating characteristic (ROC) curve (AUC), C index, net
reclassification improvement (NRI), integrated discrimination improvement (IDI), and
median improvement in risk score, the best model was selected. Then for external
validation, compared the best model with the simplified acute physiology score II (SAPSII)
and the CardShock risk score. Reviewed by:
Ole Kristian Lerche Helgestad,
Odense University Hospital, Denmark
Haobo Li,
China-Japan Friendship
Hospital, China
Dion Stub,
The Alfred Hospital, Australia
Zhongheng Zhang,
Sir Run Run Shaw Hospital, China Reviewed by:
Ole Kristian Lerche Helgestad,
Odense University Hospital, Denmark
Haobo Li,
China-Japan Friendship
Hospital, China
Dion Stub,
The Alfred Hospital, Australia
Zhongheng Zhang,
Sir Run Run Shaw Hospital, China *Correspondence:
Kangting Ji
jikt@wmu.edu.cn
Ripen Yin
15948657@qq.com Results: A total of 919 patients were included in the study, of which 804 patients were in
the training set and 115 patients were in the verification set. Using the training set, we built
three models: the cox regression model including 6 predictors, the LASSO regression
model including 4 predictors, and the CoxBoost model including 16 predictors. Among
them, the CoxBoost model had good discrimination [AUC: 0.730; C index: 0.6958
(0.6657, 0.7259)]. Compared with the CoxBoost model, the NRI, IDI, and median
improvement in risk score of other models were all < 0. In the validation set, the CoxBoost
model was also well-discriminated [AUC: 0.770; C index: 0.7713 (0.6751, 0.8675)]. Compared with the CoxBoost model, the NRI, IDI, and median improvement in risk score
of SAPS II and the CardShock risk score were all < 0. And we constructed a dynamic
nomogram to visually display the model. BACKGROUND Medical Center (Boston, MA) and the Massachusetts Institute of
Technology (Cambridge, MA), IRB approval from our institution
was exempted. Data of validation sets were collected from the
patient data of ICU at the Second Affiliated Hospital and Yuying
Children’s Hospital of WMU. The Medical Ethics Committee of
the Second Affiliated Hospital and Yuying Children’s Hospital,
WMU approved the use of the patient data of the Second
Affiliated Hospital and Yuying Children’s Hospital (Ethical
Review Number: 2021-K-71-01). Cardiogenic shock (CS) is an extremely serious clinical condition
and occurs as a consequence of cardiac pump failure, which has a
high mortality (1, 2). In recent decades, the prevalence of CS has
increased from 4.1 to 7.7%, and the mortality rate is up to 40% (3–
5). Age itself increases the risk of CS associated with myocardial
infarction, and advanced age itself is an independent risk factor
for CS (6). This suggested that for the elderly, the risk of CS will be
higher. The WHO defines the elderly as over 65 years old; as this
aging population continues to grow, it is crucial to pay attention
to issues related to this group. Therefore, the management of
CS in the elderly is a huge clinical challenge (7, 8). Finding an
efficient method to early evaluate the prognosis is helpful for
clinicians to identify high-risk patients in time, and make better
medical decisions in clinical practice. The inclusion criteria were as follows: (1) ICU admissions
age ≥65 years; (2) CS patients in MIMIC-III database and
the Second Affiliated Hospital and Yuying Children’s Hospital
of WMU. Among them, patients from the MIMIC-III database
were diagnosed according to the International Classification
of Diseases, Ninth Revision (ICD-9) diagnostic code 785.51
or 998.01, and patients from the Second Affiliated Hospital
and Yuying Children’s Hospital of WMU were selected by
unified diagnostic criteria: minimum systolic blood pressure
(SBP) <90 mmHg, or need of vasopressors therapy or signs of
hypoperfusion. Only records of the first ICU visit were selected
for analysis to eliminate duplicate data. The specific process was
shown in Figure 1. However, in the elderly population, information on the
prevalence, determinants, and prognostic factors of CS is scarce. Citation: Rong F, Xiang H, Qian L, Xue Y, Ji K
and Yin R (2022) Machine Learning for
Prediction of Outcomes in
Cardiogenic Shock. Front. Cardiovasc. Med. 9:849688. doi: 10.3389/fcvm.2022.849688 Conclusion: In conclusion, this study showed that in predicting the 30-day mortality
of elderly CS patients, the CoxBoost model was superior to the Cox regression model,
LASSO regression model, SAPS II, and the CardShock risk score. May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org Machine Learning Predicts Cardiogenic Shock Rong et al. METHODS Data Source and Research Population Data Source and Research Population
We extracted data from MIMIC-III database version 1.4 as the
training set, which is a public and free intensive care unit (ICU)
database (20). Since the MIMIC-III database was approved by
the Institutional Review Boards (IRB) of Beth Israel Deaconess Missing Data Variables with missing values ≥40% were excluded directly. We
used multiple interpolations to deal with missing variables <40%. Patients with individual data missing by more than 10% or
outliers [values above the mean of 3 standard deviations (SD)]
were excluded. In the training set and the verification set, we
carried out the above data processing respectively. Data Extraction and Outcome Data Extraction and Outcome
We extracted the following information of patients on the
first day of admission: (1) demographic information such
as age, gender, ethnicity, and pathogeny; (2) vital sign
data including heart rate, SBP, mean blood pressure (MBP),
diastolic blood pressure (DBP), respiratory rate, temperature,
and arterial oxygen saturation (SpO2); (3) laboratory data
including white blood cell (WBC) count, red cell distribution
width (RDW), hemoglobin, hematocrit, platelet, activated partial
thromboplastin time (APTT), international normalized ratio
(INR), prothrombin time (PT), anion gap, bicarbonate, glucose,
blood lactic acid, serum creatinine, serum urea nitrogen, serum
sodium, and serum potassium; (4) comorbidities including
congestive heart failure, atrial fibrillation, coronary heart disease,
renal failure, liver disease, stroke, tumor, chronic obstructive
pulmonary disease (COPD), acute respiratory distress syndrome
(ARDS), and pneumonia; (5) traditional severity scores including
simplified acute physiology score II (SAPSII); (6) As well as
ejection fraction and the use of the vasopressor. If multiple
measurements were made in the first 24 h, the vital signs and the
laboratory data were based on the results of the first examination. The endpoint was 30-day mortality. Compared
with
traditional
forecasting
methods,
novel
machine learning techniques can process high-dimensional data,
identify complex relationships between variables and develop
precise clinical prediction models, which have received more and
more attention and recognition from clinicians (11, 12). There
are many studies that apply machine learning to the evaluation
of a variety of diseases and with good results (13–15). It has also
been used in other medical auxiliary disciplines, such as imaging
and anesthesiology (16, 17). Hou et al. (18) used XGboost
machine learning to predict 30-days mortality of patients with
sepsis. Weyer and Binder (19) developed a weighting approach
for judging the effect of patient strata on high-dimensional risk
prediction signatures using CoxBoost. Therefore, we hope to use
the CoxBoost method to help us better predict the prognosis of
elderly patients with CS. Based on the Medical Information Mart for Intensive Care
III (MIMIC-III) database and the Second Affiliated Hospital
and Yuying Children’s Hospital of Wenzhou Medical University
(WMU), the goal of this study is to build a predictive model
using CoxBoost machine learning, which can predict the 30-day
mortality of elderly patients with CS. BACKGROUND Some researchers have constructed risk prediction models to
facilitate risk assessment and predict the mortality of CS, such as
the CardShock risk score (9, 10), but these models still have some
shortcomings, such as the calculation methods are complicated,
or the included predictors of some models are not all objective
data. For example, in the CardShock risk score, the evaluation of
the patients’ consciousness depends on the subjective judgment
of clinicians. Besides, they are not completely built for the elderly
population, the evaluation effect of the prognosis of the elderly
needs further assessment. Baseline Characteristics After excluding the patients who did not meet the inclusion
criteria, a total of 919 patients were included in this study. Among
them, 804 were from the training set and 115 were from the
verification set. We divided these patients into two groups based
on their death or survival in 30-day. Table 1 summarizes the basic
distribution of all the target patients’ baseline characteristics, vital
signs, comorbidities, and other indicators. In the training set, the
difference in age, SBP, MBP, DBP, respiratory rate, temperature,
SpO2, WBC count, RDW, INR, PT, anion gap, bicarbonate,
blood lactic acid, serum creatinine, serum urea nitrogen, serum
potassium, tumor, SAPSII score, and length of stay in the
hospital between the two groups was statistically significant. In
the validation set, the difference in temperature, PT, bicarbonate,
blood lactic acid, congestive heart failure, pneumonia, SAPSII
score, and length of stay in hospital between the two groups was
statistically significant. Statistical Analysis The continuous variables were expressed as mean ± SD of the
normal distribution, while the non-normal continuous variables Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 2 Rong et al. Machine Learning Predicts Cardiogenic Shock FIGURE 1 | Flowchart of patient selection. FIGURE 1 | Flowchart of patient selection. were expressed as median (interquartile range). Wilcoxon W test
or Kruskal Wallis test was used to assess the differences among
groups. The variance inflation factor (VIF) was calculated to
verify whether multicollinearity existed. (IDI), and median improvement in risk score were used to choose
the best model. In the validation set, AUC, C index, NRI, IDI, and
median improvement in risk score were also used to evaluate the
CoxBoost model, SAPSII score model, and the CardShock risk
score model for external validation. We constructed a DynNom-
based dynamic nomogram to visually display the final model. R
software version 4.0.3 was used for all statistical analyses. P < 0.05
was considered statistically significant. y
y
In
the
model
development
stage,
three
models
were
established using the training set: the cox regression model,
the Least Absolute Shrinkage and Selection Operator (LASSO)
regression model, and the CoxBoost model. In the Cox regression
model, we used the monofactor analysis to pick out targeted
predictors and screened the predictors twice using multiple
regression analysis. After two rounds of screening, the predictive
factors were finally incorporated into the Cox regression model. The main idea of LASSO is to construct a first-order penalty
function to obtain a refined model and to carry out feature
screening by finally determining the coefficients of some variables
to be 0. In the LASSO regression model, we determined the
cutoffvalue based on ten-folds cross-validation to select the most
useful predictive variables to form the LASSO regression model. CoxBoost (https://github.com/binderh/CoxBoost) is used to fit a
Cox proportional hazards model by componentizing likelihood-
based boosting, which is particularly suitable for models with a
large number of predictors and allows for mandatory covariates
with unpenalized parameter estimates. In contrast to gradient
boosting, CoxBoost is not based on gradients of loss functions
but adapts the offset-based boosting approach for estimating Cox
proportional hazards models (21). According to the CoxBoost
machine learning analysis of the importance of the predictors,
we select targeted variables incorporated into the CoxBoost
regression model. Frontiers in Cardiovascular Medicine | www.frontiersin.org Model Development These three models were evaluated together with the
classic SAPSII score model. The area under receiver operating
characteristic (ROC) curve (AUC), C index, net reclassification
improvement (NRI), integrated discrimination improvement Based on the training set, we developed three models. In the traditional cox regression model, we first used the
monofactor analysis to pick out 8 predictors (P < 0.05), May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 3 Machine Learning Predicts Cardiogenic Shock Rong et al. TABLE 1 | Baseline characteristics of the study population of 30-day all-cause death. Model Development Training set
Validation set
Survival in 30-day
Death in 30-day
P
Survival in 30-day
Death in 30-day
P
Number of patients
500
304
53
62
Pathogeny
/
0.392
Acute coronary syndrome, n (%)
/
/
47 (88.68)
56 (90.32)
Valvopathy, n (%)
/
/
2 (3.77)
1 (1.61)
Cardiomyopathy, n (%)
/
/
2 (3.77)
4 (6.45)
Heart failure, n (%)
/
/
0 (0.00)
1 (1.61)
Atrial fibrillation, n (%)
/
/
2 (3.77)
0 (0.00)
Clinical parameters
Age, years
77.50 ± 7.39
80.01 ± 7.51
<0.001
76.28 ± 6.47
78.56 ± 7.62
0.089
Sex, n (%)
0.623
0.498
Female
223 (44.60)
141 (46.38)
24 (45.28)
32 (51.61)
Male
277 (55.40)
163 (53.62)
29 (54.72)
30 (48.39)
Ethnicity, n (%)
0.279
/
White
346 (69.20)
217 (71.38)
/
/
Black
31 (6.20)
11 (3.62)
/
/
Others
123 (24.60)
76 (25.00)
53 (100)
62 (100)
Vital signs
Heart rate, beats/minute
87.09 ± 16.08
89.44 ± 17.29
0.051
99.75 ± 23.97
104.05 ± 19.98
0.299
SBP, mmHg
104.97 ± 13.53
100.44 ± 13.57
<0.001
124.58 ± 33.65
114.49 ± 28.03
0.083
MBP, mmHg
72.45 ± 8.99
69.70 ± 9.73
<0.001
89.36 ± 24.28
83.15 ± 21.53
0.150
DBP, mmHg
55.25 ± 8.85
53.21 ± 9.33
0.002
71.75 ± 21.96
67.48 ± 20.81
0.288
Respiratory rate, times/minute
19.50 ± 3.84
20.49 ± 4.27
<0.001
20.51 ± 6.11
23.02 ± 7.94
0.065
Temperature, ◦C
36.73 ± 0.76
36.53 ± 1.08
0.003
36.78 ± 0.88
36.40 ± 0.97
0.034
SpO2, %
96.69 ± 4.09
95.31 ± 6.78
<0.001
95.36 ± 8.62
94.48 ± 7.78
0.575
Laboratory parameters
WBC count, 109/L
12.50 ± 5.69
14.20 ± 7.40
<0.001
15.03 ± 5.52
15.80 ± 5.63
0.466
RDW, %
15.07 ± 1.93
15.62 ± 2.57
<0.001
14.38 ± 1.72
14.03 ± 1.54
0.262
Hemoglobin, g/dl
11.07 ± 2.18
11.08 ± 2.02
0.944
11.71 ± 2.81
11.65 ± 2.14
0.904
Hematocrit, %
33.40 ± 6.37
33.58 ± 6.04
0.704
0.36 ± 0.08
0.36 ± 0.07
0.913
Platelet, 109/L
229.84 ± 110.60
223.86 ± 113.18
0.461
242.68 ± 93.47
210.02 ± 101.88
0.081
APTT, s
53.02 ± 35.10
58.47 ± 49.84
0.069
99.00 ± 65.95
94.00 ± 61.63
0.681
INR
1.78 ± 1.54
2.16 ± 2.20
0.004
1.54 ± 1.59
1.75 ± 1.03
0.403
PT, s
17.49 ± 9.65
20.11 ± 15.97
0.004
16.09 ± 3.00
19.31 ± 7.89
0.006
Anion gap, mmol/L
16.44 ± 4.47
18.84 ± 5.34
<0.001
15.99 ± 5.96
19.41 ± 6.41
0.070
Bicarbonate, mmol/L
22.11 ± 4.69
20.40 ± 6.08
<0.001
18.96 ± 5.20
15.67 ± 6.09
0.003
Glucose, mg/dl
181.99 ± 94.06
183.43 ± 106.79
0.842
181.27 ± 91.40
205.57 ± 71.03
0.212
Blood lactic acid, mmol/L
3.09 ± 2.68
4.27 ± 3.64
<0.001
4.34 ± 4.09
7.64 ± 5.73
<0.001
Serum creatinine, mg/dl
1.76 ± 1.39
2.14 ± 1.52
<0.001
1.67 ± 1.35
1.86 ± 1.20
0.420
Serum urea nitrogen, mg/dl
35.57 ± 21.61
43.71 ± 27.42
<0.001
31.51 ± 20.86
36.33 ± 23.95
0.262
Serum sodium, mg/dl
137.11 ± 4.81
136.97 ± 5.82
0.705
138.06 ± 7.44
138.96 ± 5.76
0.468
Serum potassium, mg/dl
4.32 ± 0.79
4.46 ± 1.05
0.039
6.09 ± 13.73
4.34 ± 0.78
0.319
Comorbidities
Congestive heart failure, n (%)
109 (21.80)
70 (23.03)
0.685
3 (5.66)
14 (22.58)
0.011
Atrial fibrillation, n (%)
258 (51.60)
146 (48.03)
0.326
9 (16.98)
18 (29.03)
0.129
Coronary heart disease, n (%)
151 (30.20)
84 (27.63)
0.437
44 (83.02)
53 (85.48)
0.717
Renal failure, n (%)
118 (23.60)
77 (25.33)
0.579
19 (35.85)
27 (43.55)
0.401
Liver disease, n (%)
7 (1.40)
7 (2.30)
0.343
8 (15.09)
10 (16.13)
0.879
Stroke, n (%)
14 (2.80)
4 (1.32)
0.168
17 (32.08)
15 (24.19)
0.347
Tumor, n (%)
41 (8.20)
42 (13.82)
0.011
2 (3.77)
2 (3.23)
0.873
(Continued) TABLE 1 | Baseline characteristics of the study population of 30-day all-cause death. Model Development Pneumonia, n (%)
156 (31.20)
98 (32.24)
0.759
40 (75.47)
27 (43.55)
<0.001
Ejection fraction, %
/
/
/
41.74 ± 10.89
42.04 ± 13.93
0.905
Vasopressor, n (%)
416 (83.20)
266 (87.50)
0.099
50 (94.34)
58 (93.55)
0.860
Severity of illness
SAPSII score
47.36 ± 13.29
55.61 ± 14.98
<0.001
42.13 ± 8.00
59.94 ± 15.07
<0.001
Length of stay in hospital, day
14.72 ± 12.54
6.89 ± 6.64
<0.001
21.12 ± 13.23
6.73 ± 11.01
<0.001
The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s
Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width;
APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress
syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. TABLE 3 | LASSO regression model. TABLE 3 | LASSO regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0231–1.0544)
<0.0001
Vital signs
SBP
0.9846 (0.9765–0.9928)
0.0002
Laboratory parameters
Anion gap
1.0588 (1.0342–1.0840)
<0.0001
Blood lactic acid
1.0433 (1.0050–1.0830)
0.0262
SBP, systolic blood pressure. TABLE 2 | Cox regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0229–1.0545)
<0.0001
Vital signs
Heart rate
1.0118 (1.0047–1.0189)
0.0010
Temperature
0.7894 (0.6897–0.9036)
0.0006
Laboratory parameters
WBC count
1.0281 (1.0110–1.0454)
Anion gap
1.0580 (1.0332–1.0833)
0.0012
Blood lactic acid
1.0548 (1.0168–1.0943)
<0.0001
WBC, white blood cell. TABLE 3 | LASSO regression model. model had good discrimination (AUC: 0.730) in the training
set, which was better than others (Figure 2A). Besides, using the
CoxBoost model as a reference, the Cox regression model, LASSO
regression model, and SAPSII score model did worse in the C
index (cox regression model: 0.6835; LASSO regression model:
0.6786; SAPSII: 0.6490), NRI (cox regression model: −0.0590;
LASSO regression model: −0.1480; SAPSII: −0.1630), IDI (cox
regression model: −0.0040; LASSO regression model: −0.0300;
SAPSII: −0.0530), and median improvement in risk score (cox
regression model: −0.0040; LASSO regression model:−0.0220;
SAPSII: −0.0570) (Table 5). Therefore, we choose the CoxBoost
model as the target model. the results are presented in Supplementary Table 1. Then, we
screened the predictors twice using multiple regression analysis
(Supplementary Table 2). Model Development The final Cox regression model was
shown in Table 2, a total of 6 predictors including age, heart
rate, temperature, WBC count, anion gap, and blood lactic
acid. In the LASSO regression model, we determined the cutoff
value based on the Loess smoothing function and the Youden
index. In this way, 36 features were reduced to 4 potential
predictors (Supplementary Table 3), including age, SBP, anion
gap, and blood lactic acid (Table 3). According to the CoxBoost
machine learning analysis of the importance of the predictors
(Supplementary Table 4), we selected 17 predictors (P < 0.05)
to construct the CoxBoost model, considering the existence of
multicollinearity, we removed MBP. The final model was shown
in Table 4, including age, heart rate, SBP, DBP, respiratory rate,
temperature, SpO2, WBC count, RDW, INR, PT, anion gap,
bicarbonate, blood lactic acid, serum urea nitrogen, and tumor. VIF proved there was no significant multicollinearity in all three
models (VIF ≤3). Frontiers in Cardiovascular Medicine | www.frontiersin.org SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width;
APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress
syndrome; SAPSII, simplified acute physiology score II. Model Development According to the CoxBoost
machine learning analysis of the importance of the predictors
(Supplementary Table 4), we selected 17 predictors (P < 0.05)
to construct the CoxBoost model, considering the existence of
multicollinearity, we removed MBP. The final model was shown
TABLE 3 | LASSO regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0231–1.0544)
<0.0001
Vital signs
SBP
0.9846 (0.9765–0.9928)
0.0002
Laboratory parameters
Anion gap
1.0588 (1.0342–1.0840)
<0.0001
Blood lactic acid
1.0433 (1.0050–1.0830)
0.0262
SBP, systolic blood pressure. model had good discrimination (AUC: 0.730) in the training
set, which was better than others (Figure 2A). Besides, using the
CoxBoost model as a reference, the Cox regression model, LASSO
regression model, and SAPSII score model did worse in the C
index (cox regression model: 0.6835; LASSO regression model:
0.6786; SAPSII: 0.6490), NRI (cox regression model: −0.0590;
LASSO regression model: −0.1480; SAPSII: −0.1630), IDI (cox
regression model: −0.0040; LASSO regression model: −0.0300;
SAPSII: −0.0530), and median improvement in risk score (cox
regression model: −0.0040; LASSO regression model:−0.0220;
SAPSII: −0.0570) (Table 5). Therefore, we choose the CoxBoost
model as the target model. Model Comparisons
In the validation set, we further evaluated and validated the
CoxBoost model. The CoxBoost model was well-discriminated TABLE 1 | Continued
Training set
Validation set
Survival in 30-day
Death in 30-day
P
Survival in 30-day
Death in 30-day
P
COPD, n (%)
6 (1.20)
4 (1.32)
0.886
2 (3.77)
1 (1.61)
0.469
ARDS, n (%)
6 (1.20)
7 (2.30)
0.229
1 (1.89)
1 (1.61)
0.911
Pneumonia, n (%)
156 (31.20)
98 (32.24)
0.759
40 (75.47)
27 (43.55)
<0.001
Ejection fraction, %
/
/
/
41.74 ± 10.89
42.04 ± 13.93
0.905
Vasopressor, n (%)
416 (83.20)
266 (87.50)
0.099
50 (94.34)
58 (93.55)
0.860
Severity of illness
SAPSII score
47.36 ± 13.29
55.61 ± 14.98
<0.001
42.13 ± 8.00
59.94 ± 15.07
<0.001
Length of stay in hospital, day
14.72 ± 12.54
6.89 ± 6.64
<0.001
21.12 ± 13.23
6.73 ± 11.01
<0.001
The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s
Hospital of Wenzhou Medical University. Model Development SBP systolic blood pressure; DBP diastolic blood pressure; MBP mean blood pressure; SpO2 arterial oxygen saturation; WBC white blood cell; RDW red cell distribution width; TABLE 1 | Continued
Training set
Validation set
Survival in 30-day
Death in 30-day
P
Survival in 30-day
Death in 30-day
P
COPD, n (%)
6 (1.20)
4 (1.32)
0.886
2 (3.77)
1 (1.61)
0.469
ARDS, n (%)
6 (1.20)
7 (2.30)
0.229
1 (1.89)
1 (1.61)
0.911
Pneumonia, n (%)
156 (31.20)
98 (32.24)
0.759
40 (75.47)
27 (43.55)
<0.001
Ejection fraction, %
/
/
/
41.74 ± 10.89
42.04 ± 13.93
0.905
Vasopressor, n (%)
416 (83.20)
266 (87.50)
0.099
50 (94.34)
58 (93.55)
0.860
Severity of illness
SAPSII score
47.36 ± 13.29
55.61 ± 14.98
<0.001
42.13 ± 8.00
59.94 ± 15.07
<0.001
Length of stay in hospital, day
14.72 ± 12.54
6.89 ± 6.64
<0.001
21.12 ± 13.23
6.73 ± 11.01
<0.001
The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s
Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width;
APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress
syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0229–1.0545)
<0.0001
Vital signs
Heart rate
1.0118 (1.0047–1.0189)
0.0010
Temperature
0.7894 (0.6897–0.9036)
0.0006
Laboratory parameters
WBC count
1.0281 (1.0110–1.0454)
Anion gap
1.0580 (1.0332–1.0833)
0.0012
Blood lactic acid
1.0548 (1.0168–1.0943)
<0.0001
WBC
hit bl
d
ll
TABLE 3 | LASSO regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0231–1.0544)
<0.0001
Vital signs
SBP
0.9846 (0.9765–0.9928)
0.0002
Laboratory parameters
Anion gap
1.0588 (1.0342–1.0840)
<0.0001
Blood lactic acid
1.0433 (1.0050–1.0830)
0.0262
SBP, systolic blood pressure. Model Development May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 4 Machine Learning Predicts Cardiogenic Shock Rong et al. Rong et al. Machine Learning Predicts Cardiogenic Shock
TABLE 1 | Continued
Training set
Validation set
Survival in 30-day
Death in 30-day
P
Survival in 30-day
Death in 30-day
P
COPD, n (%)
6 (1.20)
4 (1.32)
0.886
2 (3.77)
1 (1.61)
0.469
ARDS, n (%)
6 (1.20)
7 (2.30)
0.229
1 (1.89)
1 (1.61)
0.911
Pneumonia, n (%)
156 (31.20)
98 (32.24)
0.759
40 (75.47)
27 (43.55)
<0.001
Ejection fraction, %
/
/
/
41.74 ± 10.89
42.04 ± 13.93
0.905
Vasopressor, n (%)
416 (83.20)
266 (87.50)
0.099
50 (94.34)
58 (93.55)
0.860
Severity of illness
SAPSII score
47.36 ± 13.29
55.61 ± 14.98
<0.001
42.13 ± 8.00
59.94 ± 15.07
<0.001
Length of stay in hospital, day
14.72 ± 12.54
6.89 ± 6.64
<0.001
21.12 ± 13.23
6.73 ± 11.01
<0.001
The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s
Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width;
APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress
syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. HR (95%CI)
P
Clinical parameters
Age
1.0386 (1.0229–1.0545)
<0.0001
Vital signs
Heart rate
1.0118 (1.0047–1.0189)
0.0010
Temperature
0.7894 (0.6897–0.9036)
0.0006
Laboratory parameters
WBC count
1.0281 (1.0110–1.0454)
Anion gap
1.0580 (1.0332–1.0833)
0.0012
Blood lactic acid
1.0548 (1.0168–1.0943)
<0.0001
WBC, white blood cell. the results are presented in Supplementary Table 1. Then, we
screened the predictors twice using multiple regression analysis
(Supplementary Table 2). The final Cox regression model was
shown in Table 2, a total of 6 predictors including age, heart
rate, temperature, WBC count, anion gap, and blood lactic
acid. In the LASSO regression model, we determined the cutoff
value based on the Loess smoothing function and the Youden
index. In this way, 36 features were reduced to 4 potential
predictors (Supplementary Table 3), including age, SBP, anion
gap, and blood lactic acid (Table 3). Model Comparisons In the validation set, we further evaluated and validated the
CoxBoost model. The CoxBoost model was well-discriminated
in the external validation set (AUC: 0.770), which was greater
than the SAPSII score model (AUC: 0.724) and the CardShock
risk score (Supplementary Table 5) (AUC: 0.677) (Figure 2B). In the C index, the CoxBoost model has the best performance
(C index: CoxBoost model 0.7713, SAPSII score model 0.7341,
CardShock risk score 0.6628, Table 5). Using the CoxBoost
model as a reference, the NRI of the SAPSII score model These three models were evaluated together with the classic
SAPSII score model to choose the best one. The CoxBoost Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 5 Machine Learning Predicts Cardiogenic Shock Rong et al. respectively (Table 5), all of which suggested that the CoxBoost
model was better. and the CardShock risk score were −0.3620 and −0.3480, the
IDI of the two models were −0.1740 and −0.2490, and the
median improvement in risk scores were −0.2380 and −0.1910 median improvement in risk scores were −0.2380 and −0.1910
TABLE 4 | CoxBoost model. Variables
P
Clinical parameters
Age
<0.0001
Vital signs
Heart rate
0.0224
SBP
<0.0001
DBP
0.0204
Respiratory rate
0.0020
Temperature
0.0020
SpO2
<0.0001
Laboratory parameters
WBC count
<0.0001
RDW
0.0020
INR
0.0143
PT
0.0082
Anion gap
<0.0001
Bicarbonate
0.0061
Blood lactic acid
<0.0001
Serum urea nitrogen
0.0020
Comorbidities
Tumor
0.0143
SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen
saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international
normalized ratio; PT, prothrombin time. Model Presentation p
TABLE 4 | CoxBoost model. Variables
P
Clinical parameters
Age
<0.0001
Vital signs
Heart rate
0.0224
SBP
<0.0001
DBP
0.0204
Respiratory rate
0.0020
Temperature
0.0020
SpO2
<0.0001
Laboratory parameters
WBC count
<0.0001
RDW
0.0020
INR
0.0143
PT
0.0082
Anion gap
<0.0001
Bicarbonate
0.0061
Blood lactic acid
<0.0001
Serum urea nitrogen
0.0020
Comorbidities
Tumor
0.0143
SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen
saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international
normalized ratio; PT, prothrombin time. We constructed a DynNom-based dynamic nomogram to
visually display the final model (Table 4) (https://CoxBoost-
model.shinyapps.io/DynNomapp/), which could directly obtain
the patient’s in-hospital mortality by inputting the values of the
relevant predictors. The final model formula and its regression
coefficients was as follows: survival possibility in 30-day = 0.0339
∗age + 0.0104 ∗heart rate – 0.0070 ∗SBP – 0.0127 ∗DBP +
0.0126 ∗respiratory rate – 0.1959 ∗temperature – 0.0112 ∗SpO2
+ 0.0250 ∗WBC count + 0.0422 ∗RDW + 0.0176 ∗INR +
0.0021 ∗PT + 0.0355 ∗anion gap – 0.0055 ∗bicarbonate + 0.0463
∗blood lactic acid + 0.0026 ∗serum urea nitrogen + 0.2125 ∗
(tumor = 1). DISCUSSION Based on the data of the training set, we developed three models
altogether: the Cox regression model, the LASSO regression
model, and the CoxBoost model. After extensive evaluation,
the CoxBoost model was chosen as the best model. The model
includes 16 predictors, which can simply and effectively predict
the 30-day mortality of CS patients. In external validation,
the discrimination of the CoxBoost model was better than the
SAPSII and the CardShock risk score. And we developed a
dynamic nomogram. Over the years, various scoring systems have been widely
used in the ICU (22, 23). However, in order to be suitable for
various types of critical patients, the sensitivity and specificity of
SAPSII are low. And the accuracy of the results of the assessment SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen
saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international
normalized ratio; PT, prothrombin time. FIGURE 2 | (A) Receiver operating characteristic (ROC) comparison of training set models. (B) ROC comparison of validation set models. | (A) Receiver operating characteristic (ROC) comparison of training set models. (B) ROC comparison of validation set models. Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 Machine Learning Predicts Cardiogenic Shock Rong et al. TABLE 5 | Model comparison. Model
C index (95%CI)
NRI
IDI
Median improvement in risk score
Training set
CoxBoost model
0.6958 (0.6657, 0.7259)
Cox regression model
0.6835 (0.6529, 0.7141)*
−0.0590
−0.0040*
−0.0040
LASSO regression model
0.6786 (0.6489, 0.7084)*
−0.1480**
−0.0300**
−0.0220**
SAPSII score model
0.6490 (0.6181, 0.6799)**
−0.1630**
−0.0530**
−0.0570**
Validation set
CoxBoost model
0.7713 (0.6751, 0.8675)
SAPSII score model
0.7341 (0.6448, 0.8234)*
−0.3620*
−0.1740
−0.2380
The CardShock risk Score model
0.6628 (0.5518, 0.7738)**
−0.3480*
−0.2490*
−0.1910*
*Compared with the CoxBoost model P < 0.05; **Compared with the CoxBoost model P < 0.0001. NRI, net reclassification improvement; IDI, integrated discrimination improvement. the anion gap was identified as a significant predictor of poor
prognosis in patients with CS (34). It could be linked to lactic
acid levels and keto, because elevated serum anion gap is usually
associated with excess production of organic acid anions and
reduced anion excretion (35). More experiments are needed to
confirm this. system depends on the experience of practitioners. There are also
some small studies that used SASPAII to predict the prognosis of
patients with CS (24, 25). DISCUSSION But the integrated ICU severity score
cannot accurately and reliably predict the mortality of elderly
patients with CS. The CoxBoost model constructed in this study
was targeted at elderly patients with CS, with higher sensitivity
and specificity. In the results of our study, it can be found that
the performance of the CoxBoost model was relatively better than
SAPSII in the both training set and validation set. This research was a multi-center retrospective study, the
main advantage was that the CoxBoost model was used for the
first time to predict the 30-day mortality of elderly patients
with CS. Multiple validation methods were used to compare
the CoxBoost model with traditional regression analysis, LASSO
regression analysis, and clinical scoring systems. The dynamic
nomogram was developed to facilitate users. However, there are
some limitations in this study: first, due to the relatively low
incidence of CS, the sample size of patients selected in our
study was relatively small. Second, there are potential differences
between the training set and the validation set in terms of patient
demography and research years. Third, the objective limitations
of the database may produce bias. Such as the use of diagnostic
codes to select patients may occur selective bias to a certain
extent. Or cause a lack of potential predictors. Fourth, there
was no further exploration of the database, which may make
the model imperfect. We will expand the sample size and refine
the sample data to conduct more in-depth research to validate
our model. Overall, we believe that the model developed in this
study may be useful in evaluating the prognosis of elderly patients
with CS. g
In recent years, models have been developed specifically
to assess the prognosis of patients with CS, but also have
some drawbacks (26, 27). For example, the IABP-SHOCK
II study established a scoring system for predicting 30-day
mortality in patients with CS (9), but it is more suitable
for patients with CS after emergency percutaneous coronary
intervention (PCI). The CardShock risk score (10) need
complicated calculation and scoring when it is used and partly
depend on the subjective judgment of clinicians. Hongisto
et al. evaluated the prognostic ability of two models in
elderly patients with CS and the results showed that the
predictive power was not very good (28). CONCLUSION The 16 factors that made up the CoxBoost model included all
the predictive factors in the cox model and LASSO model, which
showed that the CoxBoost approach has better performance and
accuracy. In the factors that made up the CoxBoost model, blood
lactic acid, WBC count, and anion gap were the three most
important laboratory indicators. Among them, blood lactate was
recognized as an important independent prognostic factor for CS
(29–31). WBC count could assess the prognosis of patients, which
may be related to the systemic inflammatory response caused
by hypoperfusion during CS (32, 33). But the mechanism for
the anion gap’s prediction was unclear. Zhang et al. found that In conclusion, this study showed that in predicting the 30-day
mortality of elderly patients with CS, the CoxBoost model was
superior to the Cox regression model, LASSO regression model,
SAPSII, and the CardShock risk score. It is a simple and objective
score that can be applied in clinical practice. DISCUSSION The CoxBoost model
was applicable to all types of elderly patients, and external
verification showed that its prediction ability was better than
the CardShock risk score. Last but not least, the CoxBoost
model could evaluate the short-term prognosis of elderly
CS patients by simply collecting patients’ vital signs, simple
laboratory data, and relevant medical history at admission,
all the selected predictors are objective data. The dynamic
nomogram further simplified the use of the model through an
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made available by the authors, without undue reservation. May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 7 Machine Learning Predicts Cardiogenic Shock Rong et al. ACKNOWLEDGMENTS We thank for the Second Affiliated Hospital and Yuying
Children’s Hospital of WMU for supporting our work. We thank for the Second Affiliated Hospital and Yuying
Children’s Hospital of WMU for supporting our work. SUPPLEMENTARY MATERIAL KJ took responsibility for the content of the manuscript,
including the data and analysis. FR had full access to all
of the data in the study and take responsibility for the
integrity of the data and the accuracy of the data analysis. The Supplementary Material for this article can be found
online
at:
https://www.frontiersin.org/articles/10.3389/fcvm. 2022.849688/full#supplementary-material ETHICS STATEMENT All authors contributed substantially to the study design, data
analysis and interpretation, and the writing of the manuscript. All authors contributed to the article and approved the
submitted version. The studies involving human participants were reviewed and
approved by the Medical Ethics Committee of the Second
Affiliated Hospital and Yuying Children’s Hospital of Wenzhou
Medical University. Written informed consent for participation
was not required for this study in accordance with the national
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https://openalex.org/W2130598050 | https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-8-r157 | English | null | An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer | GenomeBiology.com | 2,007 | cc-by | 16,673 | Open Access
2007
Teschendorff
et al.
Volume 8, Issue 8, Article R157
Research
An immune response gene expression module identifies a good
prognosis subtype in estrogen receptor negative breast cancer
Andrew E Teschendorff*, Ahmad Miremadi†, Sarah E Pinder†, Ian O Ellis‡
and Carlos Caldas*† Addresses: *Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology,
University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK. †Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University
Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK. ‡Histopathology, Nottingham City Hospital NHS Trust and
Department of Pathology, University of Nottingham, Nottingham NG5 1PB, UK. Correspondence: Andrew E Teschendorff. Email: aet21@cam.ac.uk. Carlos Caldas. Email: cc234@cam.ac.uk Published: 2 August 2007
Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157)
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2007/8/8/R157 Published: 2 August 2007
Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157) Received: 14 March 2007
Revised: 25 June 2007
Accepted: 2 August 2007 © 2007 Teschendorff et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Breast cancer prognosis
<p>A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and
prognostic markers in estrogen receptor negative breast cancer showing that it is a heterogeneous disease with at least four main sub
types </p> Open Access
2007
Teschendorff
et al.
Volume 8, Issue 8, Article R157
Research
An immune response gene expression module identifies a good
prognosis subtype in estrogen receptor negative breast cancer
Andrew E Teschendorff*, Ahmad Miremadi†, Sarah E Pinder†, Ian O Ellis‡
and Carlos Caldas*†
Addresses: *Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology,
University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK. †Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University
Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK. ‡Histopathology, Nottingham City Hospital NHS Trust and
Department of Pathology, University of Nottingham, Nottingham NG5 1PB, UK.
Correspondence: Andrew E Teschendorff. Email: aet21@cam.ac.uk. Carlos Caldas. Email: cc234@cam.ac.uk
© 2007 Teschendorff et al.; licensee BioMed Central Ltd.
Published: 2 August 2007
Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157)
Received: 14 March 2007
Revised: 25 June 2007
Accepted: 2 August 2007
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2007/8/8/R157 Open Access Open Access The FDR is higher in ER- breast cancer The FDR is higher in ER- breast cancer g
To understand why in ER- breast cancer it has not been possi-
ble to derive a validated prognostic signature using conven-
tional approaches, we compared the FDR for ER+ and ER-
disease. We used as cohorts integrated datasets obtained by
merging together three of the largest profiled breast cancer
cohorts [5,9,18] using the z-score transformation, a proce-
dure that we validated previously [17]. Briefly, the z-score
transformation shifts the mean of each gene expression vec-
tor in each cohort to zero, while scaling its variance to unity. The transformed gene expression vectors are then merged
across cohorts. This merging step resulted in integrated
expression matrices of 186 ER- and 527 ER+ tumors profiled
over a common set of 5,007 genes. To enable the comparison,
we selected at random 186 ER+ tumors from the 527 available. We then used the univariate Cox proportional hazards model
with time to distant metastasis (TTDM) and overall survival
as end-points to obtain P values of significance for all the
genes. Next, we estimated, for each choice of significance
threshold, the number of false positives using the q-value
approximation [20]. The numbers of significant genes and
false positives as a function of the significance threshold were
then plotted for ER+ and ER- breast cancer and for the two dif-
ferent end-points used (Figure 1). We verified that the curves
for ER+ breast cancer were robust to random selections of the
186 ER+ tumors. This showed that the FDR is much higher in
ER- tumours and motivated us to develop a different feature
selection approach based on a pattern recognition algorithm
(PACK) [17]. In spite of these clinical advances, ER+ and ER- breast cancers
remain heterogeneous diseases, and little is known regarding
why patients with the same histopathologic characteristics
may have widely different clinical outcomes [1]. This is partic-
ularly true for the basal subtype of ER- breast cancer, which is
commonly defined by over-expression of cytokeratin markers
(CK 5/6 and CK 14) and which is often also HER2 negative
(HER2-) [2]. Most recent efforts to obtain a molecular under-
standing of the observed heterogeneity have focused on ER+
breast cancer, where gene expression signatures that are
either prognostic or predictive of response to hormone ther-
apy have been derived [3-10]. In contrast, few studies have
thus far attempted to derive a prognostic signature within ER-
breast cancer. Background ER- breast cancer and, if possible, to find different prognostic
subclasses and the corresponding prognostic markers. g
It is widely recognized that estrogen receptor (ER)-positive
(ER+) and ER-negative (ER-) breast cancers are two different
disease entities. Generally, ER- tumours tend to be of high
grade, are more frequently p53 mutated, and have worse
prognosis compared with ER+ disease. Moreover, while ER+
disease can be treated with hormone therapy, the only tar-
geted therapy available for ER- patients is a monoclonal anti-
body that binds to the ERBB2 receptor and that is effective
only for those ER- tumours with HER2/ERBB2 over-expres-
sion. Abstract Background: Estrogen receptor (ER)-negative breast cancer specimens are predominantly of high
grade, have frequent p53 mutations, and are broadly divided into HER2-positive and basal subtypes. Although ER-negative disease has overall worse prognosis than does ER-positive breast cancer, not
all ER-negative breast cancer patients have poor clinical outcome. Reliable identification of ER-
negative tumors that have a good prognosis is not yet possible. Results: We apply a recently proposed feature selection method in an integrative analysis of three
major microarray expression datasets to identify molecular subclasses and prognostic markers in
ER-negative breast cancer. We find a subclass of basal tumors, characterized by over-expression of
immune response genes, which has a better prognosis than the rest of ER-negative breast cancers. Moreover, we show that, in contrast to ER-positive tumours, the majority of prognostic markers
in ER-negative breast cancer are over-expressed in the good prognosis group and are associated
with activation of complement and immune response pathways. Specifically, we identify an immune
response related seven-gene module and show that downregulation of this module confers greater
risk for distant metastasis (hazard ratio 2.02, 95% confidence interval 1.2-3.4; P = 0.009),
independent of lymph node status and lymphocytic infiltration. Furthermore, we validate the
immune response module using two additional independent datasets. Conclusion: We show that ER-negative basal breast cancer is a heterogeneous disease with at
least four main subtypes. Furthermore, we show that the heterogeneity in clinical outcome of ER-
negative breast cancer is related to the variability in expression levels of complement and immune
response pathway genes, independent of lymphocytic infiltration. information Genome Biology 2007, 8:R157 R157.2 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.2 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 The FDR is higher in ER- breast cancer Although cytokeratin markers have been
shown to correlate with poor prognosis in breast cancer [11-
14], an attempt to correlate basal markers with survival
within ER- disease has shown that these markers were not
predictive of outcome [15]. Based on our work presented
here, it appears that the prognostic 'signal' in ER- breast can-
cer is much weaker than that in ER+ disease. This precludes
the use of traditional supervised approaches, which assume a
sufficiently low false discovery rate (FDR) for deriving gene
expression based classifiers. A similar observation was
reported by others [16]. Finding ER- subclasses using PACK g
g
If the aim is to identify subclasses within a tumor type, then it
is natural that unsupervised methods be applied to sample
sets that are composed entirely of this tumor type. In fact,
given the hierarchical ER+/ER- subdivision for breast cancer,
it is questionable whether ER- subgroups can be correctly
defined based on clusters that were derived by using both ER+
and ER- samples, as was done in other studies (for example
[21-23]). To see this, assume that all tumor types and genes
are used in the clustering algorithm. It is very likely that the
clusters within ER- tumors reflect not only the interesting var-
iability of genes within ER- tumors but also the variability of
genes that are important for classification of ER+ tumors. The
variability of these genes in ER- tumors may represent unde-
sired noise, which, if not removed, can affect the inferred
clusters. Thus, in order to identify relevant subtypes of ER-
tumors more robustly, we decided to use ER- tumors only. Moreover, in view of the relatively high FDR in ER- disease,
we decided to apply the PACK methodology, which has
already been shown to provide a more reliable identification
of molecular classifiers [17]. Because PACK requires large Recently, we proposed a novel feature selection method (Pro-
file Analysis using Clustering and Kurtosis [PACK]) [17], that
selects genes using a pattern recognition method and that
may significantly reduce the FDR. Using PACK in an inte-
grated cohort of 186 ER- samples and 1,200 genes, we were
able to identify distinct molecular subtypes, including a good
prognosis subclass characterized by over-expression of
immune response genes. However, these results were not val-
idated in external cohorts. The purpose of this work is to extend our preliminary findings
[17] by applying PACK to the same three breast cancer data-
sets [5,9,18], but now using a much larger set of common
genes (we rescued a significantly larger number of genes from
our study [9] by imputing missing data, which led to a much
larger number of overlapping genes, approximately 5,000,
with the other two arrays.), and to further validate our find-
ings using two external independent cohorts [7,19]. More
generally, our goal is to elucidate the molecular taxonomy of Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. Finding ER- subclasses using PACK R157.3 http://genomebiology.com/2007/8/8/R157 FDR comparison in ER- and ER+ breast cancer
Figure 1
FDR comparison in ER- and ER+ breast cancer. For various significance
thresholds (sigth), we plot the fraction of observed genes with P values
less than the significance threshold (black) as well as the corresponding
fraction of false positives, as estimated using a q value analysis (red). (a)
Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast
cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to
distant metastasis for ER- breast cancer. P values were obtained from the
log-rank test using Cox regression models. ER, estrogen receptor; FDR,
false discovery rate. 0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
OS
(a)
ER+
0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
OS
(b)
ER−
0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
DM
(c)
ER+
0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
DM
(d)
ER− datasets used are summarized in Table 1 by platform type,
number of ER- samples, and number of poor outcome events. 0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
OS
(a)
ER+ 0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
OS
(b)
ER− Briefly, we review the concepts that underpin PACK (see
Materials and methods, below, and Figure 2). The hypothesis
is that genes that play an important role as classifiers or
biomarkers are more likely to have expression profiles that
are mixtures of gaussian distributions. On the other hand,
false positives, in spite of their spurious association with a
phenotype, are less likely to be described by a mixture of dis-
tributions. Thus, selecting genes based on whether they have
structure in their expression profiles is likely to pick out the
relevant markers from those that are just false positives. Next,
we propose to focus on those genes that define the largest
subgroups. Although genes that define small subgroups are
also of interest, it is natural to identify first those genes that
define the largest subclasses. While such features can be
found from the inferred cluster sizes, it turns out that such
features are generally also characterized by a negative (or
close to zero) kurtosis profile (see Materials and methods,
below) [17]. As shown previously, negative kurtosis expres-
sion profiles are in effect a mixture of at least two (gaussian)
distributions of approximately equal weights. Finding ER- subclasses using PACK Thus, by select-
ing those genes that have the most negative kurtosis expres-
sion profiles, we have identified the markers that define the
largest subclasses within the sample set (Figure 2). It is clear
that many of these features will be highly correlated because
they define almost the same subclasses. It follows that further
application of traditional clustering algorithms over these
negative kurtosis profiles will enable reliable identification of
the major subclasses within the sample set. We note that
because we are interested in the most negative kurtosis pro-
files and because the clusters in the individual gene profiles
are only needed to study the cluster distribution of pheno-
types, the cluster inference step on the individual gene pro-
files (known as PAC) can be performed after computation of
kurtosis (known as PAK) on the selected subset of negative
kurtosis profiles (Figure 2). 0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
DM
(d)
ER− 0.00
0.04
0.08
0.0
0.1
0.2
0.3
0.4
Sigth
DM
(c)
ER+ (c) (d) FDR comp
Figure 1 p
g
FDR comparison in ER- and ER+ breast cancer. For various significance
thresholds (sigth), we plot the fraction of observed genes with P values
less than the significance threshold (black) as well as the corresponding
fraction of false positives, as estimated using a q value analysis (red). (a)
Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast
cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to
distant metastasis for ER- breast cancer. P values were obtained from the
log-rank test using Cox regression models. ER, estrogen receptor; FDR,
false discovery rate. p
g
FDR comparison in ER- and ER+ breast cancer. For various significance
thresholds (sigth), we plot the fraction of observed genes with P values
less than the significance threshold (black) as well as the corresponding
fraction of false positives, as estimated using a q value analysis (red). (a)
Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast
cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to
distant metastasis for ER- breast cancer. P values were obtained from the
log-rank test using Cox regression models. ER, estrogen receptor; FDR,
false discovery rate. sample sizes (for small sample sizes, kurtosis estimates can
have large variance and clustering algorithms that aim to pre-
dict the optimal number of clusters have a high false negative
rate), we applied it to the integrated data matrix derived pre-
viously. Two additional independent ER- cohorts [7,19] were
left out to serve as validation studies. The five microarray Table 1
Breast cancer datasets used
Ref. Cohort name
Oligo microarray platform
ER-
ER+
n
Death/distant
metastasis (n)
n
Death/distant
metastasis (n)
[18]
NKI2
Agilent
69
34
226
45
[5]
EMC
Affymetrix
77
27
208
80
[9]
NCH
Agilent
40
14
93
21
[19]
UPP
Affymetrix
34
6
213
49
[7]
JRH-2
Affymetrix
24
6
72
17
ER, estrogen receptor. PACK flow
Figure 2 PACK flowchart
Figure 2
PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is
computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further
unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust
prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster
inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian
profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the
categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis
gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. C
owc a t
gu e
PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is
computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further
unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust
prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster
inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian
profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the
categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis
gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. ized by the expression patterns of four gene clusters that were
found to be strongly enriched for specific gene ontologies
(Figure 3a and Additional data file 3). Table 1 information Genome Biology 2007, 8:R157 R157.4 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 PACK flowchart
Figure 2
PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is
computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further
unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust
prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster
inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian
profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the
categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis
gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. −3
−2
−1
0
1
2
3
0.0
0.1
0.2
0.3
0.4
Gene expression
Density
K < 0
Bi-modal: major subgroups
−2
−1
0
1
2
0.0
0.2
0.4
0.6
Gene expression
Density
K > 0
Bi-modal: outlier subgroups
Gene expression profile
Compute kurtosis (PAK)
K < 0
K > 0
Feature selection
Estimate optimal number of clusters (PAC)
C=2
C=1
Fisher’s test to correlate with phenotype
(a)
(b) Gene expression profile
Compute kurtosis (PAK)
K < 0
K > 0
Feature selection
Estimate optimal number of clusters (PAC)
C=2
C=1
Fisher’s test to correlate with phenotype
(a) −3
−2
−1
0
1
2
3
0.0
0.1
0.2
0.3
0.4
Gene expression
Density
K < 0
Bi-modal: major subgroups
−2
−1
0
1
2
0.0
0.2
0.4
0.6
Gene expression
Density
K > 0
Bi-modal: outlier subgroups
(b) −3
−2
−1
0
1
2
3
0.0
0.1
0.2
0.3
0.4
Density
K < 0
Bi-modal: major subgroups
(b) (a) (b) Gene expression
−2
−1
0
1
2
0.0
0.2
0.4
0.6
Gene expression
Density
K > 0
Bi-modal: outlier subgroups A subgroup of good prognosis in ER- breast cancer It further follows from these observations that ER- normal
and luminal A samples were predominantly characterized by
over-expression of ECM genes. ER- basal tumors, on the other
hand, exhibited a more complex pattern and appeared to
divide into at least four subgroups (CC+/IR+, CC+, ECM+, and
IR+). To investigate further the relation of our five ER- subclasses
with the intrinsic subtypes, we considered to which ER- sub-
class ER+ samples of known intrinsic subtype were most sim-
ilar. To this end we first constructed, for each of the five ER-
subclasses, mean centroids over the 813 negative kurtosis
genes (Additional data file 5). To validate the centroids, the
same ER- samples were assigned a subclass using a nearest
centroid criterion (samples for which the largest Pearson cor-
relation coefficient was <0.25 were considered unclassified;
see Materials and methods, below), which showed that 156
(84%) were classified, of which 143 (92%) were assigned the
correct subclass. Next, using the SSP to classify the 527 ER+
samples into the intrinsic subtypes, we then assigned each of
the 527 ER+ samples into an ER- subclass based on the same
nearest centroid criterion (Table 3). As expected, only 4% of
ER+ tumors were classified as basal, whereas the majority
(82%) of them were luminal. Moreover, the analysis showed
that ER+ luminal B samples were most similar to CC+ and
CC+/IR+ ER- samples, which is consistent with the fact that all
of these samples over-express cell cycle and cell proliferation
genes. In contrast, ER+ luminal A samples were most similar
to ECM+ (63%), IR+ (26%), and SR+ (8%) ER- samples. Not
surprisingly, almost all (16/19 [84%]) 'normal' ER+ samples
were most similar to ECM+ ER- samples. All basal ER+ sam- To further confirm our findings, we also generated Kaplan-
Meier survival curves for the five identified subclasses using
TTDM as the end-point (Figure 3b). This showed that the SR+
and CC+ subclasses had worst prognosis, whereas the IR+ sub-
class was the group with best prognosis. Specifically, relative
to the IR+ subclass the SR+ subgroup had a hazard ratio (HR)
of 3.70 (95% confidence interval [CI] 1.49 to 9.24; P = 0.005),
whereas the CC+ subgroup had an HR of 2.75 (95% CI 1.07 to
7.05; P = 0.035). A subgroup of good prognosis in ER- breast cancer A subgroup of good prognosis in ER- breast cancer
We next considered whether the five identified clusters were
associated with different prognostic groups. Because we had
merged different cohorts, and it is questionable whether sur-
vival data can be also merged together, we decided to test first
the clusters for association with clinical outcome by using a
dichotomized outcome variable. Specifically, poor outcome
was defined as any death or distant metastasis event, whereas
good outcome was defined as a patient alive or with no distant
metastasis. By studying the distribution of good and poor out-
come events in the respective clusters, significant associa-
tions with prognosis could be found by means of Fisher's
exact test (Table 2). Interestingly, this showed that the IR+
subgroup had better prognosis when compared with the
ECM+ (P = 0.08), CC+ (P = 0.03), and SR+ (P = 0.005)
subclasses. In order to relate the five identified molecular subtypes to the
intrinsic breast cancer classification [21,26], we used the
recently validated single sample predictor (SSP) [23] to clas-
sify the 186 ER- samples into the various intrinsic subtypes
(Figure 3a and Table 2). In addition, we studied the expres-
sion profiles of recently validated basal markers [27] and
genes in the ERBB2 amplicon across the five identified clus-
ters (Figure 3a and Additional data file 4). Based on these fig-
ures and Table 2, we could draw the following conclusions. First, the SR+ cluster was highly correlated with the usual
HER2+ intrinsic subtype. Second, the CC+/IR+ and CC+ clus-
ters defined distinct subtypes of basal tumors. Third, the
ECM+ cluster was mostly basal, but it contained a relatively
high proportion of normal-like and luminal-A-like ER-
tumors; it also exhibited the most varied grade distribution,
with most low-grade ER- tumors falling into this class. Finally, the main constituents of the IR+ cluster were basal
and HER2+. Compared with the CC+/IR+ subgroup it also had better prog-
nosis, although the difference was not statistically significant
(P = 0.19). We thus combined the CC+/IR+ and IR+ subclasses
together and evaluated the prognosis of this larger subclass
relative to the rest of ER- samples. Consistent with our
previous result [17] we found that the ER- tumors over-
expressing immune response genes had better prognosis than
ER- samples that did not (P = 0.02). A subgroup of good prognosis in ER- breast cancer Similarly, relative to the CC+/IR+ subclass,
the SR+ subgroup had an HR of 2.35 (95% CI 1.13 to 4.88;
P = 0.02), whereas for the CC+ subgroup it did not quite reach
statistical significance (HR 1.80, 95% CI 0.83 to 3.89;
P = 0.13). We verified the statistical significance of these sur-
vival differences by 10,000 random permutations of the sam-
ples, which showed that the theoretical P value estimates
above were essentially identical to the empirically derived P
values. PACK flow
Figure 2 One group was charac-
terized by over-expression of ERBB2, the steroid hormone
receptor AR, and genes related to steroid estrogen response
(such as GATA3, TFF1, and DNALI1). This subtype is there-
fore similar to the apocrine subclass, recently proposed
[24,25], which is characterized by over-expression of AR and
genes that are either direct targets of ER or responsive to
estrogen [24,25]. Thus, we decided to call this ER- subtype
(over-expressing steroid response genes) 'SR+', although it is
clear that it also defines the well known HER2+ subtype. Distinct molecular subgroups of ER breast cancer
Applying PAK to the integrated ER- data matrix of 5,007
genes, we found 813 genes with a negative kurtosis profile
(Additional data file 1). Interestingly, applying the same anal-
ysis to ER+ breast cancer, we found only a much smaller
number (193) of negative kurtosis profiles (Additional data
file 2), despite there being roughly twice as many bimodal
profiles in ER+ breast cancer (about 4500 in ER+ versus about
2,500 in ER-). We verified by explicit simulation that the sig-
nificantly lower proportion of negative kurtosis profiles in
ER+ disease could not be explained by the larger sample size
in ER+ (527) compared with ER- disease (186; data not
shown). The other four groups were characterized mainly by absent or
lower expression of these steroid response genes. One of these
four clusters was characterized by over-expression of genes
related to cell cycle and cell proliferation pathways (CC+), and
another cluster also had over-expression of immune response Having identified the relevant features, we next clustered the
ER- tumors over these. Using hierarchical clustering with
Pearson correlation metric and complete linkage, we found
that samples clustered into five main groups, each character- Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.5 http://genomebiology.com/2007/8/8/R157 genes (CC+/IR+). For the remaining two clusters, one was
characterized by over-expression of extracellular matrix
genes (ECM+), and the other was characterized by over-
expression of immune response genes (IR+) only. ples had expression profiles most similar to CC+/IR+ and CC+
subtypes. Interestingly, only 16 of the 42 (38%) ER+ HER2+
tumors exhibited significantly correlated expression profiles
to any one of the five ER- subclasses, with most of these (11)
mapping to the CC+/IR+ subtype. Prognostic markers in ER- tumors are associated with
immune response functions The better prognosis of the IR+ subclass is likely due to spe-
cific genes that are individually prognostic. In order to find
these, we applied the PAC algorithm to the 813 genes with
negative kurtosis expression profiles. Briefly, this procedure Genome Biology 2007, 8:R157 R157.6 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 (a)
CC+/IR+
CC+
ECM+
SR+
IR+
FBN1
SPARC
MMP11
ERBB2
AR
C1QA
HLA-F
IGLC2
CDK2AP1
CDKN2A
KRT17
CRYAB
CDC25B (a)
CC+/IR+
CC+
ECM+
SR+
IR+
FBN1
SPARC
MMP11
ERBB2
AR
C1QA
HLA-F
IGLC2
CDK2AP1
CDKN2A
KRT17
CRYAB
CDC25B Genome Biology 2007, 8:R157
Figure 3 (see legend on next page)
SSP
LYM.INF. GRADE
BASAL.MARK. ERBB2.AMP. 0
2
4
6
8
10
12
0.0
0.2
0.4
0.6
0.8
1.0
(b)
(c)
HLA-F
IGLC2
LY9
TNFRSF17
SPP1
XCL2
C1QA
0
2
4
6
8
10
12
0.0
0.2
0.4
0.6
0.8
1.0
HR=2.02 (1.2-3.4) p=0.009
(d)
p = 0.003 SSP
LYM.INF. GRADE
BASAL.MARK. ERBB2.AMP. SSP
LYM.INF. GRADE
BASAL.MARK. ERBB2.AMP. (b)
(c)
(d) (c)
F
2
9
7
2
A (c)
0
2
4
6
8
10
12
0.0
0.2
0.4
0.6
0.8
1.0
HR=2.02 (1.2-3.4) p=0.009
(d) (c) (b) (d) 0
2
4
6
8
10
12
0.0
0.2
0.4
0.6
0.8
1.0
p = 0.003 Figure 3 (see legend on next page) Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.7 http://genomebiology.com/2007/8/8/R157 Molecular subclasses in ER- breast cancer
Figure 3 (see previous page)
Molecular subclasses in ER- breast cancer. (a) Complete linkage hierarchical clustering of 186 ER- breast tumors over 813 genes with negative kurtosis
profiles. Five sample clusters were identified and characterized in terms of the patterns of over-expression and under-expression of four gene clusters
related to cell cycle (CC; blue), immune response (IR; red), extracellular matrix (ECM; green), and steroid hormone response (SR; pink) functions. Panels
show the distribution of the SSP subtype [23], the lymphocytic infiltration score, histologic grade, basal marker [27], and ERBB2+ amplifier subtype. Panel
color codes: SSP (pink = HER2, brown = basal, dark green = normal, sky blue = luminal A, and blue = luminal B); LYM.INF (black = high, gray = low, and
white = missing); GRADE (black = high, blue = intermediate, sky blue = low, and white = missing), BASAL.MARK. (black = high and white = low), ERBB2-
AMP (black = high and white = low). Prognostic markers in ER- tumors are associated with
immune response functions The BASAL.MARK. profile represents an average over validated basal markers in [27], whereas the ERBB2-AMP
profile was calculated as an average over three genes in the ERBB2 amplicon (ERBB2, STARD3, GRB7). (b) Kaplan-Meier curves for time to distant
metastasis (years) and for the five subclasses identified in panel (a). (c) Partitioning around medoids clustering over the seven-gene prognostic immune
response module. Panel color codes: purple = cluster over-expressing module, yellow = cluster under-expressing module, black = poor outcome samples,
gray = good outcome samples, green = relative under-expression, and red = relative over-expression. (d) Kaplan-Meier curves for time to distant
metastasis for the two groups identified in panel (c). Hazard ratio, 95% confidence interval, and log-rank test P values are shown. ER, estrogen receptor;
SSP, single sample predictor. Machine [28] showed that immune/defense response was the
most enriched GO, with seven genes falling into this category
(C1QA, IGLC2, LY9, TNFRSF17, SPP1, XCL2, and HLA-F). The expression profiles for these seven genes confirmed the
presence of distinct clusters with nonrandom distributions of
good and poor outcome samples (Figure 4 provides detailed
profiles of C1QA and IGLC2). selects features based on whether their expression profiles
are best described as a mixture of gaussians or not, and then
evaluates whether the distribution of good and poor outcome
events among the inferred clusters is statistically different
from random or not. Applying PAC, we found 22 genes with a
Fisher test P < 0.05 (Additional data file 1). A Gene Ontology
(GO) enrichment analysis of these 22 genes using the GOTree Table 2
Distribution of ER- samples among clusters, prognostic groups and intrinsic subtypes
Cluster
n
Outcome
LI
ER-
Good
Poor
High
Low
Luminal B
Luminal A
Normal
Basal
HER2
CC+/IR+
39
25
14
7
2
0
0
0
38
1
CC+
37
18
17
3
5
0
0
1
33
3
ECM+
45
26
18
1
14
0
9
9
22
5
SR+
36
16
20
2
4
1
1
0
2
32
IR+
29
23
6
6
6
0
4
2
9
14
For the five clusters of Figure 2a, we give the number of samples per cluster (n) and their distributions over good/poor outcome, high/low
lymphocytic infiltration (LI) score, and intrinsic subtypes as determined by the single sample predictor (SSP) classifier. Prognostic markers in ER- tumors are associated with
immune response functions Clusters were labeled by the
main Gene Ontology of genes over-expressed in the group: CC+ (cell cycle), CC+/IR+ (cell cycle and immune response), ECM+ (extracellular matrix),
SR+ (steroid hormone response), and IR+ (immune response). ER, estrogen receptor. Table 2 Distribution of ER- samples among clusters, prognostic groups and intrinsic subtypes For the five clusters of Figure 2a, we give the number of samples per cluster (n) and their distributions over good/poor outcome, high/low
lymphocytic infiltration (LI) score, and intrinsic subtypes as determined by the single sample predictor (SSP) classifier. Clusters were labeled by the
main Gene Ontology of genes over-expressed in the group: CC+ (cell cycle), CC+/IR+ (cell cycle and immune response), ECM+ (extracellular matrix),
SR+ (steroid hormone response), and IR+ (immune response). ER, estrogen receptor. Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44
ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson
correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Table 3 Classification of ER+ intrinsic subtypes, medullary breast cancer, and BRCA1 tumors into ER- subclasses
ER+
MBC
DBC
BRCA1
Luminal B
Luminal A
Normal
Basal
HER2
n
97
337
32
19
42
22
44
18
n classifiable
37
113
19
17
16
20
33
16
CC+/IR+
17
2
0
13
11
14
4
13
CC+
20
2
0
4
1
3
3
2
ECM+
0
71
16
0
0
1
3
1
SR+
0
9
0
0
0
0
20
0
IR+
0
29
3
0
4
2
3
0
Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44
ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson
correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Classification of ER+ intrinsic subtypes, medullary breast cancer, and BRCA1 tumors into ER- subclasses Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44
ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson
correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Genome Biology 2007, 8:R157 R157.8 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007 R157.8 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 Expression profiles of selected prognostic markers in ER- breast cancer
Figure 4
Expression profiles of selected prognostic markers in ER- breast cancer. Expression profile (on a log2 scale) of selected prognostic markers (a) IGLC2 and
(b) C1QA in the integrated cohort of 186 ER- tumours (NKI2 + EMC + NCH), and in the validation cohorts UPP and JRH-2. Good outcome samples are
shown in green, and poor outcome samples in blue. Clusters were inferred using the variational Bayesian approach in NKI2 + EMC + NCH and the pam
algorithm in the UPP and JRH-2 cohorts. Infered clusters are indicated by different shapes (triangles and diamonds). ER, estrogen receptor; pam,
partitioning around medoids. Expression
Figure 4 Expression profiles of selected prognostic markers in ER breast cancer
Figure 4
Expression profiles of selected prognostic markers in ER- breast cancer. Expression profile (on a log2 scale) of selected prognostic markers (a) IGLC2 and
(b) C1QA in the integrated cohort of 186 ER- tumours (NKI2 + EMC + NCH), and in the validation cohorts UPP and JRH-2. Good outcome samples are
shown in green, and poor outcome samples in blue. Clusters were inferred using the variational Bayesian approach in NKI2 + EMC + NCH and the pam
algorithm in the UPP and JRH-2 cohorts. Infered clusters are indicated by different shapes (triangles and diamonds). ER, estrogen receptor; pam,
partitioning around medoids. In contrast, application of the same method to ER+ breast
cancer yielded 29 genes (out of a possible 193) with P < 0.05
(Additional data file 2). In spite of there being only 29 genes
in this list, there were many with mitotic cell cycle functions,
notably UBE2C, MAD2L1, E2F1 and KIFC1, and GO enrich-
ment analysis confirmed that the cell cycle GO was the most
significantly enriched category followed by transcription
regulatory activity. This result for ER+ breast cancer confirms
findings reported elsewhere that poor prognosis in ER+ breast
cancer is related mainly to over-expression of genes in cell
cycle and cell proliferation pathways [3,5,7]. Notably, none of
the identified prognostic genes were related to immune
response functions. ters significantly associated with clinical outcome. Specifi-
cally, the partitioning around medoids (pam) clustering
algorithm [29] with two centers predicted one cluster with 52
good outcome and 56 poor outcome patients, and another
cluster with 56 good outcome and only 19 poor outcome
events, which was highly significant under Fisher's exact test
(P = 0.0004; Figure 3c). Kaplan-Meier and Cox regression
analyses further confirmed that the group not over-express-
ing the seven-gene module (out of the seven genes the major-
ity [six] are not over-expressed) had a greater risk for distant
metastasis (HR 2.02, 95% CI 1.2 to 3.4; P = 0.009; Figure 3d). In contrast, application of the same method to ER+ breast
cancer yielded 29 genes (out of a possible 193) with P < 0.05
(Additional data file 2). Expression
Figure 4 In spite of there being only 29 genes
in this list, there were many with mitotic cell cycle functions,
notably UBE2C, MAD2L1, E2F1 and KIFC1, and GO enrich-
ment analysis confirmed that the cell cycle GO was the most
significantly enriched category followed by transcription
regulatory activity. This result for ER+ breast cancer confirms
findings reported elsewhere that poor prognosis in ER+ breast
cancer is related mainly to over-expression of genes in cell
cycle and cell proliferation pathways [3,5,7]. Notably, none of
the identified prognostic genes were related to immune
response functions. Table 3 0
50
100
150
−2
−1
0
1
2
3
NKI2+EMC+NCH
(a)
0
5
10
20
30
−2
−1
0
1
2
3
UPP
5
10
15
20
−2
−1
0
1
2
3
JRH−2
0
50
100
150
−2
−1
0
1
2
3
NKI2+EMC+NCH
(b)
0
5
10
20
30
−2
−1
0
1
2
3
UPP
5
10
15
20
−2
−1
0
1
2
3
JRH−2 0
50
100
150
−2
−1
0
1
2
3
NKI2+EMC+NCH
(a)
NKI2+EMC+NCH
(b) 5
10
15
20
−2
−1
0
1
2
3
JRH−2 0
5
10
20
30
−2
−1
0
1
2
3
UPP 0
5
10
20
30
−2
−1
0
1
2
3
UPP (b) 5
10
15
20
−2
−1
0
1
2
3
JRH−2 0
50
100
150
−2
−1
0
1
2
3 Relation to STAT1 and IFN cluster Next, we investigated the relation of the good prognosis sub-
group identified here with the novel IFN regulated cluster
identified recently [23]. As shown previously [23], the IFN
cluster, defined by over-expression of interferon regulated Having identified a prognostic module of seven immune
response genes (henceforth called the IR module), we next
confirmed that clustering over this module resulted in clus- Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.9 http://genomebiology.com/2007/8/8/R157 genes, including the transcriptional regulator STAT1, was
most closely related to the basal subclass and had a prognos-
tic performance similar to that of luminal B samples when
compared with the luminal A and normal subtypes. Interest-
ingly, when compared with the basal and HER2+ subclasses,
the IFN group had better prognosis, although a formal com-
parison was not conducted by Hu and coworkers [23]. measured for example by a higher degree of lymphocytic
infiltration (LI). The association of high LI with good progno-
sis is well known [31-34], and although a few conflicting
results have also been reported [35-37], we thought it natural
to consider whether upregulation of the identified immune
response module conferred good prognosis independently of
LI. To this end, we scored the samples in the NCH cohort for
LI (see Materials and methods, below) and combined these
with the available LI score information from the NKI2 cohort,
yielding a total of 50 scored samples. We found that although
there were proportionally more tumors with high LI scores in
the group over-expressing the immune response genes (spe-
cifically there were 11 high LI and 9 low LI samples versus 8
high LI and 22 low LI in the under-expressed group; Fisher
test, P = 0.07), a multivariate Cox regression with TTDM as
the outcome variable and the seven-gene IR module and LI
score as predictors showed that the immune response module
was still a strong predictor of clinical outcome, independent
of LI (HR 2.05, 95% CI 0.71 to 5.97; P = 0.19; Table 4). (The P
value is only marginally below statistical significance, which
is most likely due to the relatively small sample size.)
Supporting this result further, we did not find in ER- tumors
any significant association between LI and clinical outcome
(Table 4). Relation to medullary and BRCA1 ER- breast cancer Relation to medullary and BRCA1 ER- breast cancer
To further confirm the independent prognostic power of the
IR module from LI, we investigated the relationship of the
identified good prognosis tumors with medullary breast
cancers (MBCs), which are characterized by high LI scores
and relatively good prognosis [38]. Thus, we considered to
which ER- subclass the 22 MBC expression profiles from the
report by Bertucci and coworkers [38] were most similar
(Table 3). (For completeness and reference, we also per-
formed the analysis for the 44 ductal breast cancers [DBCs],
also profiled by Bertucci and coworkers [38].) This showed
that of the 22 MBCs, 20 showed reasonably strong correlation
to one of the ER- subclass centroids, 14 of which (70%) were
most similar to the CC+/IR+ subtype, whereas only two (11%)
were most similar to the IR+ subtype. In contrast, for the 33
DBC which could be classified, only four (12%) and three (9%)
were most similar to the CC+/IR+ and IR+ subtypes. These
results mirror the distribution of LI scores across the five ER-
subclasses (Figure 3a and Table 2) and further confirms that
the best prognostic group (IR+) is not related to MBC,
whereas CC+/IR+ is. A similar analysis was performed for BRCA1 mutant tumors. Of the 16 BRCA1 mutants from the NKI2 cohort [3], which
were also deemed classifiable based on a 0.25 correlation
threshold, 13 (81%) had expression profiles most similar to
the CC+/IR+ subtype (Table 3). None showed similarity to the
IR+ subclass. Therefore, this suggests that ER- BRCA1
mutants, in common with MBCs, are most similar to the CC+/
IR+ subclass identified here. Relation to STAT1 and IFN cluster Among the 98 genes in the immune response gene cluster
(Figure 3a and Additional data file 1), we identified a total of
14 with interferon related functions, including STAT1, SP110,
NFKBI, IFI44, IFNGR1, ISGF3G, and IRF7. Interestingly,
however, none of these genes showed association with prog-
nosis except SP110. Thus, although it appears that our sub-
class is related to the IFN class discovered by Hu and
coworkers [23], it is also distinct in that the associated prog-
nostic markers are not in the IFN cluster. Immune response module predicts outcome
independently of lymph node status p
y
y
p
Because our IR gene cluster included STAT1 and interferon-
induced genes, and these genes have been shown to be asso-
ciated with lymph node (LN) metastasis [30], we considered
whether the subgroup of ER- samples over-expressing the 98-
gene IR cluster was significantly associated with LN status. Because all patients in the ECM cohort were LN negative, this
analysis was only performed on the NKI2 and NCH cohorts
(109 ER- patients, of whom 42 had LN involvement). Using
pam clustering with two centers over these 98 genes and 109
samples, we found subgroups with similar proportions of LN
metastases (43 LN negative and 28 LN positive versus 24 LN
negative and 14 LN positive; Fisher's exact test P = 0.84). Moreover, clustering only over the 14 genes involved in the
IFN subcluster still did not show a significantly nonrandom
distribution of LN metastases among the clusters (P = 0.23),
although in agreement with Huang and coworkers [30] the
cluster over-expressing the IFN genes had proportionally
more LN metastases. Similarly, the distribution of LN metas-
tases among the two clusters predicted by the IR module was
not significantly different from random (P = 0.48). While LN
status itself was a significant predictor of distant metastasis
both in univariate (HR 2.28, 95% CI 1.36 to 3.85; P = 0.002)
and multivariate (HR 2.16, 95% CI 1.28 to 3.64; P = 0.004)
Cox regression analysis (this result is for a multivariate model
including LN status and the IR module as predictors.), impor-
tantly, the IR module remained a prognostic predictor for
TTDM (HR 1.93, 95% CI 1.14 to 3.26; P = 0.015) in the multi-
variate model that included LN status (Table 4). This showed
that the IR module identified here adds independent prog-
nostic value over LN status in ER- breast cancer. External validation To confirm the robustness of our findings, we used the pam
algorithm to classify patients in the two external cohorts into
clusters over-expressing and under-expressing the IR module
(Figure 5a,b). Remarkably, the predicted 20-sample cluster
over-expressing the module was composed entirely of good
outcome patients, whereas the remaining 35-sample cluster
included 12 poor outcome events (Figure 5c), which was
highly significant under Fisher's exact test (P = 0.002; the HR
is singular because one cluster did not have any events). Having identified a prognostic module related to immune
response, we next attempted to validate this finding using two
independent breast cancer cohorts [7,19]. Specifically, the
hypothesis to be tested was that over-expression of the iden-
tified prognostic markers is associated with good prognosis,
except for SPP1, for which good prognosis is hypothesized to
be associated with under-expression. Because of the relatively
small sample size of the two external cohorts, an algorithm
that attempts to learn the optimal number of clusters (as
implemented in PACK) is unlikely to capture structure
because of a large false negative rate [39]. Hence, in order to
define groups of over-expression and under-expression, we
applied the pam algorithm with two centers to each of the
seven genes in each of the two cohorts (Figure 4 and Addi-
tional data files 6 and 7). Because the small number of events,
six, in each of the two external cohorts implied a highly
discrete P value distribution, Fisher test P values would be too
conservative and poor approximations for type I errors [40]. To overcome this difficulty, we also considered the distribu-
tion of good and poor outcome samples over the combined
clusters of over-expression and under-expression (Table 5). This showed that four of the seven genes (C1QA, IGLC2,
TNFRSF17, and LY9) were also highly prognostic in these two
external cohorts, thus confirming the validity of our finding. Moreover, as in the three original cohorts, over-expression of
these genes in the two external cohorts was associated with
good prognosis (Figure 4 and Additional data files 6 and 7). For the other three genes (HLA-F, SPP1, and XCL2), P values
did not reach statistical significance (P about 0.2), yet their
expression profile trends were entirely consistent with those
found in the integrated cohort, thus confirming their role as
members of a robust prognostic module (Additional data files
6 and 7). Immune response module predicts outcome
independently of lymphocytic infiltration To confirm the robustness of our findings, we used the pam
algorithm to classify patients in the two external cohorts into
clusters over-expressing and under-expressing the IR module
(Figure 5a,b). Remarkably, the predicted 20-sample cluster
over-expressing the module was composed entirely of good
outcome patients, whereas the remaining 35-sample cluster
included 12 poor outcome events (Figure 5c), which was
highly significant under Fisher's exact test (P = 0.002; the HR
is singular because one cluster did not have any events). Immune response module predicts outcome
independently of lymphocytic infiltration The upregulation of immune response genes in good progno-
sis tumors could be explained by the fact that these tumors
elicit a stronger immune and inflammatory response, as Genome Biology 2007, 8:R157 R157.10 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 Table 4
Univariate and Multivariate Cox-regression model
ER- (n = 186)
ER+ (n = 527)
HR (95% CI)
P
HR (95% CI)
P
LN
2.28 (1.36-3.85)
0.002
2.07 (1.47-2.90)
<10-4
LI
1.06 (0.66-1.70)
0.9
1.50 (0.72-3.14)
0.58
IRM
2.02 (1.19-3.41)
0.009
1.25 (0.91-1.71)
0.19
LNa + IRM
2.16 (1.28-3.64)
0.004
2.10 (1.49-2.96)
<10-4
LN + IRMa
1.93 (1.14-3.26)
0.015
1.29 (0.94-1.76)
0.11
LIa + IRM
0.86 (0.32-2.28)
0.76
1.75 (0.41-7.47)
0.45
LI + IRMa
2.05 (0.71-5.97)
0.19
0.57 (0.27-1.19)
0.13
LNa + LI + IRM
1.79 (0.70-4.62)
0.22
1.48 (0.68-3.19)
0.32
LN + LIa + IRM
0.84 (0.51-1.38)
0.72
1.65 (0.38-7.07)
0.5
LN + LI + IRMa
2.22 (0.76-6.50)
0.15
0.57 (0.27-1.20)
0.14
The table summarizes the hazard ratio (HR), 95% confidence interval (CI), and log-rank test P values of univariate Cox proportional hazards
regression models, with lymph node status (LN = 1/0 for LN +/-), level of lymphocytic infiltration (LI = 1 for low infiltration score, and LI = 0 for high
infiltration score) and the classification based on the seven-gene immune response related module (IRM; 2 = down-regulation of module, 1 =
upregulation of module) as predictors. aCorresponding values in the multivariate Cox models including LN, LI, and IR module as predictors. The
table compares the values for estrogen receptor (ER)- and ER+ breast cancer. Table 4 Univariate and Multivariate Cox-regression model The table summarizes the hazard ratio (HR), 95% confidence interval (CI), and log-rank test P values of univariate Cox proportional hazards
regression models, with lymph node status (LN = 1/0 for LN +/-), level of lymphocytic infiltration (LI = 1 for low infiltration score, and LI = 0 for high
infiltration score) and the classification based on the seven-gene immune response related module (IRM; 2 = down-regulation of module, 1 =
upregulation of module) as predictors. aCorresponding values in the multivariate Cox models including LN, LI, and IR module as predictors. The
table compares the values for estrogen receptor (ER)- and ER+ breast cancer. Table 5 In fact, GO analysis
(using GOTree Machine) of the top 500 genes obtained from
this rank sum test (all with q-values < 0.05) showed that cell
cycle and transcription regulator activity related GOs were
the only categories with highly significant P values (uncor-
rected P < 10-6), and that the only enriched immune response
related GO was that of humoral immune response, with 11
represented genes (including BLM, FADD, C3, C7, BCL2,
NFKB1, and the IR module member TNFRSF17), and which
was only marginally enriched (uncorrected P = 0.005). Although we verified that this humoral immune response
module was associated with prognosis in the integrated ER+
cohort independent of LN status and LI (HR 2.26, 95% CI
0.97 to 5.26; P = 0.06) we were unable to validate this prog-
nostic module in the external UPP and JRH-2 cohorts
(Additional data file 8). Moreover, the co-regulation patterns
for the genes in this module were less coherent than those for
the IR module in ER- breast cancer (Figure 5 and Additional
data file 8). Hence, independent of the methodology used, an
IR related prognostic module in ER+ breast cancer could not
be identified, which seems to suggest that a good prognosis
subtype related to IR is specific to ER- disease. We believe that these differences between ER+ and ER- dis-
ease are related to the different histopathologic characteris- Pam clustering over IR module in external ER- cohorts
Figure 5
Pam clustering over IR module in external ER- cohorts. Heatmap of gene
expression of seven-gene IR-module in ER- samples of the (a) UPP and (b)
JRH-2 cohorts. Shown are the clusters over-expressing (purple) and
under-expressing (yellow) the IR module, as predicted by the pam
algorithm. Good outcome samples are shown in gray, and poor outcome
samples in black. Green indicates relative under-expression, and red
indicates relative over-expression. (c) Kaplan-Meier survival curves over
combined external cohorts (for UPP end-point was disease-specific
survival, and for JRH-2 it was recurrence-free survival), with the number
of events and samples in each of the two predicted groups. ER, estrogen
receptor; pam, partitioning around medoids. Table 5 We believe that these differences between ER+ and ER- dis-
External validation of immune response prognostic module: distribution of poor and good outcome patients in over-and-under-
expressed subgroups
Gene
UPP
JRH-2
Combined
Poor
Good
P
Poor
Good
P
Poor
Good
P
IGLC2
High
0
12
0.04
0
7
0.09
0
19
0.003
Low
6
13
6
11
12
24
LY9
High
1
16
0.05
0
6
0.14
1
22
0.007
Low
5
9
6
12
11
21
TNFRSF17
High
1
16
0.05
0
10
0.02
1
26
0.001
Low
5
9
6
8
11
17
C1QA
High
0
12
0.04
0
9
0.04
0
21
0.001
Low
6
13
6
9
12
22 mmune response prognostic module: distribution of poor and good outcome patients in over-and-under- External validation of immune response prognostic module: distribution of poor and good outcome patie
expressed subgroups with clinical outcome [5,10,18,22], in ER- disease no such
prognostic signatures have thus far been reported. Moreover,
although in ER+ tumors subtypes of different prognostic
risks, the luminal A and B subtypes, have been defined
[21,22], no such subdivisions have been noted for ER- breast
cancer. It is known that the two main subtypes of ER- breast
cancer (ER-/HER2+ and basals) have worse prognosis com-
pared with the luminal A subtype, but no outcome differences
between the ER-/HER2+ and basal subtypes have been
observed [15,21-23,26]. confirmed by application of PAC, which showed that, with the
exception of XCL2, none of the other six genes were individu-
ally prognostic. In this context, it is worth noting once again the absence of
immune response related genes among the 29 PAC derived
prognostic genes in ER+ disease, which would suggest that a
good prognosis IR related subtype is absent in ER+ breast
cancer. To investigate this further we checked, by performing
Wilcoxon rank sum tests on the 5,007 genes, that the absence
of immune response GOs was not just an artefact of the small
number of genes picked out by PACK. Pam cluste
Figure 5 g
g
Pam clustering over IR module in external ER- cohorts. Heatmap of gene
expression of seven-gene IR-module in ER- samples of the (a) UPP and (b)
JRH-2 cohorts. Shown are the clusters over-expressing (purple) and
under-expressing (yellow) the IR module, as predicted by the pam
algorithm. Good outcome samples are shown in gray, and poor outcome
samples in black. Green indicates relative under-expression, and red
indicates relative over-expression. (c) Kaplan-Meier survival curves over
combined external cohorts (for UPP end-point was disease-specific
survival, and for JRH-2 it was recurrence-free survival), with the number
of events and samples in each of the two predicted groups. ER, estrogen
receptor; pam, partitioning around medoids. information Table 5 (a)
HLA−F
IGLC2
LY9
TNFRSF17
SPP1
XCL2
C1QA
(b)
HLA−F
IGLC2
LY9
TNFRSF17
SPP1
C1QA
0
2
4
6
8
10
0.0
0.2
0.4
0.6
0.8
1.0
(c)
0/20
12/35 (a)
HLA−F
IGLC2
LY9
TNFRSF17
SPP1
XCL2
C1QA
(b)
HLA−F
IGLC2
LY9
TNFRSF17
SPP1
C1QA
0
2
4
6
8
10
0.0
0.2
0.4
0.6
0.8
1.0
(c)
0/20
12/35 The prognostic value of the IR module is specific to ER-
tumours To confirm that the good prognosis conferred by activation of
the IR module is specific to ER- breast cancer, we applied the
same pam clustering algorithm over the seven genes to the
integrated dataset of 527 ER+ breast tumors. This gave two
clusters with unequal distributions of good and poor outcome
samples (209 good and 99 poor for the cluster under-express-
ing the genes versus 163 good and 47 poor for the cluster over-
expressing the genes; P = 0.02). Although this suggested to us
that over-expression of this seven-gene module also con-
ferred better prognosis in ER+ samples, the association was
much weaker than for ER- samples. Univariate Cox regression
with TTDM as the outcome variable confirmed that under-
expression of this seven-gene module conferred a much
greater risk for distant metastasis in ER- tumors (HR 2.02,
95% CI 1.2 to 3.4; P = 0.009) than in ER+ tumors (HR 1.25,
95% CI 0.9 to 1.7; P = 0.16; Table 4). It is also noteworthy that,
in contrast to the ER- case, in the multivariate model setting
for ER+ tumors, a low LI score and LN involvement were
stronger predictors of TTDM than the seven-gene module
(HR 1.65, 95% CI 0.4 to 7.1 for LI score and HR 1.48, 95% CI
0.7 to 3.2 for LN involvement, versus HR <1; Table 4). The
specificity of our prognostic module to ER- breast cancer was Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.11 http://genomebiology.com/2007/8/8/R157 Table 5 confirmed by application of PAC, which showed that, with the
with clinical outcome [5,10,18,22], in ER- disease no such
Table 5
External validation of immune response prognostic module: distribution of poor and good outcome patients in over-and-under-
expressed subgroups
Gene
UPP
JRH-2
Combined
Poor
Good
P
Poor
Good
P
Poor
Good
P
IGLC2
High
0
12
0.04
0
7
0.09
0
19
0.003
Low
6
13
6
11
12
24
LY9
High
1
16
0.05
0
6
0.14
1
22
0.007
Low
5
9
6
12
11
21
TNFRSF17
High
1
16
0.05
0
10
0.02
1
26
0.001
Low
5
9
6
8
11
17
C1QA
High
0
12
0.04
0
9
0.04
0
21
0.001
Low
6
13
6
9
12
22 confirmed by application of PAC, which showed that, with the
exception of XCL2, none of the other six genes were individu-
ally prognostic. In this context, it is worth noting once again the absence of
immune response related genes among the 29 PAC derived
prognostic genes in ER+ disease, which would suggest that a
good prognosis IR related subtype is absent in ER+ breast
cancer. To investigate this further we checked, by performing
Wilcoxon rank sum tests on the 5,007 genes, that the absence
of immune response GOs was not just an artefact of the small
number of genes picked out by PACK. In fact, GO analysis
with clinical outcome [5,10,18,22], in ER- disease no such
prognostic signatures have thus far been reported. Moreover,
although in ER+ tumors subtypes of different prognostic
risks, the luminal A and B subtypes, have been defined
[21,22], no such subdivisions have been noted for ER- breast
cancer. It is known that the two main subtypes of ER- breast
cancer (ER-/HER2+ and basals) have worse prognosis com-
pared with the luminal A subtype, but no outcome differences
between the ER-/HER2+ and basal subtypes have been
observed [15,21-23,26]. Discussion A striking difference between ER+ and ER- disease is emerg-
ing at the level of mRNA expression. Although in ER+ disease
a significant number of genes have been found that correlate Genome Biology 2007, 8:R157 R157.12 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 tics of the tumors. The prognostic signatures derived for ER+
breast cancer are characterized by genes related to cell cycle
and cell proliferation pathways, and are also highly correlated
with the histologic grade of the tumors [7,22]. It is not a
coincidence that most luminal B tumours are of high grade,
whereas the great majority of luminal A tumours are of low
grade [7,22]. It appears that there may be a whole plethora of
diverse oncogenic pathways that drive the over-activation of
cell cycle and cell growth pathways in poor prognosis tumors. This would explain the larger number of prognostic genes
found in ER+ disease (the great majority of which are related
to cell cycle ontologies) as well as the stronger prognostic sig-
nals (relatively large differences in log2 expression between
poor and good prognosis tumours), an effect that is probably
driven by oncogenic amplifications. This interpretation
would also fit in well with our finding that most bimodal pro-
files in ER+ breast cancer have positive kurtosis values,
because this could be a reflection of a more diverse range of
small amplifier subgroups in ER+ breast cancer. number of genes in the 98-gene IR cluster show expression
variability that is not explained by LI. This is confirmed fur-
ther by two recent studies that profiled breast cancer cell lines
[27,38], which showed that a considerable number of
immune response related genes do exhibit significant
variable expression across the basal cell subtype. Moreover,
we found that two (SPP1 and HLA-F) of the three IR module
genes that we could map to good quality probes in [27,38]
showed twofold changes across the eight basal cell lines. Thus, these findings together suggest that a significant pro-
portion of the expression of the IR module genes in the good
prognosis tumors is tumor-intrinsic in origin. Discussion That tumor-
intrinsic expression of IR genes can have an impact on prog-
nosis of breast cancer patients is plausible in view of recent
studies that show, for example, how amplification of kinase
oncogenes can activate the nuclear factor-κB pathway, and
hence immune response pathways, in both breast cancer cell
lines and patient derived breast tumors [41]. Similarly,
another recent study [42] used breast cancer cell lines to show
how BRCA1/IFN-γ pathways may regulate target genes
involved in innate immune response, providing another pos-
sible mechanism for tumor intrinsic IR gene expression
variability. In contrast, most ER- tumours are of high grade, which would
explain why any differences in clinical outcome within ER-
disease are not related to differential activation of cell cycle
pathways. Instead, the work presented here shows that differ-
ences in clinical outcome within ER- disease are mainly
related to differentially expressed genes in the complement
and immune response pathways, and that the association
with prognosis can be independent of lymphocytic infiltration
(LI) and LN status. In fact, for ER- tumors we observed that
even though there were proportionally more high LI samples
in the group over-expressing the IR module, these did not
necessarily have better prognosis. The fact that LI could not
explain the observed association of the IR module with out-
come was supported further by our finding that medullary
breast cancers, which are characterized by high LI scores, had
expression profiles most similar to the CC+/IR+ subtype
rather than the IR+ subtype, which had the best prognosis
overall. The better prognosis of the CC+/IR+ subtype relative
to CC+ and SR+ ER- breast cancer is therefore entirely
consistent with the CC+/IR+ subclass being medullary breast
cancers (MBCs), as MBC is known to have marginally better
prognosis than other basal tumors [38]. On the other hand,
the IR+ subclass, which had the best prognosis among the five
ER- subclasses, was only marginally associated with high LI
and was unrelated to MBC. Also consistent with these obser-
vations, it is important to note again the distinction between
the identified seven-gene prognostic IR module and the 98-
gene IR cluster that was derived from unsupervised hierarchi-
cal clustering. Clearly, we found a strong statistical associa-
tion between high LI and over-expression of the 98-gene IR
cluster. Discussion Specifically, there were 13 high LI and eight low LI
samples in the combined IR+ and CC+/IR+ clusters relative to
six high LI and 23 low LI samples in the rest of the cohort
(Fisher test P = 0.007). In contrast, the association between
high LI and over-expression of the IR module was much
weaker (P = 0.07). Again, this suggests that a significant In spite of identifying only a relatively small module of prog-
nostic genes, we were nevertheless able to validate their prog-
nostic potential in two external cohorts. It is likely that an
integrative analysis similar to the one used here but applied to
multiple cohorts that were all profiled on exactly the same
genome-wide platform would allow further expansion of this
module to include other members of the complement and
immune response pathways. Interestingly, from the seven
prognostic markers that composed the IR module, two have
already been associated with clinical outcome in breast can-
cer. Specifically, C1QA, which is a gene involved in the classi-
cal complement pathway, was recently shown to harbor a
single nucleotide polymorphism that correlated with distant
metastasis in breast cancer [43]. Two recent studies also
implicated SPP1 (osteopontin) in metastatic breast cancer
[44,45]. It is important also to note that the robustness of the identi-
fied prognostic markers is a consequence of the PACK meth-
odology. Despite being a conservative procedure that filters
out many true positives, PACK allows, by efficient removal of
false positives, a more reliable identification of prognostic
markers. We tested this further by applying two popular sta-
tistical tools, singular value decomposition (SVD) [46] and
the shrunken centroids classifier (PAMR) [47], to the inte-
grated ER- dataset to determine whether we could derive a
similar if not identical prognostic IR module. Using SVD we
found that none of the inferred SVD components showed a
correlation with prognosis (Wilcoxon rank sum test P > 0.05),
whereas at a FDR threshold of 0.3 PAMR yielded 21 prognos-
tic genes, of which only two (the IR module member Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.13 http://genomebiology.com/2007/8/8/R157 TNFRSF17 and KLRD1) had immune response related func-
tions. PACK: profile analysis using clustering and kurtosis PACK: profile analysis using clustering and kurtosis
The hypothesis underlying PACK [17] is that genes that are
true biologic or clinical markers have expression profiles that
are generated by a mixture of two or more underlying distri-
butions, whereas spurious features are more likely to have
profiles generated by a single distribution. The biologic valid-
ity of this assumption was proved through a FDR analysis
[17]. PACK can be viewed as a semi-supervised algorithm, consist-
ing of two main steps: a feature selection criterion and a
supervised step, in which the selected features are correlated
to a phenotype (Figure 2). It is important to note that PACK is
a flexible modular algorithm in that the feature selection step
can be applied on its own. In this case, there are two possible
versions of the algorithm: PAC and PAK. The precise way in
which these two algorithms are used in PACK will depend on
the purpose of the exercise. Below, we describe the PACK
strategy implemented in this paper, which is slightly different
from that applied previously [17]. Besides identifying a module of genes that is prognostic in
over 240 ER- breast tumors, PACK also provided us with a
novel subclassification of ER- breast cancer. Specifically, clus-
tering over PACK selected genes identified five different sub-
types (CC+, CC+/IR+, IR+, ECM+, and SR+) characterized by
the over-expression patterns of four distinct gene clusters,
each enriched for IR, ECM, CC, and SR genes, respectively. Moreover, we related these subtypes to the gene expression
based intrinsic subclasses. This showed that the basal sub-
group was a heterogeneous group with at least four distinct
subtypes (CC+, CC+/IR+, ECM+, and IR+), whereas the ER-/
HER2+ subgroup showed strong overlap with the SR+ and IR+
subtypes. Conclusion
hil i
b While in ER+ breast cancer prognostic markers are associated
mainly with cell cycle pathways, in ER- disease prognostic
markers are associated with immune response pathways. In
particular, we have identified a subclass of ER- tumors that
over-express immune response genes and that has a good
prognosis compared with the rest of ER- breast tumors, inde-
pendently of LN status or LI. Furthermore, we have identified
an associated module of complement and immune response
genes that define prognostic markers valid in over 240 ER-
samples. where X is any random variable and E denotes the expecta-
tion. For a gaussian
, so that
K(X) = 0. Most nongaussian distributions necessarily have
either K > 0, in which case they are called supergaussian or
leptokurtic, or K < 0, in which case they are called subgaus-
sian or platykurtic. Specifically, a mixture of two approxi-
mately equal mass gaussians must have negative kurtosis
because the two modes on either side of the center of mass
effectively flatten out the distribution. To see this, consider a
gene whose expression profile is described by a mixture of
two gaussians. Then, the kurtosis, K, is a function of two
parameters (we assume for simplicity that the gaussians are
of equal variance σ2, although this assumption is not needed
for the result below); the effect size of the gene, as defined by
the effective separation e between the two gaussians (e = μ/σ,
where μ is the separation), and the ratio of cluster weights (π1,
E X
X
E X
X
[(
) ]
[(
) ]
−
=
−
4
2 2
3 where X is any random variable and E denotes the expecta- where X is any random variable and E denotes the expecta-
tion. For a gaussian
, so that
K(X) = 0. Most nongaussian distributions necessarily have
either K > 0, in which case they are called supergaussian or
leptokurtic, or K < 0, in which case they are called subgaus-
sian or platykurtic. Specifically, a mixture of two approxi-
mately equal mass gaussians must have negative kurtosis
because the two modes on either side of the center of mass
effectively flatten out the distribution. To see this, consider a
gene whose expression profile is described by a mixture of
two gaussians. Feature selection with PAK: using negative kurtosis to
find genes defining major subclasses Kurtosis is related to the fourth central moment and can con-
veniently be defined as follows [49]: K X
(
)
[(
) ]
[(
) ]
≡
−
−
−
E X
X
E X
X
4
2 2
3
(1) (1) Conclusion
hil i
b Then, the kurtosis, K, is a function of two
parameters (we assume for simplicity that the gaussians are
of equal variance σ2, although this assumption is not needed
for the result below); the effect size of the gene, as defined by
the effective separation e between the two gaussians (e = μ/σ,
where μ is the separation), and the ratio of cluster weights (π1,
E X
X
E X
X
[(
) ]
[(
) ]
−
=
−
4
2 2
3 Discussion Thus, in agreement with findings presented previously
[17], this reinforces the advantage of PACK over other pattern
recognition tools and supervised methods that do not use
pattern recognition steps, such as for example those based on
t-tests. TNFRSF17 and KLRD1) had immune response related func-
tions. Thus, in agreement with findings presented previously
[17], this reinforces the advantage of PACK over other pattern
recognition tools and supervised methods that do not use
pattern recognition steps, such as for example those based on
t-tests. ther normalized, if necessary, by transforming them onto a
common log2 scale and shifting the median of each array to
zero. We also created an automated computational pipeline
(Perl scripts on a Linux platform) to crosslink the annotation
provided for each dataset with UniGene. For some datasets,
the linkage relied on Ensembl [48] external database identifi-
ers. Thus each probe was associated with a universal gene
name. This procedure generated a nonredundant set of gene
identifiers for the subsequent integrative analysis. The absence of a prognostic IR module in ER+ breast cancer
is intriguing. The seven-gene IR module was only marginally
associated with prognosis in ER+ disease, and importantly
this association was not independent of LI or LN status. Repeating the same unsupervised analysis (PAK) and semi-
supervised analysis (PACK) in ER+ breast cancer also did not
find a prognostic immune response module. By using a tradi-
tional supervised method, a prognostic IR module was iden-
tifiable but failed to validate in the two external cohorts. Thus,
to determine fully whether such a robust prognostic IR mod-
ule exists for ER+ breast cancer, it may be necessary to con-
duct larger integrative studies that use the same microarray
platform so that the analysis can be performed over a larger
set of common genes. Software packages used where
and σ are the mean and standard deviation esti-
mates of the profile. A standard error estimate of K was
obtained by performing 10,000 random simulations, with n =
186 (number of ER- samples), which showed that the stand-
ard error estimate, 0.36, was essentially identical to the theo-
retical estimate, √(24/n) [50]. x All analyses were performed using the R statistical program-
ming language [55]. The following add-on packages were
used: vabayelMix for the PACK implementation, survival for
the Cox regression models, qvalue for FDR estimation, and
cluster for the partitioning around medoids (pam) clustering
algorithm. Two notes with the feature selection step are in order. First,
the kurtosis threshold used to select features depends on how
large the smallest subgroup must be. Generally, given the
effective separation values that are typical for differential
gene expression, we find that a zero kurtosis threshold (as
used in this report) generally picks out subgroups within the
individual gene expression profiles that are at least as large as
30% of the total sample size [17]. Second, in principle, genes
defining major subclasses could be found using a clustering
step to infer two clusters (PAC) and setting a lower bound
threshold (for instance, 30%) on the size of the smallest clus-
ter. However, this approach is computationally more expen-
sive, because PAC attempts to estimate the optimal number of
clusters in the profile. However, this model selection step is a
necessary one to ensure that profiles for which there is no
objective evidence of bimodality are excluded (see below). Datasets and gene annotation One possibility is to use the EM algorithm to
learn the parameters for the two different models C = 1 and C
= 2, and perform model selection using the Bayesian Infor-
mation Criterion (BIC) score [51,52]. Alternatively, the opti-
mal number of clusters, C, can be inferred using a lower
bound on the model evidence, as provided by a variational
Bayesian (VB) approach [39,53,54]. The results we report
here were obtained using the VB algorithm for model selec-
tion. Thus, genes for which C = 1 were excluded from further
analysis. Finally, association with the phenotype (here prog-
nosis) was determined using Fisher's exact test to test
whether poor outcome events were unevenly distributed
across the two clusters. (2) where a and b are the quadratic roots 2 ± √3. Thus, for e ≠ 0,
the kurtosis is negative if and only if (2 - √3) < R < (2 + √3). This in turn requires the smallest cluster weight, πmin, to be in
the range (approximately) of 0.22 <πmin < 0.5. It follows that
for the case of approximately equal weights, where R ≅ 1 (πmin
≅ 0.5), the kurtosis is always negative and in the limit of large
cluster separations (when e >> 1) the kurtosis decreases
monotonically, asymptotically approaching the lower bound -
2. Thus, kurtosis provides a useful measure for ranking genes
based on how platykurtic their profiles are. Given a gene's expression profile x = (x1, ..., xn), an unbiased
estimate for the kurtosis [50] is as follows: K x
n n
x
x
n
n
n
n
n
n
i
i
n
( )
(
)
(
)
(
)(
)(
)
(
)
(
)(
)
+
−
−
−
−
−
−
−
−
=
∑
1
1
2
3
3
1
2
3
4
1
4
2
σ
(3) (3) The SSP classifier The classification of the samples in the NKI2, EMC, and NCH
cohorts into the intrinsic subtypes was performed using the
single sample predictor (SSP) [23] and was done for each
cohort separately because this guaranteed a larger number of
overlapping genes. In the SSP, samples were assigned the
intrinsic subtype for which the corresponding Spearman rank
correlation between the sample and SSP centroid was maxi-
mal [23]. The ER- subclass centroids From the hierarchical clustering with Pearson correlation
metric and complete linkage diagram (Figure 3a) we con-
structed mean centroids for each of the five subclasses. Clas-
sification of external samples to these centroids was
performed using the nearest centroid criterion. Because these
centroids were defined over ER- samples only, external sam-
ples (which may not be ER-) may not show strong correlation
to any of these centroids. We thus validated, through 10,000
Monte Carlo (MC) randomisations, that samples with a max-
imal pearson coefficient larger than 0.25 were significantly
correlated with the corresponding centroid (P < 0.0001). Samples with maximal correlation coefficients smaller than
0.25 were deemed to be unclassifiable. Datasets and gene annotation The microarray breast cancer datasets considered in this
work are described elsewhere [5,7,9,18,19]. For these cohorts
we used the normalized data, which are available in the public
domain (see [5,7,9,18,19]). The retrieved datasets were fur- Genome Biology 2007, 8:R157 sue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 R157.14 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 π2), that is R = π1/(1 - π1). Specifically, a short computation
reveals that R = π1/(1 - π1). Specifically, a short computation p x
G x
i
k
i
k
k
k
CM
(
| )
(
|
,
)
θ
π
μ
σ
=
=∑
1
(4) (4) K e R
e
R R
a
R
b
R
R
R
e
( ,
)
(
)(
)
(
) (
(
)
)
=
−
−
+
+
+
4
4
2
2 2
1
1
1
(2) Where πk are the weights of the components, (μk, σk) are the
mean and standard deviation of the univariate gaussian k,
and θ denotes the set of all parameters. In the above, CM
denotes the maximum number of clusters that can be
inferred, which in our application we set to 2. The optimal
number of clusters, C, can be inferred using one of various
approaches. One possibility is to use the EM algorithm to
learn the parameters for the two different models C = 1 and C
= 2, and perform model selection using the Bayesian Infor-
mation Criterion (BIC) score [51,52]. Alternatively, the opti-
mal number of clusters, C, can be inferred using a lower
bound on the model evidence, as provided by a variational
Bayesian (VB) approach [39,53,54]. The results we report
here were obtained using the VB algorithm for model selec-
tion. Thus, genes for which C = 1 were excluded from further
analysis. Finally, association with the phenotype (here prog-
nosis) was determined using Fisher's exact test to test
whether poor outcome events were unevenly distributed
across the two clusters. Where πk are the weights of the components, (μk, σk) are the
mean and standard deviation of the univariate gaussian k,
and θ denotes the set of all parameters. In the above, CM
denotes the maximum number of clusters that can be
inferred, which in our application we set to 2. The optimal
number of clusters, C, can be inferred using one of various
approaches. Additional data files The following additional data are available with the online
version of this manuscript. Additional data file 1 is a table
showing the 813 genes with negative kurtosis expression
profiles over 186 ER- tumors, together with the predicted
number of clusters and Fisher's test P value with outcome as
binary phenotype. Additional data file 2 is a table showing the
193 genes with negative kurtosis expression profiles over 527
ER+ samples, together with the predicted number of clusters
and Fisher's test P value with outcome as binary phenotype. Additional data file 3 is a figure showing hierarchical cluster-
ing over 186 ER- breast cancers (gene annotated version). Additional data file 4 is a figure showing the distribution of
basal and ERBB2 markers among ER- subtypes. Additional
data file 5 is a table showing the centroids of gene expression
for each of the five identified ER- subtypes. Additional data
file 6 is a figure showing expression profiles of immune
response module genes in ER- samples of the external UPP
cohort. Additional data file 7 is a figure showing expression
profiles of immune response module genes in ER- samples of
the external JRH-2 cohort. Additional data file 8 is a figure
showing the clustering of ER+ samples over the humoral
immune response gene module in the two external UPP and
JRH-2 cohorts. Additional data files Additi
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fil 10. Additional data files 10. Teschendorff AE, Naderi A, Barbosa-Morais NL, Pinder SE, Ellis IO,
Aparicio S, Brenton JD, Caldas C: A consensus prognostic gene
expression classifier for ER positive breast cancer. Genome
Biol 2006, 7:R101. 11. van de Rijn M, Perou CM, Tibshirani R, Haas P, Kallioniemi O,
Kononen J, Torhorst J, Sauter G, Zuber M, Kochli OR, et al.: Expres-
sion of cytokeratins 17 and 5 identifies a group of breast car-
cinomas with poor clinical outcome. Am J Pathol 2002,
161:1991-1996. 12. Malzahn K, Mitze M, Thoenes M, Moll R: Biological and prognostic
significance of stratified epithelial cytokeratins in infiltrating
ductal breast carcinomas. Virchows Arch 1998, 433:119-129. 13. Rakha EA, El-Rehim DA, Paish C, Green AR, Lee AH, Robertson JF,
Blamey RW, Macmillan D, Ellis IO: Basal phenotype identifies a
poor prognostic subgroup of breast cancer of clinical
importance. Eur J Cancer 2006, 42:3149-3156. p
J
14. Rakha EA, El-Sayed ME, Green AR, Lee AH, Robertson JF, Ellis IO:
Prognostic markers in triple-negative breast cancer. Cancer
2007, 109:25-32. 15. Jumppanen M, Gruvberger-Saal S, Kauraniemi P, Tanner M, Bendahl
PO, Lundin M, Krogh M, Kataja P, Borg A, Ferno M, et al.: Basal-like
phenotype is not associated with patient survival in estro-
gen-receptor-negative breast cancers. Breast Cancer Res 2007,
9:R16. 16. Eden P, Ritz C, Rose C, Ferno M, Peterson C: 'Good Old' clinical
markers have similar power in breast cancer prognosis as
microarray gene expression profilers. Eur J Cancer 2004,
40:1837-1841. 17. Teschendorff AE, Naderi A, Barbosa-Morais NL, Caldas C: PACK:
Profile Analysis using Clustering and Kurtosis to find molec-
ular classifiers in cancer. Bioinformatics 2006, 22:2269-2275. 18. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW,
Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al.: A gene-
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p
y
6. Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Hol-
mberg L, Huang F, Klaar S, et al.: Gene expression profiling spares
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and validated in two population-based cohorts. Breast Cancer
Res 2005, 7:R953-R964. For the samples from our NCH cohort [9] we used the follow-
ing scoring method. Lymphocytic infiltration (LI) was
assessed in whole tumour sections from frozen sections
stained with hematoxylin and eosin. The intensity of lym-
phocytic infiltrate was first graded semi-quantitatively as
minimal or mild (1), moderate (2), and marked (3). The LI
scores were then dichotomized (we considered mild and
moderate as low LI and marked as high LI) to make them
comparable with the binary LI scores used by van 't Veer and
coworkers [3]. 7. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H,
Farmer P, Praz V, Haibe-Kains B, et al.: Gene expression profiling
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Cufer T, Sieuwerts AM, Talantov D, Span PN, et al.: Multicenter val-
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24:1665-1671. 9. Naderi A, Teschendorff AE, Barbosa-Morais NL, Pinder SE, Green
AR, Powe DG, Robertson JF, Aparicio S, Ellis IO, Brenton JD, et al.: A
gene-expression signature to predict survival in breast can-
cer across
independent
data
sets. Oncogene
2007,
26:1507-1516. References The basal marker used in Figure 3 was derived by first map-
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[27] onto the integrated data set of 5,007 genes. For each of
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expression or 'basalness'. For each sample in the integrated
cohort an average rank was then computed over the ten basal
markers. The average ranks were then rescaled onto the unit
interval (0,1), with '1' indicating highest expression for basal
markers. The marker for the ERBB2 subtype was obtained in
an analogous manner using three genes in the ERBB2 ampli-
con (ERBB2, GRB7, and STARD3). 1. Brenton JD, Carey LA, Ahmed AA, Caldas C: Molecular classifica-
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g
Having selected the genes defining the largest subclasses, we
next apply PAC to each of these genes to remove those for
which there is no evidence of bimodality (gaussian profiles
that spuriously have negative kurtosis values). Specifically,
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https://openalex.org/W3153210820 | https://ir.lib.hiroshima-u.ac.jp/52804/files/4185 | Japanese | null | Carnosic Acid and Carnosol Activate AMPK, Suppress Expressions of Gluconeogenic and Lipogenic Genes, and Inhibit Proliferation of HepG2 Cells | International journal of molecular sciences | 2,021 | cc-by | 210 | 【背景】 【背景】 ローズマリーは古くから香辛料や薬草として使用されており、解毒作用や抗酸化作用、血行改
善作用、炎症抑制作用など多くの効能を有し、糖尿病や脂肪肝などを含む様々な代謝疾患に対す
る治療的側面を有している可能性があり注目されている。 ローズマリーは古くから香辛料や薬草として使用されており、解毒作用や抗酸化作用、血行改
善作用、炎症抑制作用など多くの効能を有し、糖尿病や脂肪肝などを含む様々な代謝疾患に対す
る治療的側面を有している可能性があり注目されている。 これまでにローズマリー抽出物の成分であるcarnosic acid (CA)、carnosol (CL)、rosmarinic
acid (RA) の代謝改善作用に関して、特に骨格筋でAMPK を介して問う取り込みを亢進させる
ことが報告されている (Clin Exp Pharmacol Physiol. 2016, Int J Mol Sci. 2018, Molecules. 2017)。一方で、その肝臓における作用に関しては、マウスを用いた実験で脂肪肝改善作用が複
数報告されているものの、その機序についてはCA がPPARγ発現低下を介して肝脂肪蓄積を抑
制するがAMPK に依らずEGFR/MAPK 依存的である (J Gastroenterol. 2012) という報告も
あり、AMPK の寄与については不明な点が多い。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化
を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には
AMPK を介する機序についての報告はほとんどない。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化
を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には
AMPK を介する機序についての報告はほとんどない。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化
を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には
AMPK を介する機序についての報告はほとんどない。 これらのことから私はHepG2 細胞を用いてCA、CL のAMPK を介した培養肝細胞での糖代
謝や脂質代謝、細胞増殖に対する影響について検討を行った。 これらのことから私はHepG2 細胞を用いてCA、CL のAMPK を介した培養肝細胞での糖代
謝や脂質代謝、細胞増殖に対する影響について検討を行った。 【方法
結果】
はじめにローズマリー抽出物 (RM-21B base) のAMPK 活性化をC2C12 細胞 (myotube) で
確認したところ、濃度依存的にAMPK の活性化がみられた。またローズマリー抽出物に含まれ
る主要な構成成分であるCA、CL、RA についてAMPK の活性化を評価したところ、CA、CL
でのみ濃度依存的にAMPK の活性化がみられた。そこで以降の実験では、CA、CL 共にAMPK
が活性化した最低濃度 (10 µM) を用いて実験を行った。 我々は以前にAMPK 活性化が糖新生抑制に働くことを報告している (Horike N, et al. J Biol
Chem. 2008) が、CA、CL 添加によりForskolin 刺激時の糖新生律速酵素遺伝子 (Pck1、G6pc)
の誘導が抑制され、ルシフェラーゼアッセイでの検討においてもPck1 promoter 活性の抑制が
認められ、CA、CL は糖新生を抑制することが示唆された。 我々は以前にAMPK 活性化が糖新生抑制に働くことを報告している (Horike N, et al. J Biol
Chem. 2008) が、CA、CL 添加によりForskolin 刺激時の糖新生律速酵素遺伝子 (Pck1、G6pc)
の誘導が抑制され、ルシフェラーゼアッセイでの検討においてもPck1 promoter 活性の抑制が
認められ、CA、CL は糖新生を抑制することが示唆された。 次に脂肪酸合成や脂肪酸酸化に及ぼす影響について評価を行った。肝がん細胞株HepG2 をCA、
CL とともに24h incubation し脂肪酸合成及び脂肪酸酸化に関わる遺伝子発現量を検討したと
ころ、CA、CL の添加によって脂肪酸合成に働くFAS、ACC1、SREBP-1c の発現量は減少し、
一方で脂肪酸酸化に働くCPT1a の発現量は増加傾向を示し、AMPK 阻害剤Compound C の添
加によってcancel された。以上からCA、CL は脂肪酸酸化を亢進し脂肪酸合成を抑制するので
はないかと示唆された。 次に脂肪酸合成や脂肪酸酸化に及ぼす影響について評価を行った。肝がん細胞株HepG2 をCA、
CL とともに24h incubation し脂肪酸合成及び脂肪酸酸化に関わる遺伝子発現量を検討したと
ころ、CA、CL の添加によって脂肪酸合成に働くFAS、ACC1、SREBP-1c の発現量は減少し、
一方で脂肪酸酸化に働くCPT1a の発現量は増加傾向を示し、AMPK 阻害剤Compound C の添
加によってcancel された。以上からCA、CL は脂肪酸酸化を亢進し脂肪酸合成を抑制するので
はないかと示唆された。 さらにCA、CL の細胞増殖への影響についてHepG2 を用いて検討した。MTT assay での添加
24h 後の細胞の生存率は、CA、CL 投与群では低下し、Compound C の添加により回復した。
またCA、CL 添加によりAMPK 依存的なp53 リン酸化の亢進及びmTORC1 活性の低下が認め
られ、CA ではcleaved caspase-3 の発現増加も見られapoptosis 亢進も示唆された。以上から CA、CL はAMPK 依存的にp53 を活性化、mTORC1 活性を抑制することで、細胞増殖抑制に
働く可能性が示唆された。 働く可能性が示唆された。 【結論】 ローズマリー抽出物の成分であるcarnosic acid、carnosol は糖新生抑制、脂肪酸合成抑制、脂
肪酸酸化亢進作用ならびに細胞増殖抑制作用を呈し、少なくともその機序の一部はAMPK 依存
的であると示唆された。 |
https://openalex.org/W3172015668 | https://www.mdpi.com/2076-2615/11/6/1645/pdf?version=1623207553 | English | null | Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias | Animals | 2,021 | cc-by | 11,731 | Citation: Romito, G.; Guglielmini, C.;
Poser, H.; Baron Toaldo, M. Lorenz
Plot Analysis in Dogs with Sinus
Rhythm and Tachyarrhythmias.
Animals 2021, 11, 1645. https://
doi.org/10.3390/ani11061645 animals animals animals Keywords: electrocardiography; Holter; Poincaré plot; heart rate variability; canine Lorenz Plot Analysis in Dogs with Sinus Rhythm
and Tachyarrhythmias
Citation: Romito, G.; Guglielmini, C.;
Poser, H.; Baron Toaldo, M. Lorenz
Plot Analysis in Dogs with Sinus
Rhythm and Tachyarrhythmias. Animals 2021, 11, 1645. https://
doi.org/10.3390/ani11061645
Academic Editors: Paola
Giuseppina Brambilla and
Chiara Locatelli
Received: 28 April 2021
Accepted: 28 May 2021
Published: 1 June 2021
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil- animals animals Lorenz Plot Analysis in Dogs with Sinus Rhythm
and Tachyarrhythmias Giovanni Romito 1
, Carlo Guglielmini 2,*
, Helen Poser 2
and Marco Baron Toaldo 1,† Giovanni Romito 1
, Carlo Guglielmini 2,*
, Helen Poser 2
and Marco Baron Toaldo 1,† Giovanni Romito 1 1
Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna,
40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.) 1
Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna,
40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.)
2
Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, Italy;
helen.poser@unipd.it 1
Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna,
40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.)
2
Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, Italy;
helen.poser@unipd.it g
y g
2
Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, It
helen.poser@unipd.it *
Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505 *
Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505
†
Current address: Department for Small Animals, Division of Cardiology, Clinic for Small Animal Internal
Medicine, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland. Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505
†
Current address: Department for Small Animals, Division of Cardiology, Clinic for Small Animal Internal
Medicine, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland. Simple Summary: The Lorenz plot (LP) is a geometrical method to assess the dynamics of heart rate
variability. It consists of a two-dimensional Cartesian coordinate system derived from electrocar-
diographic monitoring, in which each recorded R-R interval is plotted as a function of the previous
R-R interval, and the values of each pair of successive R-R interval define a dot in the plot. The
resultant clusters of dots can be evaluated quantitatively and qualitatively, and categorized into
distinct geometrical patterns. In humans, several studies have demonstrated that the analysis of LP
patterns (LPPs) has the potential to speed-up and improve the accuracy of arrhythmia detection and
differentiation, especially in patients with tachyarrhythmias. As data on LP analysis are limited in
dogs, this study describes the graphic features of LP derived from Holter recordings obtained in
dogs with sinus rhythm and tachyarrhythmias, and analyzes the usefulness of LPP recognition in
this species. We sought to evaluate if distinct cardiac rhythms imprint distinct and reproducible LPPs
in dogs, as previously described in humans, and if each LLP can be used as a sensitive and specific
indicator of a particular cardiac rhythm in this species. 1. Introduction A variety of Holter software algorithms have emerged in the last decades to speed-
up rhythm analysis and simplify the interpretation of complex cardiac rhythms. Lorenz
plots (LP), also known as Poincaré plots or scatterplots, provide visual representation of
oscillations in the period between consecutive heartbeats, by plotting each R-R interval
against the next one in a two-dimensional Cartesian coordinate system and depicting it as
a dot. In this way, recorded beats are organized into clusters of dots with particular shapes,
sizes, and positions according to the R-R interval fluctuations and the underlying cardiac
rhythm [1,2]. In humans, analysis of such clusters in patients with sinus rhythm (SR) and
tachyarrhythmias has allowed for the identification of 10 distinct LP patterns, each one
having its own specific graphic characteristics, nomenclature, and excellent diagnostic
accuracy for rhythm diagnosis [2]. Therefore, LPs could represent an attractive diagnostic
tool in veterinary cardiology as well. Regrettably, only a few studies have described the
graphic features of LP in dogs with and without arrhythmias [3–7], and the only study
aimed at characterizing the LP patterns in arrhythmic dogs evaluated LPs generated from
1-h Holter recordings [6]. Therefore, the purposes of this study are threefold: (1) to evaluate the graphic charac-
teristics of LPs derived from long-term Holter analysis obtained from dogs with SR and
tachyarrhythmias; (2) to assess the reproducibility of LP pattern classification; and (3) to de-
termine the diagnostic performance of LP patterns in identifying different cardiac rhythms. We hypothesized that distinct cardiac rhythms would imprint distinct and recognizable LP
patterns in dogs. 2. Materials and Methods
2.1. Study Population Holter recordings from all dogs that underwent a Holter analysis as part of the di-
agnostic evaluation at the veterinary teaching hospitals of the University of Bologna and
Padova between June 2006 and January 2019 were retrospectively reviewed. Holter record-
ings belonged to dogs with cardiac and/or extra-cardiac disorders associated with rhythm
irregularities detected during cardiac auscultation and/or surface electrocardiogram, or to
clinically healthy dogs of predisposed canine breeds (e.g., Doberman Pinschers) screened
for dilated cardiomyopathy. Inclusion was restricted to good quality Holter recordings
with ≥20 h of valid data and a Holter diagnosis of SR or tachyarrhythmias, either supraven-
tricular or ventricular. For the purpose of this study, Holter recordings obtained from dogs
with atrial fibrillation (AF) were included only if this tachyarrhythmia was observed for
the entire duration of the monitoring. Recordings showing advanced or complete atrioven-
tricular blocks, and those consistent with sick sinus syndrome, were excluded. Information
regarding signalment, underlying cardiac or extracardiac disorders, and ongoing cardiac
treatment at the time of Holter recording were obtained from medical records.
Abstract: The Lorenz plot (LP), a graphical representation of heart rate variability, has been poorly
studied in dogs to date. The present study aimed to describe the graphic features of LP in dogs with
sinus rhythm (SR) and tachyarrhythmias, and to analyze the usefulness of its pattern recognition. One hundred and nineteen canine Holter recordings were retrospectively evaluated. Cardiac rhythms
were classified as: SR; SR with frequent (>100) premature ectopies (atrial, SR-APCs; ventricular,
SR-VPCs; atrial and ventricular, SR-APCs-VPCs); atrial fibrillation (AF); and AF with frequent VPCs
(AF-VPCs). Lorenz plots were studied qualitatively and quantitatively, and classified by distinct LP
patterns (LPPs). Repeatability and reproducibility of LPP classification and diagnostic value were
determined. Recordings included: 48 SR, 9 SR-APCs, 35 SR-VPCs, 5 SR-APCs-VPCs, 4 AF, and 18 AF-
VPCs. Ten LPPs were identified: comet (n = 12), torpedo (n = 3), Y-shaped (n = 6), diamond (n = 10),
diamond with a central silent zone (n = 17), double side-lobe (DSL) (n = 47), triple side-lobe (n = 1),
quadruple side-lobe (n = 2), fan (n = 18), and fan with DSL (n = 3). Repeatability and reproducibility
of LPP classification were excellent. The DSL pattern was both highly sensitive (91.3%) and specific
(94.5%) for SR with frequent premature ectopies, either APCs, or VPCs, or both. The remaining LPPs
had lower diagnostic value (high specificity but low sensitivity). Distinct rhythms imprint distinct
and reproducible LPPs in dogs. The majority of canine LPPs are specific but insensitive indicators of
SR and tachyarrhythmias. Academic Editors: Paola
Giuseppina Brambilla and
Chiara Locatelli Received: 28 April 2021
Accepted: 28 May 2021
Published: 1 June 2021 Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
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iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
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and
conditions of the Creative Commons
Attribution (CC BY) license (https:// Keywords: electrocardiography; Holter; Poincaré plot; heart rate variability; canine creativecommons.org/licenses/by/ Animals 2021, 11, 1645. https://doi.org/10.3390/ani11061645 https://www.mdpi.com/journal/animals 2 of 13 Animals 2021, 11, 1645 2.2. Holter Monitoring and Rhythm Analysis Holter recordings were obtained at the two centers using the same standardized
technique [8] and analyzed using a commercially available software program designed
for humans (Cube Holter software, Cardioline S.p.A.). The monitoring was conducted in
the dog’s home environment during their daily routines, and the owners were instructed
to note all activities in a diary. Holter data were acquired with a resolution of 10-bit and
at a sampling frequency of 250 Hz and were then transferred to a computer for analysis. A standard protocol for semiautomatic arrhythmia analysis was performed as previously
described [9–11]. Initially, a single board-certified cardiologist (GR) manually checked
the entire recording to assess its quality, ensure that the software triggered correctly on
every complex, and label possible unidentified complexes. Based on R-R intervals, the
software automatically calculated minimum, mean, and maximal heart rates. Subsequently,
events marked by the software were manually checked by the same operator to confirm
correct classification. The software distinguished QRS complex of sinus and supraventric- Animals 2021, 11, 1645 3 of 13 3 of 13 ular origin (N) from wide QRS complexes (‘atypical’). The software defined more than
3 successive N at a heart rate <60 beats per minute as bradycardia, and N-N intervals
>2 s as sinus pauses. The software also noted events with an NN interval at least 80%
shorter than the previous N-N interval. These events were manually differentiated into
atrial premature complexes ([APCs], i.e., abnormal P waves conducting normal-appearing
QRS complexes [12,13]) and premature normal complexes (i.e., premature sinus complexes
during sinus arrhythmia; the latter was defined as a regularly irregular SR, which is charac-
terized by cyclic variations of the R-R intervals and is associated with a rate appropriate for
temperament and level of activity of the dog [9–11]). Atypical complexes were manually
checked to confirm if they were ectopic complexes of ventricular origin (i.e., wide and
abnormal looking QRS not associated with sinus P waves [12,13]). The software defined
atypical complexes with a coupling interval at least 5% shorter than the previous N-N
interval as ventricular premature complexes (VPCs). For the purposes of this study, only
the number of APCs and VPCs, and not their organization into atrial and ventricular
allorhythmias, was considered. 2.2. Holter Monitoring and Rhythm Analysis Presence of AF entirely relied on manual analysis and was
based on standard criteria (i.e., replacement of isoelectric baseline and sinus P waves by
sequential less-defined deflections varying in amplitude, morphology and cycle length, as-
sociated with normal-appearing QRS complexes, and irregular ventricular rhythm [12,13]). In light of arrhythmias analysis, the same operator made a final rhythm diagnosis for
each recording. g
For statistical analysis, given the wide range of electrocardiographic abnormali-
ties identified on Holter recordings, cardiac rhythms were arbitrarily divided into the
following classes: (1) SR: SR (with/without phases of SR arrhythmia) as dominant
rhythm throughout the recording, including both pure SR and SR associated with in-
frequent (<100/Holter [14,15]) APCs or VPCs; (2) SR-APCs: SR associated with frequent
(>100/Holter) APCs, both isolated and organized into atrial allorhythmias; (3) SR-VPCs:
SR associated with frequent VPCs (>100/Holter), both isolated and organized into ven-
tricular allorhythmias; (4) SR-APCs-VPCs: SR associated with frequent APCs and VPCs
(in both cases, >100/Holter), both isolated and organized into atrial and/or ventricular
allorhythmias; (5) AF: AF as dominant rhythm throughout the recording, including both
pure AF and AF associated with infrequent VPCs (<100/Holter); and (6) AF-VPCs: AF
associated with frequent VPCs (>100/Holter), both isolated and organized into ventricular
allorhythmias. In Holter recordings from the last class, particular attention was paid to
manually differentiate true VPCs from QRS-complex changes related to rate-dependent
aberrancy due to the Ashman phenomenon. Such differentiation was primarily based
on the following electrocardiographic criteria: (1) the coupling interval of the wide QRS
complex with the previous beat (true VPCs typically have a fixed coupling interval, while
the Ashman phenomenon systematically results from a long R-R/short R-R sequence);
(2) the presence or absence of a pause after the wide QRS complex (true VPCs are typically
followed by a post-extrasystolic pause, whereas such pause is not expected in the case of
the Ashman phenomenon); (3) the morphology of the wide QRS complex (the morphology
of true VPCs can vary over the same recording due to the occurrence of VPCs arising
from different ectopic foci, whereas the QRS-configuration tends to be stable in the case
of Ashman phenomenon); and (4) the tendency of the wide QRS complex beats to form
groups (VPCs tend to organize in couplets, triplets, or bigeminy, whereas such type of
organization is atypical for the Ashman phenomenon) [16]. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti Once the aforementioned steps were completed, the arrhythmia filter was disabled,
and the complete population of recorded complexes was used to create LPs from the entire
time of recording. On LPs, each R-R interval (R-Rn, dots depicted on the X-axis) was plotted
against the following one (R-Rn + 1, dots depicted on the Y-axis), so that the coordinates of
each dot were: R-R, R-R + 1 (Figure 1). Once the aforementioned steps were completed, the arrhythmia filter was disabled,
and the complete population of recorded complexes was used to create LPs from the entire
time of recording. On LPs, each R-R interval (R-Rn, dots depicted on the X-axis) was plot-
ted against the following one (R-Rn + 1, dots depicted on the Y-axis), so that the coordi-
nates of each dot were: R-R, R-R + 1 (Figure 1). Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bot-
tom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R-
R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause
(PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two
R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R
interval is premature (b); therefore, the correspondent dot moves below the line to point B. The
fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to
point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot
moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns
to point A. Repetition of this process using the entire population of R-R intervals recorded during a
Holter monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure
bottom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular
R-R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause
(PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two
R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R
interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth
R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to
point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point
A. Repetition of this process using the entire population of R-R intervals recorded during a Holter
monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bot-
tom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R-
R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause
(PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two
R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R
interval is premature (b); therefore, the correspondent dot moves below the line to point B. The
fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to
point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot
moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns
to point A. Repetition of this process using the entire population of R-R intervals recorded during a
Holter monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure
bottom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular
R-R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause
(PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. 2.3. Heart Rate Variability Analysis The software allowed analysis of heart rate variability (HRV), including both time- and
frequency-domain analysis. Complexes of ventricular origin were automatically excluded
from HRV analysis. Consequently, NN intervals included in the HRV analysis comprised
sinus complexes and APCs [9–11]. For the purposes of this study, only time-domain
variables were considered, including: the standard deviation of all the N-N intervals; the
standard deviation of the means of the N-N intervals for all 5 min segments; the mean of Animals 2021, 11, 1645 4 of 13
time-
N N the standard deviations of all the N-N intervals for all 5 min segments; the percentage of
interval differences of successive N-N intervals more than 50 ms; and the square root of the
mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the
SR class was categorized as ‘normal’ or ‘reduced’ based on data previously reported in the
canine literature [17]. the mean of the standard deviations of all the N N intervals for all 5 min segments; the
percentage of interval differences of successive N-N intervals more than 50 ms; and the
square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV
of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previ-
ously reported in the canine literature [17]. the standard deviations of all the N-N intervals for all 5 min segments; the percentage of
interval differences of successive N-N intervals more than 50 ms; and the square root of the
mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the
SR class was categorized as ‘normal’ or ‘reduced’ based on data previously reported in the
canine literature [17]. the mean of the standard deviations of all the N N intervals for all 5 min segments; the
percentage of interval differences of successive N-N intervals more than 50 ms; and the
square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV
of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previ-
ously reported in the canine literature [17]. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti Note
that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. Table 1 Quantitative and qualitative features of Lorenz plot patterns
Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter
recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster of
dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained
from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both
CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that
both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of
identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-axis of the plot. (C): Example
Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart
rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note that both arms are clearly
attached to the CC, acting as its direct continuation and not as distinct ECs. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti Table 1 reports the criteria of classification of LP patterns. The nomenclature already proposed in humans [2] and dogs [5–7] was used when the
characteristics of patterns obtained from dogs included in the study were similar to those
previously described; otherwise, a new nomenclature was proposed. identity were defined as ‘central’ and ‘eccentric’, respectively [2]. When more than one CC
was present, the term ‘main’ was used to define the cluster of dots located at the left lower
corner of the graph. Table 1 reports the criteria of classification of LP patterns. The no-
menclature already proposed in humans [2] and dogs [5–7] was used when the character-
istics of patterns obtained from dogs included in the study were similar to those previ-
ously described; otherwise, a new nomenclature was proposed. Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter
recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster
of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording
obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature
complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the
graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then
extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-
axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm
associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note
that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. Table 1 Quantitative and qualitative features of Lorenz plot patterns
Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter
recording obtained from a dog with atrial fibrillation. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two
R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R
interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth
R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to
point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point
A. Repetition of this process using the entire population of R-R intervals recorded during a Holter
monitoring creates the final Lorenz plot. The resulting cloud of dots was characterized by: (1) a shape, fitted to the plot with
the mean R-R interval as its center; (2) a length, the major axis passing through the mean
R-R interval along the bisector (line of identity); and (3) a width, the minor axis passing
through the mean R-R interval perpendicular to the major axis [1,2,5]. Then, as previously
described in humans [2], each LP was studied qualitatively by assessing the specific shape
The resulting cloud of dots was characterized by: (1) a shape, fitted to the plot with
the mean R-R interval as its center; (2) a length, the major axis passing through the mean
R-R interval along the bisector (line of identity); and (3) a width, the minor axis passing
through the mean R-R interval perpendicular to the major axis [1,2,5]. Then, as previously
described in humans [2], each LP was studied qualitatively by assessing the specific shape
of the contour of the main central cluster (CC) of dots, and also quantitatively by assessing
three geometrical indexes: (1) the ratio of the maximal length to the maximal width;
(2) the number of CCs and eccentric clusters (ECs) of dots; and (3) the number of branches
arising from the main CC (Figure 2). Clusters of dots located along and outside the line Animals 2021, 11, 1645 5 of 13
essing
th; (2) of identity were defined as ‘central’ and ‘eccentric’, respectively [2]. When more than
one CC was present, the term ‘main’ was used to define the cluster of dots located at the
left lower corner of the graph. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti Maximal length (Lmax) and maximal width (Wmax) of the cluster of
dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained
from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both
CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that
both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of
identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-axis of the plot. (C): Example
Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart
rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note that both arms are clearly
attached to the CC, acting as its direct continuation and not as distinct ECs. Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter
recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster
of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording
obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature
complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the
graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then
extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-
axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm
associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. CC: central cluster; CSZ: central silent zone; DSL: double side lobe; EC: eccentric cluster; Lmax/Wmax: ratio of the maximal length to the
maximal width; LP: Loren plot; NA: not applicable; QSL: quadruple side lobe; TSL: triple side lobe. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti Animals 2021, 11, 1645 6 of 13 2.5. Statistical Analysis 2.5. Statistical Analysis Statistical analysis was performed with dedicated software (Microsoft Excel, version
2016, Microsoft Corporation; R, version 3.5.2, R Foundation for Statistical Computing,
Vienna, Austria). The Shapiro–Wilk test was used to verify data distribution. Normally and
non-normally distributed data were expressed as mean, standard deviation, and median
(interquartile range), respectively. Repeatability and reproducibility of the classification
of LP patterns were determined through intraobserver and interobserver agreement, re-
spectively. The intraobserver agreement was determined from data generated by the same
observer (GR) who evaluated blindly, four months apart, 20 randomly selected LPs. The in-
terobserver agreement was determined from data generated by a second blinded observer
(MBT) who analyzed the same 20 LPs used for intraobserver agreement. Intra and interob-
server agreement were measured using the kappa statistics, as previously described [18]. The diagnostic value of LP analysis in identifying different rhythm classes was quantified
in terms of sensitivity and specificity using standard formulas [19]. 2.4. Lorenz Plot Analysis
2.4. Lorenz Plot Analysis
O
th
f
ti q
p
p
LP Pattern
Lmax/Wmax
CC
(No.)
EC
(No.)
Branches from CC
(No.)
LP Morphology
Comet
>1
1
0
0
Comet/club
Torpedo
>1
1
0
0
Cigarette
Y-shaped
NA
1
0
2
Y
Diamond
1 or >1
1
0
0
Diamond/rhombus
Diamond with CSZ
1 or >1
2
0
0
Diamond/rhombus with a
central rarefaction area
DSL
NA, <1, 1 or >1
1 or 2
2
0 or 2
One of the first five morphologies with two
lateral fusiform ECs
(one left-sided and one right-sided)
TSL
NA, <1, 1 or >1
1 or 2
3
0 or 2
One of the first five morphologies with three
lateral small and fusiform ECs
(two left-sided and one right-sided)
QSL
NA, <1, 1 or >1
1 or 2
4
0 or 2
One of the first five morphologies with four
lateral small and fusiform ECs
(two left-sided and two right-sided)
Fan
1 or <1
1
0
0
Triangular
Table 1. Quantitative and qualitative features of Lorenz plot patterns. LP Pattern
Lmax/Wmax
CC
(No.)
EC
(No.)
Branches from
CC (No.)
LP Morphology
Comet
>1
1
0
0
Comet/club
Torpedo
>1
1
0
0
Cigarette
Y-shaped
NA
1
0
2
Y
Diamond
1 or >1
1
0
0
Diamond/rhombus
Diamond with
CSZ
1 or >1
2
0
0
Diamond/rhombus with a
central rarefaction area
DSL
NA, <1, 1 or >1
1 or 2
2
0 or 2
One of the first five morphologies with two
lateral fusiform ECs
(one left-sided and one right-sided)
TSL
NA, <1, 1 or >1
1 or 2
3
0 or 2
One of the first five morphologies with three
lateral small and fusiform ECs
(two left-sided and one right-sided)
QSL
NA, <1, 1 or >1
1 or 2
4
0 or 2
One of the first five morphologies with four
lateral small and fusiform ECs
(two left-sided and two right-sided)
Fan
1 or <1
1
0
0
Triangular
Fan with DSL
1 or <1
1
2
0
Triangular with two lateral small and
fusiform ECs
(one left-sided and one right-sided)
CC: central cluster; CSZ: central silent zone; DSL: double side lobe; EC: eccentric cluster; Lmax/Wmax: ratio of the maximal length to the
maximal width; LP: Loren plot; NA: not applicable; QSL: quadruple side lobe; TSL: triple side lobe. Lmax/Wmax
CC
EC
Branches from CC
LP
Table 1. Quantitative and qualitative features of Lorenz plot patterns. No. of dogs
Age (years)
Body weight (kg)
Sex (M/NM/F/NF) 3.1. Study Population and Holter Analysis The study population included 119 Holter recordings from 102 client-owned dogs,
with 11 animals undergoing more than one Holter monitoring. Sixteen (15.7%) and eighty-
four (82.3%) dogs were clinically healthy and affected by cardiac or systemic diseases,
respectively, whereas clinical diagnosis was not available in the remaining two (2%) dogs. Of the 119 Holter recordings, 62 (52.1%) were obtained from dogs without any cardiac
treatment, 56 (47.1%) from dogs receiving at least one cardiac drug at the time of monitoring,
whereas no data were available for one dog (0.8%) (Table 2). Table 2. Demographic data from dogs used in this study. Variable
No. of dogs
102
Age (years)
10.0 (6.5–12)
Body weight (kg)
25.8 (13.8–35.0)
Sex (M/NM/F/NF)
49/8/22/23
Breed (No. of dogs)
Mixed breed (24)
Doberman Pinscher (10)
Boxer (9)
German Shepherd, Labrador Retriever (5)
English Bulldog, Golden Retriever (4)
Cocker Spaniel, Corso (3)
American Staffordshire Terrier, Cavalier King Charles Spaniel, English Pointer,
Italian Hound, Pug (2)
Basset Hound, Bolognese, Bouvier des Flandres, Briard, Czechoslovak Wolfdog,
Dogo Argentino, English Setter, French Bulldog, Great Danes, Irish Setter, Irish
Terrier, Jack Russell Terrier, Leonberger, Miniature Pinscher, Neapolitan Mastiff,
Newfoundland, Nova Scotia Duck Tolling Retriever, Parson Russell Terrier, Poodle,
Rottweiler, Shih Tzu, Vizsla, Weimaraner, West Highland White Terrier, Yorkshire
Terrier (1)
Clinical status (H/D/NA)
16/84/2
D: systemic and/or cardiac disease; F: female; H: healthy; M: male; NA: not available; NF: neutered female; NM: neutered male. Table 2. Demographic data from dogs used in this study. No. of dogs
Age (years)
Body weight (kg)
Sex (M/NM/F/NF) Breed (No. of dogs) Clinical status (H/D/NA) c and/or cardiac disease; F: female; H: healthy; M: male; NA: not available; NF: neutered female; NM: neutered male. The mean duration of Holter monitoring was 23.3 ± 1 h and all recordings had good
quality ECGs that included the whole night. The SR was the most numerous class, followed
by the SR-VPCs, and the AF-VPCs classes, whereas the SR-APCs, the SR-APCs-VPCs, and
the AF classes were less frequent. Table 3 presents detailed information on rhythm classes
and clinical diagnosis. 7 of 13 Animals 2021, 11, 1645 Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. Holter Diagnosis (No.)
Clinical Diagnosis (No.)
Ongoing Cardiac Treatment (No.)
SR (48)
(No. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns Lorenz plot analysis allowed for the identification of 10 distinct patterns (Figure 3
and Table 4). Features of six patterns were similar to those previously described in both
humans and dogs, including comet, torpedo, Y-shaped, double side lobe (DSL), triple side
lobe (TSL), and fan. The following nomenclature was proposed for the remaining four LP
patterns: diamond, diamond with a central silent zone (CSZ) (i.e., a well-defined region
of low density of dots within a PP pattern), quadruple side-lobe (QSL), and fan with DSL. The terms DSL, TSL, and QSL were used when one among the comet, torpedo, Y-shaped,
diamond, or diamond with CSZ configuration was associated with two, three, and four
ECs, respectively. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used
in this study. Lorenz Plot Pattern (No.)
Rhythm Classes (No.)
Comet (12)
SR with normal HRV (12)
Torpedo (3)
SR with reduced HRV (3)
Y-shaped (6)
SR with normal HRV (6)
Diamond (10)
SR with normal HRV (8); SR-APCs (1); SR-VPCs (1)
Diamond with CSZ (17)
SR with normal HRV (15); SR-APCs (1); AF (1)
Double side lobe (47)
SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5);
SR with normal HRV (4)
Triple side lobe (1)
SR-VPCs (1)
Quadruple side lobe (2)
SR-VPCs (2)
Fan (18)
AF-VPCs (16); AF (2)
Fan with double side lobe (3)
AF-VPCs (2); AF (1)
AF: atrial fibrillation; APC: atrial premature complex; CSZ: central silent zone; HRV: heart rate variability; SR:
sinus rhythm; VPC: ventricular premature complex. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used
in this study. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used
in this study. 3.1. Study Population and Holter Analysis of VPCs: 2 (0–9))
cMMVD (16); AH (13); cardiac
tumor, CHD (3); DCM, dMMVD,
NA, suspected myocarditis,
NM-TLoC, PH (2);
Pheochromocytoma (1)
pimobendan (5); benazepril, furosemide (4); sotalol
(3); amiodarone, atenolol, mexiletine (2);
spironolactone (1)
SR-APCs (9)
(No. of APCs: 2444 (1578–3502))
cMMVD (4); dMMVD (3); AH,
non-specific LV cardiomyopathy (1)
benazepril, pimobendan (3); furosemide (2);
amiodarone, amlodipine, hydrochlorothiazide,
sildenafil, spironolactone, torasemide (1)
SR-VPCs (35)
(No. of VPCs: 1589 (389–11,751))
cMMVD (8); DCM (6); suspected
myocarditis (5); AC, CHD (4);
cardiac tumor (3); AH, dMMVD (2);
non-specific BV cardiomyopathy (1)
amiodarone (6); pimobendan (5); furosemide, sotalol
(4); benazepril (3); atenolol, mexiletine (1)
SR-APCs-VPCs (5)
(No. of APCs: 953 (332–3992))
(No. of VPCs: 1049 (175–2822))
dMMVD (2); cardiac tumor, DCM,
suspected myocarditis (1)
benazepril, furosemide, pimobendan (4); amlodipine
(2); atenolol, mexiletine (1)
AF (4)
(No. of VPCs: (33 (8–65)
DCM (2); dMMVD, suspected
myocarditis (1)
benazepril, furosemide, pimobendan (3); digoxin (2);
diltiazem (1)
AF-VPCs (18)
(No. of VPCs: 982 (366–2369))
dMMVD (9); cMMVD (4); DCM (3);
HWD, CHD (1)
pimobendan (14); benazepril, furosemide (10);
diltiazem (8); digoxin (7); torasemide (3);
amlodipine, hydrochlorothiazide, spironolactone (1)
AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular;
CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine
stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary
Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated
transient loss of consciousness; PH: pulmonary hypertension; SR: sinus rhythm; VPC: ventricular premature complex. Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. Holter Diagnosis (No.)
Clinical Diagnosis (No.)
Ongoing Cardiac Treatment (No.)
SR (48)
(No. of VPCs: 2 (0–9))
cMMVD (16); AH (13); cardiac
tumor, CHD (3); DCM, dMMVD,
NA, suspected myocarditis,
NM-TLoC, PH (2);
Pheochromocytoma (1)
pimobendan (5); benazepril, furosemide (4); sotalol
(3); amiodarone, atenolol, mexiletine (2);
spironolactone (1)
SR-APCs (9)
(No. of APCs: 2444 (1578–3502))
cMMVD (4); dMMVD (3); AH,
non-specific LV cardiomyopathy (1)
benazepril, pimobendan (3); furosemide (2);
amiodarone, amlodipine, hydrochlorothiazide,
sildenafil, spironolactone, torasemide (1)
SR-VPCs (35)
(No. of VPCs: 1589 (389–11,751))
cMMVD (8); DCM (6); suspected
myocarditis (5); AC, CHD (4);
cardiac tumor (3); AH, dMMVD (2);
non-specific BV cardiomyopathy (1)
amiodarone (6); pimobendan (5); furosemide, sotalol
(4); benazepril (3); atenolol, mexiletine (1)
SR-APCs-VPCs (5)
(No. 3.1. Study Population and Holter Analysis of APCs: 953 (332–3992))
(No. of VPCs: 1049 (175–2822))
dMMVD (2); cardiac tumor, DCM,
suspected myocarditis (1)
benazepril, furosemide, pimobendan (4); amlodipine
(2); atenolol, mexiletine (1)
AF (4)
(No. of VPCs: (33 (8–65)
DCM (2); dMMVD, suspected
myocarditis (1)
benazepril, furosemide, pimobendan (3); digoxin (2);
diltiazem (1)
AF-VPCs (18)
(No. of VPCs: 982 (366–2369))
dMMVD (9); cMMVD (4); DCM (3);
HWD, CHD (1)
pimobendan (14); benazepril, furosemide (10);
diltiazem (8); digoxin (7); torasemide (3);
amlodipine, hydrochlorothiazide, spironolactone (1)
AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular;
CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine
stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary
Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. SR-VPCs (35)
(No. of VPCs: 1589 (389–11,751)) SR-APCs-VPCs (5)
(No. of APCs: 953 (332–3992))
(No. of VPCs: 1049 (175–2822))
AF (4)
(No. of VPCs: (33 (8–65)
AF-VPCs (18)
(No. of VPCs: 982 (366–2369)) AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular;
CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine
stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary
Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated
transient loss of consciousness; PH: pulmonary hypertension; SR: sinus rhythm; VPC: ventricular premature complex. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns Lorenz Plot Pattern (No.)
Rhythm Classes (No.)
Comet (12)
SR with normal HRV (12)
Torpedo (3)
SR with reduced HRV (3)
Y-shaped (6)
SR with normal HRV (6)
Diamond (10)
SR with normal HRV (8); SR-APCs (1); SR-VPCs (1)
Diamond with CSZ (17)
SR with normal HRV (15); SR-APCs (1); AF (1)
Double side lobe (47)
SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5);
SR with normal HRV (4)
Triple side lobe (1)
SR-VPCs (1)
Quadruple side lobe (2)
SR-VPCs (2)
Fan (18)
AF-VPCs (16); AF (2)
Fan with double side lobe (3)
AF-VPCs (2); AF (1)
AF: atrial fibrillation; APC: atrial premature complex; CSZ: central silent zone; HRV: heart rate variability; SR:
sinus rhythm; VPC: ventricular premature complex. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used
in this study. 8 of 13 Animals 2021, 11, 1645 Fig-
ure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E):
diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe
(QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric
clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the
diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a
central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with
four eccentric clusters, respectively. Figure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond;
(E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe
(QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric
clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the
diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central
silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric
clusters, respectively. ure 3. Lorenz plot patterns identified in the study population. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E):
diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe
(QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric
clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the
diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a
central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with
four eccentric clusters, respectively. Figure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond;
(E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe
(QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric
clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the
diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central
silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric
clusters, respectively. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used
in this study. Lorenz Plot Pattern (No.)
Rhythm Classes (No.)
The intra- and interobserver agreement was high: K = 0.94 (standard error = 0.06;
95% confidence interval = 0.81–1.0) and K = 0.87 (standard error = 0.09; 95% confidence
interval = 0.7–1.0), respectively. Comet (12)
Torpedo (3)
3.3. Diagnostic Value of Lorenz Plot Patterns Y-shaped (6)
SR with normal HRV (6)
Diamond (10)
SR with normal HRV (8); SR-APCs (1); SR-VPCs (1)
Diamond with CSZ (17)
SR with normal HRV (15); SR-APCs (1); AF (1)
Double side lobe (47)
SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5);
Comet, torpedo, Y-shaped, diamond, and diamond with CSZ patterns were predomi-
nantly associated with SR (Table 4). Specifically, the torpedo pattern was associated with
SR with reduced HRV, while comet, Y-shaped, diamond, and diamond with CSZ patterns
were associated with SR and normal HRV (Table 5). The remaining patterns were mainly
associated with tachyarrhythmias. Specifically, the DSL was predominantly associated
with SR with frequent ectopic complexes, either APCs, VPCs, or both; the TSL and the QSL
exclusively with SR with frequent VPCs; and the fan and the fan with DSL exclusively with
AF, either with or without frequent VPCs (Table 4). Table 5. Time-domain heart rate variability parameters obtained from dogs of the sinus rhythm class, divided based on
their Lorenz plot patterns. HRV Variable
Lorenz Plot Pattern (No.)
Comparis. Intervals *
Comet
(12)
Torpedo
(3)
Y-Shaped
(6)
Diamond
(10)
Diamond with
CSZ (17)
PNN50 (%)
43.7 ± 17.2
9.3 ± 4.2
34.0
51.0
48.0
56 ± 10
(25.7–46.7)
(41.5–58.5)
(32.2–61.5)
(18–75)
RMSSD (ms)
148.8 ± 85.6
32.3 ± 6.1
130.5
174.0
204.0
325 ± 118
(85.2–307.7)
(131.0–182.0)
(122.2-289.5)
(112-610)
SDANN (ms)
124.9 ± 64.5
72.0
(69.0–93.0)
145.5
120
131.0
195 ± 52
(133.5–196.5)
(91.0–174.5)
(111.5–163.5)
(112–322)
SDNN (ms)
188.2 ± 95.3
84.0 ± 26.1
215.7 ± 111.0
204.0
208.0
331 ± 87
(179.0–224.0)
(165.2–248.2)
(148–521)
SDNNIDX (ms)
155.0 ± 88.0
53.7 ± 15.3
143.0
164.6 ± 58.7
180.5
260 ± 76
(111.7–238)
(122.2–215.5)
(88–415)
CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms;
RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN
intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the
NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman
Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. ain heart rate variability parameters obtained from dogs of the sinus rhythm class, divided based on Table 5. CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms;
RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN
intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the
NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman
Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. Comet (12)
Torpedo (3)
3.3. Diagnostic Value of Lorenz Plot Patterns Time-domain heart rate variability parameters obtained from dogs of the sinus rhythm class, d
their Lorenz plot patterns. CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms;
RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN
intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the
NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman
Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. 9 of 13 Animals 2021, 11, 1645 9 of 13 Comet, torpedo, Y-shaped, diamond, and diamond with CSZ patterns were poorly
sensitive but highly specific in diagnosing the SR class. The DSL pattern appeared more
sensitive than specific in diagnosing individually the SR-APCs, SR-VPCs, and SR-APCs-
VPCs classes. However, when used to diagnose SR with frequent premature complexes
irrespective of their origin (i.e., considering together the APCs, VPCs, and SR-APCs-VPCs
classes), both sensitivity and specificity were high. The low number of TSL and QLS
patterns limited individual statistical analysis, but when they were grouped together, low
sensitivity and high specificity in diagnosing the SR-VPCs class were found. The fan
pattern was more specific than sensitive in diagnosing both the AF and AF-VPCs classes. Similarly, the fan with DSL pattern was highly specific but poorly sensitive in diagnosing
both the AF and AF-VPCs classes (Table 6). Table 6. Diagnostic value of Lorenz plot patterns for the diagnosis of cardiac rhythms. Comet (12)
Torpedo (3)
3.3. Diagnostic Value of Lorenz Plot Patterns Lorenz Plot Pattern
Cardiac Rhythm
Se (%)
Sp (%)
(95% CI)
(95% CI)
Comet
SR
25.0 (13.6–39.6)
100 (94.9–100)
Torpedo
SR
6.2 (1.3–17.2)
100 (94.9–100)
Y-shaped
SR
12.5 (4.7–25.3)
100 (94.9–100)
Diamond
SR
16.7 (7.5–30.2)
97.2 (90.2–99.7)
Diamond with CSZ
SR
31.2 (18.7–46.3)
97.2 (90.2–99.7)
DSL
SR-APCs
77.8 (39.9–97.2)
63.6 (53.9–72.6)
SR-VPCs
88.6 (73.3–96.8)
81.0 (70.9–88.7)
SR-APCs-VPCs
100 (47.8–100)
63.2 (53.6–72)
SR with frequent ECs
of any origin (APCs,
VPCs or both)
91.3 (79.2–97.6)
94.5 (86.6–98.5)
TSL + QSL
SR-VPCs
8.8 (1.9–23.7)
100 (95.8–100)
Fan
AF
50.0 (6.8–93.2)
86.1 (78.4–91.8)
AF-VPCs
88.9 (65.3–98.6)
98.0 (93–99.8)
Fan with DSL
AF
25.0 (0.6–80.6)
98.3 (93–99.8)
AF-VPCs
11.1 (1.4–34.7)
99.0 (94.6–99.9)
AF: atrial fibrillation; APC: atrial premature complex; CI: confidence interval; CSZ: central silent zone; DSL:
double side lode; EC: ectopic complex; QSL: quadruple side lobe; Se: sensitivity; Sp: specificity; SR: sinus rhythm;
TSL: triple side lobe; VPC: ventricular premature complex. Table 6. Diagnostic value of Lorenz plot patterns for the diagnosis of cardiac rhythms. AF: atrial fibrillation; APC: atrial premature complex; CI: confidence interval; CSZ: central silent zone; DSL:
double side lode; EC: ectopic complex; QSL: quadruple side lobe; Se: sensitivity; Sp: specificity; SR: sinus rhythm;
TSL: triple side lobe; VPC: ventricular premature complex. 4. Discussion The main findings of the present study revealed that: (1) SR and tachyarrhythmias
imprint peculiar signatures on canine LPs that can be categorized into 10 patterns; (2)
the intra and interobserver agreement of LP patterns classification was excellent; and (3)
the majority of LP patterns were highly specific but less sensitive indicators of canine SR
and tachyarrhythmias. y
y
Similar to humans [2,20–23], the comet and torpedo pattern were exclusively observed
in dogs from the SR class, in particular in those with normal and reduced HRV, respectively. Graphically, comet and torpedo patterns had one CC characterized by a length bigger
than the width. However, the former is narrow at the bottom and gradually gets wider
towards the top along the line of identity showing a certain degree of asymmetry, and the
latter maintains a relatively symmetric shape with a limited width. Human studies have
demonstrated that an enhanced vagal cardiac activity leads to increased cluster width and
asymmetry [2,20–23]. This can explain why dogs with SR and severely reduced HRV had a
torpedo rather than a comet pattern. As previously observed in healthy dogs [5–7], three other LP patterns predominantly
occurred in the SR class with normal HRV, namely the Y-shaped, diamond, and diamond
with CSZ. The Y-shaped pattern showed the most intense distribution of dots at the lower
left corner of the graph, forming a stalk that extended from the X-axis at an angle of
approximately 45◦and splitting into two diverging arms approximately parallel to the
X-axis and Y-axis of the plot. The stalk represents consecutive R-R intervals of a similar Animals 2021, 11, 1645 10 of 13 10 of 13 length (i.e., phases of regular SR), while the diverging arms are created by long-short and
short-long R-R intervals (i.e., premature sinus complexes and sinus pauses during phases
of sinus arrhythmia, respectively). Other LPs had a diamond configuration due to an
additional cluster of dots filling the gap between the aforementioned arms. These dots
represent consecutive R-R intervals with a longer length (e.g., phases of sinus bradycardia). Lastly, many LPs with a diamond configuration had a CSZ. 4. Discussion This area represents a range
of R-R intervals occurring infrequently when compared to others, and is likely due to
the initiation of beats from different sinus node areas characterized by a fixed range of
discharge rates or variation in the exit block from the sinus node under the physiologic
control of the autonomic nervous system [7]. The reasons for these different LP patterns
found in dogs from the SR class with normal HRV may depend on differences in breeds,
age, sex, clinical status, and treatments [9–11,17,24–26]. Similar to human [2,27] and previous canine [6] studies, the DSL pattern was predom-
inant in dogs with frequent ectopic complexes of any origin. Graphically, the human DSL
pattern is composed by a central comet or torpedo configuration and two ECs [2]. Given the
wide range of patterns associated with canine SR, we classified a DSL pattern when either a
comet, torpedo, Y-shaped, diamond, and diamond with CSZ configuration was associated
with two ECs. Eccentric clusters arose from the lower left corner of the graph, close to
the body of the main CC, and then diverged distally, approximately parallel to the X-axis
and Y-axis of the plot. The long-short R-R intervals produced by VPCs following sinus
complexes, and the short-long R-R intervals produced by post-ectopic pauses following
VPCs, created the right-sided and the left-sided ECs, respectively. Variable EC length,
thickness, and density were observed in this study, as already reported in humans [2]. This
finding likely reflects the variable number of premature ectopic complexes observed and
the variable duration of their coupling intervals and post-ectopic pauses. In addition to
the DSL pattern, an additional left-sided EC, creating a TSL pattern, was observed in a
dog with SR + VPC. This pattern has been already described in humans and dogs with
frequent VPCs and compensatory post-ectopic pauses [2,6,27]. Two dogs from this study,
both from the SR-VPCs class, showed two left-sided and two right-sided ECs, creating a
QSL pattern. This previously unreported pattern may derive from the coexistence of two
ventricular foci, each one generating frequent VPCs with peculiar coupling intervals and
stable duration of the relative post-ectopic pauses. p
p
p
As in previous human [2,28] and canine [6] reports, the fan pattern was identified
exclusively in dogs showing AF as the dominant cardiac rhythm. Graphically, this pattern
shows widely scattered data dots organized into a single CC located along the line of
identity. 4. Discussion The shape of the most concentrated cluster resembles a triangle where the width
is often bigger than the length, and the triangular apex is at the left lower corner of the
graphs. Two dogs from the AF-VPCs class and one dog from the AF showed also two ECs,
creating a fan with DSL pattern. Interestingly, the dog from the AF class had a number of
VPCs (93 VPCs/Holter) close to the threshold beyond which the shift from the AF to the
AF-VPCs class was set. Therefore, the VPCs of this dog were frequent enough to generate
visible ECs. Intriguingly, 16/18 dogs from the AF-VPCs class had a fan rather a fan with
DSL pattern. This can be explained by the relationship between the refractory period of
the atrioventricular node during AF, and the prematurity of VPCs as well as the duration
of their post-ectopic pauses. When coupling intervals of VPCs and duration of relative
post-ectopic pauses significantly differ from R-R intervals recorded during AF, the resultant
ECs should be clearly separated from the fan pattern envelope; conversely the fan pattern
and ECs can overlap [29]. Regarding the reproducibility of LP patter classification, this study found an excellent
intra and interobserver agreement. This finding is in line with the human literature, where
good to excellent intra and interobserver agreement of LP pattern classification has been
reported [2]. The majority of observed LP patterns were highly specific but less sensitive in identify-
ing distinct rhythm classes; this was different from human LP patterns, which demonstrated Animals 2021, 11, 1645 11 of 13 11 of 13 both high sensitivity and specificity [2]. The reasons for this discrepancy are not immedi-
ately clear. Differences in study population size, rhythm classes analyzed, and software
employed for LPs analysis can be a source of discrepancy [2]. Additionally, species-related
peculiarities should be considered. For example, the discharge regularity of the human
sinus node explains why human SR imprints only two patterns on LP (comet and tor-
pedo) [2]. In contrast, the widely variable canine HRV led to five LP patterns in dogs
from the SR class (comet, torpedo, Y-shaped, diamond, and diamond with CSZ), which
inevitably reduce the sensitivity of each of them. Interestingly, the DSL pattern was both
highly sensitive and specific in diagnosing SR with frequent premature ectopic complexes
irrespective of their origin (i.e., considering together the APCs, VPCs, and SR-APCs-VPCs
classes). 4. Discussion This finding could bear relevance in small animal practice, especially in busy
hospitals. Indeed, veterinary cardiologists often deal, over the same workday, not only
with Holter analysis, but also with clinical and echocardiographic examinations, manage-
ment of hospitalized patients, and interventional procedures. This can delay the Holter
analysis completion, and, therefore, the start of antiarrhythmic treatment in some dogs
with tachyarrhythmias. Therefore, one possible clinical implication of this result could be
the strong justification to give priority to thorough Holter analysis when a DSL pattern is
present, with the aim to start rapidly an antiarrhythmic treatment, if necessary. p
p
y
y
y
This study has some limitations. First, the low frequency of some specific rhythm
classes limited the statistical analysis of the relative LP patterns. Additionally, we did
not include dogs with incessant tachyarrhythmias other than AF, which theoretically
could generate a torpedo pattern. Moreover, only the number of ectopies, but not their
organization into allorhythmias, was considered. This choice was purposefully taken,
primarily to fill the information gap regarding the effect of ectopies on canine LP. We
preferred to exclude from this initial study the analysis of the effect of the different types
of organization of ectopies (e.g., bigeminy, trigeminy, or tachycardia) on LP in order to
simplify this preliminary analysis, already rich in numerical and graphic data. However, it
is among our future goals to perform such an analysis to expand further our comprehension
on the effect of canine rhythm disturbances on LP. A second limitation relies on the variable
duration of Holter recordings, ranging from 20–24 h. However, our recordings fulfilled the
recommendations for HRV assessment in humans (i.e., at least 18 h of analyzable ECG data
that includes the whole night) [1]. Third, we focused on examining the effects of frequent
tachyarrhythmias on the LP shape, which implies that the effects of arrhythmic episodes
with a low incidence could have been obscured by the more numerous sinus complexes. A
fourth limitation could be related to our definition of ‘frequent’ ectopic complexes, which
was based on previously reported canine cut-offs [14,15]. Moreover, it is important to note
that an identical cut-off has been used in studies analyzing LPs in humans [2,27]. Author Contributions: Conceptualization, G.R. and M.B.T.; investigation, G.R.; resources, G.R., C.G.,
H.P., and M.B.T.; data curation, G.R.; writing—original draft preparation, G.R.; writing—review 4. Discussion Lastly,
given the lack of standardized and universally accepted thresholds for classifying canine
HRV as ‘normal’ and ‘reduced’, classification of time-domain HRV variables of dogs from
this study was arbitrary and based on comparison with a previous study [17]. Although
that study only included dogs of a single breed (i.e., Doberman Pinschers), we anyway
deemed appropriate to use it for comparison because it was the study analyzing the HRV
parameters of our interest in the larger group of healthy dogs [17]. 5. Conclusions For the first time in dogs, we showed that SR and tachyarrhythmias imprint peculiar
configurations on LPs that could be classified into a set of 10 patterns. Additionally,
this study demonstrated an excellent reproducibility of LP pattern classification in dogs. The majority of LP patterns were highly specific but less sensitive in identifying SR and
tachyarrhythmias in this species. Further studies are warranted to analyze LP patterns in
dogs with different cardiac rhythms. Animals 2021, 11, 1645 12 of 13 12 of 13 and editing, C.G., H.P., and M.B.T. All authors have read and agreed to the published version of
the manuscript. and editing, C.G., H.P., and M.B.T. All authors have read and agreed to the published version of
the manuscript. Funding: This research received no external funding. Funding: This research received no external funding. Institutional Review Board Statement: Ethical approval for this study was waived by the Organism
in charge of Animal Welfare (Organismo Preposto al Benessere degli Animali, OPBA) of the University
of Padova. Data Availability Statement: The data presented in this study are available on request from the
corresponding author. Data Availability Statement: The data presented in this study are available on request from the
corresponding author. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. References Holter monitoring
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https://openalex.org/W4294991290 | https://www.scielo.br/j/bjb/a/NKyDvLVjr9DTnn8xQq4NjpB/?lang=en&format=pdf | English | null | Prevalence of intestinal nematodes infection in school children of urban areas of district Lower Dir, Pakistan | Brazilian Journal of Biology | 2,022 | cc-by | 4,821 | Abstract Intestinal parasitism is the main cause of disease all over the world and described as a significant community
health problem. The current study intended to find out the occurrence and identification of hazard factors linked
with IPIs among 4-12 years aged shool-age children residing in Lower Dir district, Pakistan during 2019 - 2020. A
cross-sectional school-based study was conducted using a pre-arranged pre-tested survey. Anthropometric data
and stool collection were done to obtain the findings. The direct wet mount preparation in saline/iodine/methods
was used for stool examination. Data were investigated using the GraphPad Prism 5. A total of 400 children studied
(mean age of 8.6±3.6 years) the total incidence rate for the intestinal parasitic disease was established to be 71.75%. Of the 400 children studied, the overall prevalence rate for intestinal parasitic infections was found to 71.75%
Ascaris lumbricoides (33.1%), Trichuris trichiura (1.04%), E. vermicularis (1.39%), Hookworm (19.86%) were identified
in children living in the study area. We concluded that there is a mass scale campaigns were required to generate
alertness about health and sanitation in children and the need for the development of effective poverty control
programs because deworming (killing of worm with drugs) alone is not adequate to control parasitic infections. Keywords: nematodes infection, poly-parasitism, urban life, unhygienic, poor nutrition. Prevalência de infecção por nematoides intestinais em escolares de áreas urbanas do
distrito de Lower Dir, Paquistão H. Ur. Rahmana* , N.Khatoonb, S.Arshadb, Z.Masoodc, B.Ahmadd, W. Khand , N. Rafiqa, M. I. Khana,
M. Kabire,, Z. Ul Haqf , I. Kamalf, E. Khang, M. Rashidh, A. ul Haqi, Y. Garedaghij
aAbdul Wali Khan University Mardan, Department of Zoology, Mardan, Pakistan
bUniversity of Karachi, Karachi-Pakistan
cSardar Bahadur Khan women University, Quetta, Pakistan
dUniversity of Malakand, Department of Zoology, Lower Dir, Pakistan
eUniversity of Sargodha, Department of Biological Sciences, Sub Campus Bhakkar, Bhakkar, Punjab, Pakistan
fHazara University Mansehra, Department of Zoology, Mansehra, Pakistan
gGovernment Degree College, Department of Zoology, Thana, Malakand, Pakistan
hFederal Urdu University, Department of Zoology, Gulshan Iqbal Campus, Karachi, Pakistan
iShaheed Benazir Bhutto University, Department of Zoology, Dir Upper, Pakistan
jIslamic Azad University, Tabriz Medical Sciences, Faculty of Veterinary Medicine, Department of Parasitology, Tabriz, Iran H. Ur. Rahmana* , N.Khatoonb, S.Arshadb, Z.Masoodc, B.Ahmadd, W. Khand , N. Rafiqa, M. I. Khana,
M. Kabire,, Z. Ul Haqf , I. Kamalf, E. Khang, M. Rashidh, A. ul Haqi, Y. Garedaghij This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited. Prevalence of intestinal nematodes infection in school children
of urban areas of district Lower Dir, Pakistan Prevalência de infecção por nematoides intestinais em escolares de áreas urbanas do
distrito de Lower Dir, Paquistão *e-mail: hafeezzoologest@gmail.com
Received: October 21, 2020 – Accepted: February 21, 2021 THE INTERNATIONAL JOURNAL ON NEOTROPICAL BIOLOGY THE INTERNATIONAL JOURNAL ON NEOTROPICAL BIOLOGY ISSN 1519-6984 (Print)
ISSN 1678-4375 (Online) ISSN 1519-6984 (Print)
ISSN 1678-4375 (Online) Original Article Brazilian Journal of Biology, 2022, vol. 82, e244158 | https://doi.org/10.1590/1519-6984.244158 Resumo O parasitismo intestinal é a principal causa de doença em todo o mundo e descrito como um importante problema de
saúde comunitária. O presente estudo buscou descobrir a ocorrência e identificação de fatores de risco relacionados
a infecções parasitárias intestinais (IPIs) entre crianças em idade escolar de 4 a 12 anos residentes no distrito de
Lower Dir, Paquistão durante 2019-2020. Um estudo transversal baseado em escola foi realizado usando uma
pesquisa preestabelecida e pré-testada. Dados antropométricos e coleta de fezes foram feitos para obtenção dos
achados. A preparação de montagem úmida direta em solução salina/iodo/métodos foi usada para exame de fezes. Os dados foram investigados usando o GraphPad Prism 5. Em um total de 400 crianças estudadas (idade média
de 8,6±3,6 anos), a taxa de incidência total da parasitose intestinal foi estabelecida em 71,75%. Das 400 crianças
estudadas, a taxa de prevalência global de infecções parasitárias intestinais foi de 71,75%. Ascaris lumbricoides
(33,1%), Trichuris trichiura (1,04%), E. vermicularis (1,39%), Ancilostomíase (19,86%) foram identificados em crianças
morando na área de estudo. Concluímos que há necessidade de campanhas em massa para gerar alerta sobre saúde
e saneamento nas crianças, e a necessidade do desenvolvimento de programas efetivos de controle da pobreza,
pois a desparasitação por si só não é adequada para controlar as infecções parasitárias. Palavras-chave: infecção por nematoides, poliparasitismo, vida rural, anti-higiênico, má nutrição. 1/7 Rahman, H.Ur. et al. 3. Data Collection The questionnaire was organized on the demographic
data (age and gender) as well as socioeconomic profile of
the inhabitants. 2.1.1. Location and boundary Lower Dir is the is a part of old district Dir of Malakand
division. It is located in Hindu Kush range and the area
occupied is 5,284 km2. These days it forms two districts
of Pakistan - Upper Dir and Lower Dir (1,585km2). In the
Northside of Dir Lower the rocky mountainous peaks raise
from 1100 to 3119 meters. About every of it connects in the
basin of the Panjkora which rise in the Hindu Kush at Lat. 35.45 and connect the River Swat close to Chakdara, where
the district is naturally penetrated, at Lat. 34.40 (Figure 1). 2.1. Study sites 2.1. Study sites 2.1. Study sites 1. Introduction amid egg yield and the figure of fully developed worms is
composite. In Pakistan Ascaris lumbricoides illness is broadly
common, with changeable division in all regions of the
country. Therefore, accurate analysis of soil transmitted
helminthiasis play a key role in human being patient
organization, drug efficiency assessment, organization of
contaminated human being, detecting manage programs
and removal (McCarthy et al., 2012; Speich et al., 2014). Intestinal Helminths are prevalent in those parts of the
world where high temperature, poor cleanness, impure
water, and imperfect and crowded accommodation exist. The disease rate is maximum in family existing in Sub-
Saharan parts of Africa, after that Asia and next Caribbean
and Latin America (Silva et al., 2003; Brooker et al., 2006). There is large number of nematode worms, but a small
number for human infection. Among them, some are the
soil-transmitted helminths Ancylostoma duodenale, Necator
americanus, Ascaris lumbricoides and Trichuris trichiura
are most prevalent organisms on the earth, estimated to
infect almost one-sixth of the global population. Ascaris
lumbricoides, Trichuris trichiura and hookworm of human
origin are a group of nematode parasites infecting human
alimentary canal when ingested eggs or larva (Khan et al.,
2019b). In recent past decade various studies have been
published on intestinal parasites infecting different sectors
of human population in the region as Khan et al. (2011,
2012, 2014, 2016, 2017c,b, 2018a, b, 2019a, b), Arshad et al. (2019), Khan and Khan (2015), Noor un Nisa et al. (2011),
Khan et al. (2020, 2021a,b, 2022), Iqbal et al. (2021),
Rahman et al. (2022), Ulhaq et al. (2022). Brazilian Journal of Biology, 2022, vol. 82, e244158 2. Materials and Methods The overall weight of STHs infection shown about
70% of infection happened in Asia (Pullan et al., 2014)
as well as 26.4% of Asian study inhabitants hosted as a
minimum one STP species. In Pakistan, Ascaris lumbricoides
infection is broadly common, with changeable division
in all regions of the country. Different species of human
intestinal worms have been recorded previous workers in
different parts of the Malakand region and Pakistan as well
(Arshad et al., 2019). Three and 3.5 Billion individuals are
approximately contaminated through intestinal parasites
including 1.47 Billion with A.lumbricoides, 13 million with
A.duodenale/N.americanus and 1.05 billion with T.trichura. More than 40 million school-going children are expected
to be contaminated with STHs. Children range from
5 to 15 years in age are commonly polluted, though the
occurrence of A.duodenale/N.americanus disease tends to
increase by growing time. Therefore, young girls and women
during delivery are mainly infected with A.duodenale/N. americanus (Luong, 2003). A. lumbricoides go after extremely
equivalent lines with a stable increase initial childhood to
mean youth, and then turn down into the mature period
program. This is dissimilar as of the hookworms when
they able to initiate in near the beginning childhood and
childhood but after that go up during fully developed life
moreover attainment to upland or merely go down from
40 years or so. There were no information on age- correlated
frequency or power designed for human Strongyloides
stercoralis in the writing, and all STHs existed confront
of understanding worm mass as of the investigative tests
used (Olsen et al., 2009). 4. Laboratory Examination The stool sample was examined by naked eyes to find
out of mature or some immature stage of parasites. Then
stool samples were faced to microscopic examination, with
the help of wet-mount procedure (Lugol’s iodine solutions
and Salt solution). The formol-ether concentration was
also planned for the verification of negative cases selected
to positive. Three 3 g of stool were emulsified in 3 drops
of salt solution (0.9%) or Lugol’siodine solution (WHO,
1991). Only one drop of the suspension was placed on
the centre of the slide with the help of wooden stirrer
and after that, a cover-slip was sited. The slides with
sample suspension were studied with help of the sample
microscope first below low 10× power and after that high
40× power objectives. Salines direct smear was used for
the identification of tapeworm eggs. At the top of direct
stool microscopic assessment, one 1 gram 125 of each stool
sample was emulsified in 10% formol-ether and formalin
solution concentration technique was carry out as to elevate
the opportunity of scrutinized parasites (WHO, 1991). One characteristic of nematodes are calculated known
their predictable global occurrence was the relationship
aimed at the incidence and power of illness. Whereas
occurrence stand for the population exaggerated by
something as of one to thousands (huge infection) of worms,
the quantity of fake negatives depends on the investigative
method used. However, the disease is disadvantaged on
illness intensity and the greater part of worm load is greatly
over-dispersed by a hypothetical quantity of 80% of every
worm below 20% of those contaminated. The majority
exploratory procedure suggests not direct actions of illness,
depending on the existence of eggs within the faces, and by
greatest are merely semi-quantitative, because the affiliation Brazilian Journal of Biology, 2022, vol. 82, e244158 2/7 Nematode infection among school children of urban areas Figure 1. Location Sites of the study area in lower Dir region (Khyber, Pakhtunkhwa). Figure 1. Location Sites of the study area in lower Dir region (Khyber, Pakhtunkhwa). Figure 2. A. lumbricoides unfertile egg. 5. Parasite Identification Intestinal parasites were examined under the microscope
and recognized based on morphological characteristics of
eggs, larvae and adult stages through valid and standard keys. 6. Statistical Analysis SPSS, Graph Pad Prism and Minitab were use to calculate
the results. If P-value is less than 0.05, it will be considered
as statistically important. Brazilian Journal of Biology, 2022, vol. 82, e244158 7. Result lumbricoides, H.dimanuta, hookworm
5 (2.5)
H.nana, T.saginata, A.lumbricoides
7 (3.57)
27 (13.77)
4 species (n=12)
A.lumbricoides, hookworm, T.saginata, H. dimunuta
2 (1.02)
A.lumbricoides, E.vermicularis, H. nana, hookworm
3 (1.53)
H.nana, T. saginata, hookworm, E.vermicularis
7 (3.57)
12 (6.12)
Total poly parasitism
92 (46.93)
Total of infected individuals
196 (49)
Total No. Examined
400
Table 2. Frequency distribution of intestinal parasites identified from school children stools. Group
Parasite species
Population infected
Prevalence (%)
Helminth
Ascaris lumbricoides
95
33.1
Taenia saginata
65
22.64
Hook worms
57
19.86
Hymenolepis nana
54
18.81
Enterobius vermiculari
4
1.39
Hymenolepis.diminuta
4
1.39
Trichuris trichura
3
1.04
Taxocara spp
2
0.69
Total helminth infection
284
99.3
Total number of infection
287
71.75
Total number of individual infected
400 Rahman, H.Ur. et al. Rahman, H.Ur. et al. Table 1. Proportion of mono-parasitism and poly parasitism of intestinal parasitic infections in school children of Lower Dir, Pakistan. Type of infection
No. of species
Species associated
Cases (%)
Mono-parasitism
1species (n=121)
hookworm
27 (13.77)
Ascaris lumbricoides
70 (35.71)
Enterobius vermicularis
15 (7.65)
Trichuris trichiura
9 (4.59)
Total mono -parasitism
121 (61.73)
poly-parasitism
2 species (n=36)
A. lumbricoides, hookworm
11 (5.61)
A. lumbricoides, H. nana
10 (5.10)
T. saginata, hookworm ,
12 (6.12)
H. nana, T. trichura
1 (0.5)
A. lumbricoides, Taxocara spp
2 (1.02)
36 (18.36)
3 species (n=27)
T. saginata, A. lumbricoides, hookworm
5 (2.5)
H. nana, E.vermicularis,T. saginata
4 (2.04)
A.lumbricoides, H. nana, E. vermicularis
4 (0.04)
H. nana, T. saginata, hookworm
2 (1.02)
A. lumbricoides, H.dimanuta, hookworm
5 (2.5)
H.nana, T.saginata, A.lumbricoides
7 (3.57)
27 (13.77)
4 species (n=12)
A.lumbricoides, hookworm, T.saginata, H. dimunuta
2 (1.02)
A.lumbricoides, E.vermicularis, H. nana, hookworm
3 (1.53)
H.nana, T. saginata, hookworm, E.vermicularis
7 (3.57)
12 (6.12)
Total poly parasitism
92 (46.93)
Total of infected individuals
196 (49)
Total No. Examined
400 Table 2. Frequency distribution of intestinal parasites identified from school children stools. Group
Parasite species
Population infected
Prevalence (%)
Helminth
Ascaris lumbricoides
95
33.1
Taenia saginata
65
22.64
Hook worms
57
19.86
Hymenolepis nana
54
18.81
Enterobius vermiculari
4
1.39
Hymenolepis.diminuta
4
1.39
Trichuris trichura
3
1.04
Taxocara spp
2
0.69
Total helminth infection
284
99.3
Total number of infection
287
71.75
Total number of individual infected
400 Table 3. Prevalence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. 7. Result The prevalence of intestinal parasites is at least a
single infection was 195 (61.73%). Mixed infection was
observed in 92 (46.93%) among school children who had
an intestinal parasitic infection. Of these proportion,
36 (18.36%) are double, 27 (13.77%) triple and 12 (6.12%)
quadruple infections were observed (Table 1). Figure 2. A. lumbricoides unfertile egg. Figure 3. A. lumbricoides fertile egg. The overall prevalence of intestinal parasite was 71.75%
(n=287/400). Multiple parasitic infections were identified
in 32.05% (n=92/400) individuals (Table 1). The most
common prevalent parasite is A. lumbricoides (34.49%)
hookworm (19.86%), E. vermicularis (1.39%), T. trichiura
(1.04%) (Table 2). Table 3 demonstrated over all infection if A.lumbriciodes,
A.duodenale, E.vermicularis, T.saginata, H.nana and
H.diminuta as 33.1%, 19.8%, 1.39%, 1.04%, 22.6% 18.8%
and 1.39%. of the children below age 8 years were more
infected than above 8 years, however males were highly
infected than females. Regarding the prevalence of Toxocara
spp which showed same percent prevalence in both the
genders and ages as well. 7.1. Plaetes
Figure 2 to 7. Figure 3. A. lumbricoides fertile egg. Brazilian Journal of Biology, 2022, vol. 82, e244158 3/7 Rahman, H.Ur. et al. Table 3. Prevalence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. Parasite
Ages
Sex
Over all
%
<8
>8
Male
Female
Nematodes
Ascaris lumbricoides
57
38
77
18
95
33.1
Ancylostoma duodenale
30
27
41
16
57
19.86
Enterobius vermicularis
3
1
3
1
4
1.39
Trichuris trichura
3
-
3
-
3
1.04
Taxocara spp
1
1
1
1
2
0.69
Cestodes
Taenia saginata
45
20
48
17
65
22.64
Hymenolepis nana
36
18
45
9
54
18.81
Hymenolepis diminuta
3
1
2
2
4
1.39
Table 1. Proportion of mono-parasitism and poly parasitism of intestinal parasitic infections in school children of Lower Dir, Pakistan. Type of infection
No. of species
Species associated
Cases (%)
Mono-parasitism
1species (n=121)
hookworm
27 (13.77)
Ascaris lumbricoides
70 (35.71)
Enterobius vermicularis
15 (7.65)
Trichuris trichiura
9 (4.59)
Total mono -parasitism
121 (61.73)
poly-parasitism
2 species (n=36)
A. lumbricoides, hookworm
11 (5.61)
A. lumbricoides, H. nana
10 (5.10)
T. saginata, hookworm ,
12 (6.12)
H. nana, T. trichura
1 (0.5)
A. lumbricoides, Taxocara spp
2 (1.02)
36 (18.36)
3 species (n=27)
T. saginata, A. lumbricoides, hookworm
5 (2.5)
H. nana, E.vermicularis,T. saginata
4 (2.04)
A.lumbricoides, H. nana, E. vermicularis
4 (0.04)
H. nana, T. saginata, hookworm
2 (1.02)
A. Brazilian Journal of Biology, 2022, vol. 82, e244158 7. Result Parasite
Ages
Sex
Over all
%
<8
>8
Male
Female
Nematodes
Ascaris lumbricoides
57
38
77
18
95
33.1
Ancylostoma duodenale
30
27
41
16
57
19.86
Enterobius vermicularis
3
1
3
1
4
1.39
Trichuris trichura
3
-
3
-
3
1.04
Taxocara spp
1
1
1
1
2
0.69
Cestodes
Taenia saginata
45
20
48
17
65
22.64
Hymenolepis nana
36
18
45
9
54
18.81
Hymenolepis diminuta
3
1
2
2
4
1.39
Total No. of infection
287
71.75
Total No. of samples
400 alence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. 4/7 Nematode infection among school children of urban areas Figure 4. Hookworm egg. Figure 6. Trichuris trichiura. Figure 6. Trichuris trichiura. Figure 4. Hookworm egg. Figure 7. E. vermicularis egg. Figure 5. Trichuris trichiura. Figure 5. Trichuris trichiura. Figure 5. Trichuris trichiura. Figure 7. E. vermicularis egg. The eggs are getting out in the faces and expose in the
surroundings, afterwards establish in water, soil, impure
fruit and vegetables. Leave the eggshell out and infective
embryonated eggs swallowed, and exceed through the
liver to the blood stream, lungs, and then returned to
small intestine departure the respiratory tract and after
that swallowed. In the current study A. lumbricoides was
the most prevalent parasite 33.1% (n=95) in urban locality
of Lower Dir, which is comparable with 30.1% in District
Swat (Noor-un-Nisa et al., 2011), 39.8% in district Swat
(Khan et al., 2011), 39.8%in District Swat (Khan and Khan,
2015), 31.7% in district Swat (Khan et al., 2019b) and 33.3%
in Panjab (Dar et al., 2013). But the present prevalence
rate is high when compared with, 15% in Banu (Khan and
Khan, 2015), 17%,20.3% in Swat (Khan et al., 2018a), 1.4%
in Peshawar (Ilyas et al., 2018), 7.76% in Swat (Khan et al.,
2019a), 4.0% in Quetta % (Arshad et al., 2019), 17.5% in
Punjab (Kosar et al., 2017), 1.1% in Larkana, 5.5%in Karachi
(Arshad et al., 2019), 12% in AJK (Khan et al., 2017a).The
present prevalence rate is low when compared, 55.8%
in Swat (Khan et al., 2017c), 53.0% in Swat (Khan et al., Brazilian Journal of Biology, 2022, vol. 82, e244158 8. Discussion Albendazole
and mebendazole in the treatment of ancylostomiasis in school
children between the ages of 6-15 in Swat, Pakistan. Journal of
the Pakistan Medical Association, vol. 71, no. 8, pp. 2058-2060. KHAN, M.M., AWAN, A.K., KHAN, R.M.A., AHMED, N., HUSSAIN,
W. and KHAN, M.A., 2017a. Prevalence of worm infestation
and malnutrition in school going children and risk factors
responsible for worm infestation. International Journal of
Pathology, vol. 15, no. 1, pp. 9-14. KHAN, W. and KHAN, A., 2015. Diversity of intestinal parasites in
male and female students and workers of Education Department
of Swat, Pakistan. Pakistan Journal of Zoology, vol. 47, no. 2,
pp. 565-568. KHAN, W., ARSHAD, S., KHATOON, N., KHAN, I., AHMAD, N., KAMAL,
M., ULHASSAN, H., KHAN, N., HAQ, A.U., ILYAS, M. and ULLAH,
S., 2021a. Food handlers: an important reservoir of protozoans
and helminth parasites of public health importance. Brazilian
Journal of Biology, vol. 82. Enterobius vermicularis (pinworm) is an intestinal
nematode parasite that infection is the main agent for
contact-borne infectious helminth. The present survey
established the prevalence of E.vermicularis (1.39%), in
children of district Dir is greater than previous studies .E. vermicularis infection among children are lower than studies
conducted 22.75% in Islamabad, 10.7% Swat (Khan et al.,
2011), 10.3% in district Swat (Noor-un-Nisa et al., 2011),
10% in AJK (Khan et al., 2017a), 9.52% in Swat (Khan et al.,
2018a), 8.25% Swat (Noor-un-Nisa et al., 2011), 8.25% Swat
(Khan and Khan, 2015), 5.05% in Swat (Khan et al., 2019b),
and 14.4% Swat (Khan et al., 2017b). The prevalence rate of
E. vermicularis in children of the district Lower Dir is high
and not negligible due to highly transmittable infection. KHAN, W., IMRAN. and WAHAB, A., 2016. Intestinal obstruction
by Ascaris lumbricoides in a 12 year old boy: a case report in
Pakistan. Journal of Bacteriology & Parasitology, vol. 7, no. 1,
p. 1000262. http://dx.doi.org/10.4172/2155-9597.1000262. KHAN, W., IQBAL, M. and OMER, D.A.D., 2020. Have we forgotten
the threat posed by fascioliasis? A potential threat to public
health. Iranian Journal of Public Health, vol. 49, no. 4, pp. 814. KHAN, W., KHAN, J., KHAN, N., IQBAL, R., ULLAH, A., GHAFFAR, R.,
MEHMOOD, S.A., AHMAD, S., KHAN, S. and ULLAH, F., 2019a. Soil-transmitted helminth infections in school children of three
districts of Malakand region, Khyber Pakhtunkhwa, Pakistan. Pakistan Journal of Pharmaceutical Sciences, vol. 32, no. 2, suppl.,
pp. 799-803. PMid:31103975. 8. Discussion Parasitic infection of helminths is generally prevalent
all over the world. These parasites were changeable
according to the environmental conditions, customs
climatic, local behaviour, in the urban and rural region
the globe. Therefore, we planned to throw some light on
parasitic infections in schoolchildren. Parasitism is one of
the greatest problems in developing and underdeveloped
countries including Pakistan where population increase day
by day, low per capita income, smallest health facilities,
reduced nutrition in the joint family system particularly in
rural localities with maximum chances of contact, provide
ideal conditions for intestinal helminthic infections. In the
current study overall prevalence of intestinal parasites
infection among school children of urban areas of Lower
Dir, Pakistan was 49% (n=196/400). The highest prevalence
was recorded in Islamabad 94.4%, while the lowest in
other studies. Ascaris lumbricoides (roundworm) is the most common
parasite, infecting over 1/5 of the world population. 5/7 Rahman, H.Ur. et al. 2017b), 66.4 in district Swat, Upper Dir and Lower Dir
(Khan et al., 2019b). DAR, U.F., IQBAL, M.S., LATIF, M.Z., JAVAID, M.S., NAYYAR, U. and
NIZAMI, R., 2013. Worm infestation among children of rural
area of central Punjab. PJMHS, vol. 7, no. 3, pp. 713-715. Ancylostoma duodenale (hookworm) incidence rate is
19.86% in the present study. This nematode infection is
nearly comparable with 20% in Azad Jammu and Kasmir
(Khan et al., 2018b), 7.58% in Islamabad, 6.70%in district
Swat (Noor-un-Nisa et al., 2011), 6.91% in district Swat,
Lower and Upper Dir (Khan et al., 2019a), 6.45% in district
Swat (Khan et al., 2017b) and 5.99% in district Swat
(Khan et al., 2017c). The infection rate was high then
other studies, 3.64% in Swat (Noor-un-Nisa et al., 2011),
3.64% in district Swat (Khan and Khan, 2015), 2.90% in
Swat (Khan et al., 2018b), 3.96% (Khan et al., 2018a), 1.08%
in district Swat (Khan et al., 2019b), 0.85% in Peshawar
(Ilyas et al., 2018);m0.4% in Karachi (Arshad et al., 2019);
33.4% was found in school children of Lower district Lower
Dir, Pakistan (Khan et al., 2022) and 41.9% of prevalence
was noted by Ulhaq et al. (2022). The infection rate was
low 41.7% study conducted in Punjab (Dar et al., 2013). ILYAS, M., KHAN, I., UR REHMAN, F. and SHAHID, M., 2018. Frequency
of gastrointestinal parasites among children in clinical practices
Peshawar, KPK, Pakistan. KJMS, vol. 11, no. 1, pp. 31-36. IQBAL, M., KHAN, W., KHAN, F. and KHAN, I., 2021. 8. Discussion The current prevalence rate of Trichuris trichiura is 1.04%
in district Lower Dir. This is comparable, with 1.3% in Punjab
(Kosar et al., 2017), 1.3% in Quetta (Arshad et al., 2019) and
0.42% in Lahore (Anwar et al., 2018). The prevalence rate of
the present study is low when compared with, 26.2% Swat
(Khan et al., 2017b), 19.1% Swat (Khan and Khan, 2015),
19.1% Swat (Khan et al., 2012), 19.0% in Swat (Khan et al.,
2011), 15.9% in Swat (Noor-un-Nisa et al., 2011), 14.9% Swat
(Khan and Khan, 2015), 14.3% Swat (Khan et al., 2018a),
11% in AJK (Khan et al., 2017b), 8.73% Swat (Khan et al.,
2019a) and 8.30% in Swat (Khan et al., 2019b). The above
nematodes were found share with cestodes infection in
19.7% of the study population (Rahman et al., 2022). KHAN, W., KHAN, N.I., BUKHARI, S.N.F. and BEGUM, N., 2019b. Prevalence of Intestinal Parasitic Infection among Drug Addicts
in District Swat, Khyber Pakhtunkhwa, Pakistan. Iranian Journal
of Parasitology, vol. 14, no. 2, pp. 359-361. PMid:31543928. KHAN, W., NISA, N. and KHAN, A., 2017b. Soil transmitted
helminthiasis in different occupational groups in Swat, Khyber
Pakhtunkhwa, Pakistan. Pakistan Journal of Pharmaceutical
Sciences, vol. 30, no. 4, pp. 1345-1350. PMid:29039336. KHAN, W., NOOR-UN-NISA and KHAN, A., 2011. An investigation of
incidence of intestinal parasites in under and above 15 years
age in farmers of Swat, Pakistan. Proceedings of Parasitology,
vol. 52, pp. 43-53. References KHAN, W., NOOR-UN-NISA and KHAN, A., 2012. Endemicity of
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https://openalex.org/W1501686914 | https://www.intechopen.com/citation-pdf-url/36660 | English | null | Knowledge Representation in a Proof Checker for Logic Programs | InTech eBooks | 2,012 | cc-by | 8,598 | 7
Knowledge Representation in
a Proof Checker for Logic Programs
Emmanouil Marakakis, Haridimos Kondylakis and Nikos Papadakis
Department of Sciences, Technological Educational Institute of Crete,
Greece 7 Emmanouil Marakakis, Haridimos Kondylakis and Nikos Papadakis
Department of Sciences, Technological Educational Institute of Crete,
Greece www.intechopen.com 1. Introduction Lately the need for systems that ensure the correctness of software is increasing rapidly. Software failures can cause significant economic loss, endanger human life or environmental
damage. Therefore, the development of systems that verify the correctness of software
under all circumstances is crucial. Formal methods are techniques based on mathematics which aim to make software
production an engineering subject as well as to increase the quality of software. Formal
verification, in the context of software systems, is the act of proving or disproving the
correctness of a system with respect to a certain formal specification or property, using
formal methods of mathematics. Formal program verification is the process of formally
proving that a computer program does exactly what is stated in the program specification it
was written to realize. Automated techniques for producing proofs of correctness of
software systems fall into two general categories: 1) Automated theorem proving (Loveland,
1986), in which a system attempts to produce a formal proof given a description of the
system, a set of logical axioms, and a set of inference rules. 2) Model checking, in which a
system verifies certain properties by means of an exhaustive search of all possible states that
a system could enter during its execution. Neither of these techniques works without human assistance. Automated theorem provers
usually require guidance as to which properties are "interesting" enough to pursue. Model
checkers can quickly get bogged down in checking millions of uninteresting states if not
given a sufficiently abstract model. Interactive verifiers or proof checkers are programs which are used to help a user in building a
proof and/or find parts of proofs. These systems provide information to the user regarding
the proof in hand, and then the user can make decisions on the next proof step that he will
follow. Interactive theorem provers are generally considered to support the user, acting as
clerical assistants in the task of proof construction. The interactive systems have been more
suitable for the systematic formal development of mathematics and in mechanizing formal
methods (Clarke & Wing, 1996). Proof editors are interactive language editing systems which
ensure that some degree of “semantic correctness” is maintained as the user develops the
proof. The proof checkers are placed between the two extremes, which are the automatic
theorem provers and the proof editors (Lindsay, 1988). 2. An Overview of the main components of the proof checker This verifier of logic programs requires a lot of interaction with the user. That is why
emphasis is placed on the design of its interface. The design of the interface aims to facilitate
the proof task of the user. A screenshot of the main window of our system is shown in Fig. 1. Fig. 1. The main window of the proof-checker. Initially, all proof decisions are taken by the programmer. The design of the interface aims to
facilitate the proof task of the user. This interactive verifier of logic programs consists of
three distinct parts the interface, the prover or transformer and the knowledge base (KB). The
interface offers an environment where the user can think and decide about the proof steps
that have to be applied. The user specifies each proof step and the prover performs it. A
high-level design of our system is depicted in Fig. 2. The main components of the proof
checker with their functions are shown in this figure. The prover of the system consists of
the following two components. 1) The component “Spec Transformer” transforms a Fig. 1. The main window of the proof-checker. Fig. 1. The main window of the proof-checker. Initially, all proof decisions are taken by the programmer. The design of the interface aims to
facilitate the proof task of the user. This interactive verifier of logic programs consists of
three distinct parts the interface, the prover or transformer and the knowledge base (KB). The
interface offers an environment where the user can think and decide about the proof steps
that have to be applied. The user specifies each proof step and the prover performs it. A
high-level design of our system is depicted in Fig. 2. The main components of the proof
checker with their functions are shown in this figure. The prover of the system consists of
the following two components. 1) The component “Spec Transformer” transforms a Initially, all proof decisions are taken by the programmer. The design of the interface aims to
facilitate the proof task of the user. This interactive verifier of logic programs consists of
three distinct parts the interface, the prover or transformer and the knowledge base (KB). The
interface offers an environment where the user can think and decide about the proof steps
that have to be applied. The user specifies each proof step and the prover performs it. 1. Introduction www.intechopen.com 162 Advances in Knowledge Representation In this chapter we will present a proof checker or an interactive verifier for logic programs which
are constructed by a schema-based method (Marakakis, 1997), (Marakakis & Gallagher, 1994)
and we will focus on the knowledge representation and on its use by the core components of
the system. A meta-program is any program which uses another program, the object program,
as data. Our proof checker is a meta-program which reasons about object programs. The logic
programs and the other elements of the theory represented in the Knowledge Base (KB) of our
system are the object programs. The KB is the data of the proof checker. The proof checker
accesses and changes the KB. The representation of the underlying theory (object program) in
the proof checker (meta-program) is a key issue in the development of the proof checker. Our
System has been implemented in Sicstus Prolog and its interface has been implemented in
Visual Basic (Marakakis, 2005), (Marakakis & Papadakis, 2009) www.intechopen.com 2. An Overview of the main components of the proof checker A
high-level design of our system is depicted in Fig. 2. The main components of the proof
checker with their functions are shown in this figure. The prover of the system consists of
the following two components. 1) The component “Spec Transformer” transforms a www.intechopen.com 163 Knowledge Representation in a Proof Checker for Logic Programs specification expressed in typed FOL into structured form which is required by our
correctness method (Marakakis, 1997), (Marakakis, 2005). 2) The component “Theorem Proof
Checker supports the proof task of the selected correctness theorem. specification expressed in typed FOL into structured form which is required by our
correctness method (Marakakis, 1997), (Marakakis, 2005). 2) The component “Theorem Proof
Checker supports the proof task of the selected correctness theorem. The “KB Update” subsystem allows the user to update the KB of the system through a user-
friendly interface. The knowledge base (KB) and its contents are also shown in Fig. 2. The
KB contains the representation of specifications, theorems, axioms, lemmas, and programs
complements. It also has the representation of FOL laws in order to facilitate their selection
for application. These entities are represented in ground representation (Hill & Gallagher,
1998). The main benefit of this representation is the distinct semantics of the object program
variables from the meta-variables. It should be noted that the user would like to see
theorems, axioms, lemmas and programs in a comprehensible form which is independent of
their representation. However, the ground representation cannot be easily understood by
users. Moreover, the editing of elements in ground representation is error-prone. Part of the
interface of the system is the “Ground-Nonground Representation Transformer” component
which transforms an expression in ground representation into a corresponding one in the
standard formalism of FOL and vice-versa. The standard form of expressions helps users in
the proof task and for the update of the KB. Fig. 2. Main components of the proof-checker. Fig. 2. Main components of the proof-checker. 3. Knowledge representation Knowledge and representation are two distinct concepts. They play a central role in the
development of intelligent systems. Knowledge is a description of the world, i.e. the problem
domain. Representation is how knowledge is encoded. Reasoning is how to extract more
information from what is explicitly represented. www.intechopen.com 164 Advances in Knowledge Representation Different types of knowledge require different types of representation. Different types of
knowledge representation require different types of reasoning. The most popular
knowledge representation methods are based on logic, rules, frames and semantic nets. Our
discussion will be focused on knowledge representation based on logic. Different types of knowledge require different types of representation. Different types of
knowledge representation require different types of reasoning. The most popular
knowledge representation methods are based on logic, rules, frames and semantic nets. Our
discussion will be focused on knowledge representation based on logic. Logic is a language for reasoning. It is concerned with the truth of statements about the
world. Each statement is either “true” or “false”. Logic includes the following: a) syntax
which specifies the symbols in the language and how they can be combined to form
sentences, b) semantics which specify how to assign a truth to a sentence based on its
meaning in the world and c) inference rules which specify methods for computing new
sentences from existing sentences. There are different types of logic, i.e. propositional logic,
first-order predicate logic, fuzzy logic, modal logic, description logic, temporal logic, etc. We
are concerned on knowledge representation and reasoning based on typed first-order
predicate logic because our correctness method is based on typed FOL. Another classification of knowledge representation is procedural and declarative knowledge
representation. Declarative knowledge concerns representation of the problem domain
(world) as a set of truth sentences. This representation expresses “what something is”. On
the other hand, the procedural knowledge concerns tasks which must be performed to
reach a particular goal. In procedural representation, the control information which is
necessary to use the knowledge is embedded in the knowledge itself. It focuses on “how
something is done”. In the same way, declarative programming is concerned with writing
down “what” should be computed and much less with “how” it should be computed (Hill
& Lloyd, 1994). Declarative programming separates the control component of an
algorithm (the “how”) from the logic component (the “what”). 3. Knowledge representation The key idea of declarative
programming is that a program is a theory (in some suitable logic) and computation is
deduction from the theory (Lloyd, 1994). The advantages of declarative programming are:
a) teaching, b) semantics, c) programmer productivity, c) meta-programming and e)
parallelism. Declarative programming in Logic Programming means that programs are
theories. The programmer has to supply the intended interpretation of the theory. Control
is usually supplied automatically by the system, i.e. the logic programming language. We
have followed the declarative knowledge representation for the representation of the
knowledge base of our system. www.intechopen.com 3.1 Meta-programming, ground and non-ground representation A language which is used to reason about another language (or possibly itself) is called
meta-language and the language reasoned about is called the object language. A meta-program
is a program whose data is another program, i.e. the object program. Our proof-checker is a
meta-program which manipulates other logic programs. It has been implemented in Prolog
and the underlying theory, i.e. the logic programs being verified and the other elements of
the KB, is the object program. An important decision is how to represent programs of the
object language (i.e. the KB elements in our case) in the programs of the meta-language, i.e. in the meta-programs. Ground representation and non-ground representation are the two main
approaches to the representation of object programs in meta-programs. We have followed
the ground representation approach for the representation of the elements of the KB of our
system. Initially, ground and non-ground representation will be discussed. Then, we will
see the advantages and the drawbacks of the two representations. www.intechopen.com 165 Knowledge Representation in a Proof Checker for Logic Programs In logic programming there is not clear distinction between programs and data because data
can be represented as program clauses. The semantics of a meta-program depend on the
way the object program is represented in the meta-program. Normally, a distinct
representation is given to each symbol of the object language in the meta-language. This is
called naming relation (Hill & Gallagher, 1998). Rules of construction can be used to define
the representation of the constructed terms and formulas. Each expression in the language
of the object program should have at least one representation as an expression in the
language of the meta-program. The naming relation for constants, functions, propositions,
predicates and connectives is straightforward. That is, constants and propositions of the
object language can be represented as constants in the meta-language. Functions and
predicates of the object language can be represented as functions in the language of meta-
program. A connective of the object language can be represented either as a connective or as
a predicate or as a function in the meta-language. The main problem is the representation of
the variables of the object language in the language of the meta-program. There are two
approaches. One approach is to represent the variables of the object program as ground
terms in the meta-program. This representation is called ground representation. www.intechopen.com 3.1 Meta-programming, ground and non-ground representation The object program in our proof checker is represented as clauses. The
underlying theory is fixed for each proof task. programming. The object program in our proof checker is represented as clauses. The
underlying theory is fixed for each proof task. 3.2 Ground representation of object programs in the proof-checker The KB shown in Fig. 2 contains the representation of specifications, theorems, axioms,
lemmas and programs complements. It also has the representation of FOL laws in order to
facilitate their selection for application. These KB elements are represented in ground
representation (Hill & Gallagher, 1998).. The representation of the main symbols of the
object language which are used in this chapter is shown below. Object language symbol
Representation
constant
constant
object program variable
term v(i), i is natural
function
term g(i), i is natural
proposition, formulas of FOL
term f(i), i is natural
predicate
term p(i), i is natural
connectives (,,~,↔)
\/, /\, ~, -> , <->
exist ()
ex
for all ( )
all
length of sequence x1(#x1)
len(v(1):Type):nat
operation plus (+)
plus
operation minus (-)
minus
type variable
term tv(i), i is natural
type sequence
seq
empty sequence (<>)
nil_seq
sequence constructor
seq_cons(Head, Tail) where Head and Tail are
(Head :: Tail)
defined in ground representation
accordingly. operator / (Object/Type)
(Object : Type)
x1i /Type (e.g. x1/α1)
v(1, i:nat):Type (e.g. v(1, 1:nat):tv(1) )
equality (=)
eq
inequality (≠)
~eq
less-equal (≤)
le
greater-equal (≥)
ge
type natural (N)
nat
type integer (Z)
int
nonzero naturals (N1)
posInt Object language symbol
Representation
constant
constant
object program variable
term v(i), i is natural
function
term g(i), i is natural
proposition, formulas of FOL
term f(i), i is natural
predicate
term p(i), i is natural
connectives (,,~,↔)
\/, /\, ~, -> , <->
exist ()
ex
for all ( )
all
length of sequence x1(#x1)
len(v(1):Type):nat
operation plus (+)
plus
operation minus (-)
minus
type variable
term tv(i), i is natural
type sequence
seq
empty sequence (<>)
nil_seq
sequence constructor
seq_cons(Head, Tail) where Head and Tail are
(Head :: Tail)
defined in ground representation
accordingly. operator / (Object/Type)
(Object : Type)
x1i /Type (e.g. x1/α1)
v(1, i:nat):Type (e.g. v(1, 1:nat):tv(1) )
equality (=)
eq
inequality (≠)
~eq
less-equal (≤)
le
greater-equal (≥)
ge
type natural (N)
nat
type integer (Z)
int
nonzero naturals (N1)
posInt Predicates are represented by their names assuming that each predicate has a unique name. In case of name conflicts, we use the ground term p(i) where i is natural. Sum of n elements, i.e. 1
n
i
i
x
is represented as the following ground term: sum(1:nat, v(2):nat, v(3, i.e. 3.1 Meta-programming, ground and non-ground representation The other
approach is to represent the variables of the object program as variables (or non-ground
terms) in the meta-program. This representation is called non-ground representation. Using non-ground representation of the object program is much easier to make an efficient
implementation of the meta-program than using ground representation. In non-ground
representation, there is no need to provide definitions for renaming, unification and
application of substitutions of object language formulas. These operations which are time
consuming do not require special treatment for the object language terms. The inefficiency
in ground representation is mainly due to the representation of the variables of the object
program as constants in the meta-program. Because of this representation complicated
definitions for renaming, unification and application of substitutions to terms are required. On
the other hand, there are semantic problems with non-ground representation. The meta-
program will not have clear declarative semantics. There is not distinction of variables of the
object program from the ones of the meta-program which range over different domains. This problem can be solved by using a typed logic language instead of the standard first-
order predicate logic. The ground representation is more clear and expressive than the non-
ground one and it can be used for many meta-programming tasks. Ground representation is
suitable for meta-programs which have to reason about the computational behavior of the
object program. The ground representation is required in order to perform any complex
meta-programming task in a sound way. Its inherent complexity can be reduced by
specialization. That is, such meta-programs can be specialized with respect to the
representation of the object program (Gallagher 1993). Another issue is how the theory of the object program is represented in the meta-program. There are again two approaches. One approach is the object program to be represented in
the meta-program as program statements (i.e. clauses). In this case, the components of the
object program are fixed and the meta-program is specialized for just those programs that
can be constructed from these components. The other approach is the object program to be
represented as a term in a goal that is executed in the meta-program. In this case the object
program can be either fixed or it can be constructed dynamically. In this case the meta-
program can reason about arbitrary object programs. This is called dynamic meta- www.intechopen.com 166 Advances in Knowledge Representation programming. 3.3.2 Object program variables Object program variables and variables in specifications are expressed using the lower case
English letter x followed by a positive integer which is the unique identifier of the variables
e.g. x1, x2, x3, x4 etc. Each object variable is represented in ground form by a term of the
form v(N) where N stands for the unique identifier of the variable. For example, the ground
representation of the object variables x1, x2, x3 is v(1) ,v(2) and v(3) respectively. Note that,
the quantifier of each variable comes before the variable in the formula. Subscripted
variables of the form x1i represent elements from constructed objects. They are represented
by a term of the form v(Id, i:nat):ElementType where the first argument “Id” represents its
unique identifier and the second one represents its subscript. “Id” is a natural number. This
type of variables occurs mainly in specifications. A term like v(Id, i:nat):ElementType can be
assumed as representing either a regular compound term or an element of a structured
object like a sequence. The distinction is performed by checking the types of the elements x
and x(i). For example, for i=1 by checking x1:seq(α1) and x1(1:nat):α1, it can be inferred that
x1(1:nat):α1 is an element of x1:seq(α1). 3.3.1 Type variables The type variables are specified by the lower case Greek letter a followed by a positive
integer which is the unique identifier of the variables e.g. a1, a2, a3, a4 etc. Each type variable
is represented in ground form by a term of the form tv(N) or in simplified form tvN where N
stands for the unique identifier of the variable. For example, the ground representation of
type variables a1, a2, a3 could be tv(1) or tv1, tv(2) or tv2, tv(3) or tv3 respectively. 3.4 Representation of axioms and lemmas A set of axioms is applied to each DT including the “domain closure” and the “uniqueness”
axioms which will be also presented later on Section 3.7. Each axiom is specified by a FOL
formula. Axioms are represented by the predicates “axiom_def_ID/1” and “axiom_def/4” as
follows. The predicate 3.2 Ground representation of object programs in the proof-checker 1
n
i
i
x
is represented as the following ground term: sum(1:nat, v(2):nat, v(3, v(4):nat):Type):Type where “Type” is the type of xi. v(4):nat):Type):Type where “Type” is the type of xi. www.intechopen.com 167 Knowledge Representation in a Proof Checker for Logic Programs “axiom_def_ID(Axiom_Ids)” represents the identifiers of all axioms in the KB. Its argument “Axiom_Ids” is a list with the
identifiers of the axioms. For example, the representation “axiom_def_ID([1,2,3,4])” says
that the KB has four axioms with identifiers 1,2,3 and 4. The specification of each axiom is represented by a predicate of the following form “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. Representation: fol_law(2,’ distribution’,
[f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). fol_law(2,’ distribution’,
[f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). Representation: Similarly, lemmas are represented by the predicates “lemma_sp_ID/1” and “lemma_sp/4”. Specification: P (Q R) ↔ (P Q) (P R)
Representation:
fol_law(2,’ distribution’,
[f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. The argument “Axiom_Id” is the unique identifier of the axiom, i.e. a positive integer. “DT_name” is the name of the DT which the axiom is applied to. “Axiom_name” is the name
of axiom. “Axiom_specification” is a list which has the representation of the specification of
the axiom. Example: Domain closure axiom for sequences. Informally, this axiom says that a sequence can
be either empty or it will consist from head and tail. www.intechopen.com 168 Advances in Knowledge Representation Specification: [ x1/seq(a2),[x1= < > ( x3/a2, x4/seq(a2),[x1=x3::x4])]]
Representation:
axiom_def (1, sequences, ’domain closure’,
[all v(1):seq(tv(1)), (eq(v(1):seq(tv(1)),nil_seq) \/
[ex v(2):tv(1), ex v(3):seq(tv(1)), eq(v(1):seq(tv(1)),seq_cons(v(2):tv(1),
v(3):seq(tv(1))):seq(tv(1))) ])]). [ x1/seq(a2),[x1= < > ( x3/a2, x4/seq(a2),[x1=x3::x4])]] [ x1/seq(a2),[x1= < > ( x3/a2, x4/seq(a2),[x1=x3::x4])]] “fol_law(FOL_law_Id, FOL_law_description, FOL_law_specification).”. The argument “FOL_law_Id” is the unique identifier of the FOL law, i.e. a positive integer. “FOL_law_description” is the name of a FOL law. “FOL_law_specification” is a list which has
the ground representation of the specification of FOL law. The argument “FOL_law_Id” is the unique identifier of the FOL law, i.e. a positive integer. “FOL_law_description” is the name of a FOL law. “FOL_law_specification” is a list which has
the ground representation of the specification of FOL law. 3.5 Representation of first-order logic laws The FOL laws are equivalence preserving transformation rules. Each FOL law is specified by
a FOL formula. They are represented by predicates fol_law_ID/1 and fol_law/3 as follows. The
predicate The FOL laws are equivalence preserving transformation rules. Each FOL law is specified by
a FOL formula. They are represented by predicates fol_law_ID/1 and fol_law/3 as follows. The
predicate “fol_law_ID(FOL_laws_Ids)” represents the identifiers of all FOL laws in the KB. Its argument “FOL_laws_Ids” is a list
with the identifiers of all FOL laws. The specification of each FOL law is represented by a
predicate of the form represents the identifiers of all FOL laws in the KB. Its argument “FOL_laws_Ids” is a list
with the identifiers of all FOL laws. The specification of each FOL law is represented by a
predicate of the form “fol_law(FOL_law_Id, FOL_law_description, FOL_law_specification).”. Representation: theorem(1, progr1, spec_struct1,
[all v(1):seq(int),all v(2):int, (sum(v(1):seq(int), v(2):int):int <->
sum_s(v(1):seq(int), v(2):int))]). x1/seq(Z), x2/Z (sum(x1,x2) ↔ sums(x1,x2)) x1/seq(Z), x2/Z (sum(x1,x2) ↔ sums(x1,x2)) Comp(Pr) Spec A |= x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2)) Pr is the logic program for predicate sum/2, excluding the DT definitions. Comp(Pr) is the
complement of the program Pr. Spec is the specification of predicate sum/2, i.e. sumS(x1,x2). A is the theory for sequences, i.e. the underlying DTs for predicate sum/2, including the
specifications of the DT operations. 3.6.1 Initial theorem The theorems that have to be proved must also be represented in the KB. Each theorem is
specified by a FOL formula. They are represented by the predicates “theorem_ID/1” and
“theorem/4” as follows. The predicate “theorem/4” as follows. The predicate “theorem_ID(Theorems_Ids)” “theorem_ID(Theorems_Ids)” “theorem_ID(Theorems_Ids)” www.intechopen.com 169 Knowledge Representation in a Proof Checker for Logic Programs represents the identifiers of all theorems that are available in the KB. Its argument
“Theorems_Ids” is a list with the identifiers of all theorems. The specification of each theorem
is represented by a predicate of the form represents the identifiers of all theorems that are available in the KB. Its argument
“Theorems_Ids” is a list with the identifiers of all theorems. The specification of each theorem
is represented by a predicate of the form “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” The argument “Theorem_Id” is the unique identifier of the theorem, i.e. a positive integer. The arguments “Program_Id” and “Spec_struct_Id” are the unique identifiers of the program
and the structured specifications respectively. “Theorem_specification” is a list which has the
representation of the specification of theorem. Example: The predicate sum(x1, x2) where Type(sum) = seq(Z) Z is true iff x2 is the sum of
the sequence of integers x1. The correctness theorem for predicate sum/2 and the theory
which is used to prove it is as follows. 3.6.2 Theorems in structured form The specification of a theorem may need to be transformed into structured form in order to
proceed to the proof. The structure form of theorems facilitates the proof task. Each theorem
in structured form is specified by a FOL formula. They are represented by the predicates
“theorem_struct_ID/1” and “theorem_struct/4” as follows. The predicate “theorem_struct_ID(Theorems_Ids)” “theorem_struct_ID(Theorems_Ids)” represents the identifiers of all theorems available in the KB with the specification part in
structured form. Its argument “Theorems_Ids” is a list with the identifiers of all theorems in
structured form. The specification of each theorem is represented by a predicate of the form Representation:
3.7 An example theory and theorem
Throughout this Chapter we use the correctness theorem and theory for predicate sum/2.
That is,
Comp(Pr) Spec A |= x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2))
The ground representation of theory is also illustrated.
Theory
The logic program completion Comp(Pr) of Pr is as follows.
Representation:
progr_clause(progr1, 1,[all v(1):seq(int), all v(2):int, [sum(v(1):seq(int),v(2):int) <->
((p1(v(1):seq(int)) /\p2(v(1):seq(int), v(2):int)) \/ [ex v(3):int, ex v(4):seq(int), ex v(5):int,
x1/seq(Z),x2/Z,[sum(x1,x2)↔ (p1(x1)p2(x1,x2) [x3/Z, x4/seq(Z),
x5/Z,[~p1(x1)p3(x1,x3,x4)p4(x1,x3,x5,x2)sum(x4,x5)]])]
x1/seq(Z),[p1(x1)↔empty_seq(x1)]
x1/seq(Z),x2/Z,[p2(x1,x2) ↔neutral_add_subtr_int(x2)]
x1/seq(Z),x2/Z,x3/seq(Z),[p3(x1,x2,x3)↔p5(x1,x2,x3)p6(x1,x2,x3)]
x1/seq(Z),x2/Z,x3/seq(Z),[p5(x1,x2,x3)↔head(x1,x2)]
x1/seq(Z),x2/Z,x3/seq(Z),[p6(x1,x2,x3)↔tail(x1,x3)]
x1/seq(Z),x2/Z,x3/Z,x4/Z,[p4(x1,x2,x3,x4)↔plus_int(x3,x2,x4)]
theorem_struct(1, progr1, spec_struct1,
[all v(1):seq(int), all v(2):int, (sum(v(1):seq(int), v(2):int) <->
((eq(v(1):seq(int),nil_seq:seq(tv(1))) /\eq(v(2):int,0:int)) \/ [ex v(3):int,
ex v(4):int, ex v(5):seq(int), (eq(v(1):seq(int), seq_cons(v(4):int,
v(5):seq(int)):seq(int) ) /\ eq(v(2):int,plus(v(4):int, v(3):int)) /\
sum_s(v(5):seq(int), v(3):int) )]) )]).
x1/seq(Z), x2/Z (sums(x1,x2) ↔ [x1=<>x2=0 [x4/Z, x5/Z,
x6/seq(Z),[x1=x5::x6 x2=x5+x4 sums(x6,x4)]]]) x1/seq(Z), x2/Z (sums(x1,x2) ↔ [x1=<>x2=0 [x4/Z, x5/Z,
x6/seq(Z),[x1=x5::x6 x2=x5+x4 sums(x6,x4)]]]) “theorem_struct(Theorem_struct_Id,Program_Id,Spec_struct_Id, Theorem_specification).”. “theorem_struct(Theorem_struct_Id,Program_Id,Spec_struct_Id, Theorem_specification) The argument “Theorem_struct_Id” is the unique identifier, i.e. a positive integer, of the
theorem whose specification part is in structured form. The arguments “Program_Id” and
“Spec_struct_Id” are the unique identifiers of the program and the structured specifications
respectively. “Theorem_specification” is a list which has the representation of the specification
of theorem. www.intechopen.com 170 Advances in Knowledge Representation Theory The logic program completion Comp(Pr) of Pr is as follows. Representation:
x1/seq(Z),x2/Z,[sum(x1,x2)↔ (p1(x1)p2(x1,x2) [x3/Z, x4/seq(Z),
x5/Z,[~p1(x1)p3(x1,x3,x4)p4(x1,x3,x5,x2)sum(x4,x5)]])]
x1/seq(Z),[p1(x1)↔empty_seq(x1)]
x1/seq(Z),x2/Z,[p2(x1,x2) ↔neutral_add_subtr_int(x2)]
x1/seq(Z),x2/Z,x3/seq(Z),[p3(x1,x2,x3)↔p5(x1,x2,x3)p6(x1,x2,x3)]
x1/seq(Z),x2/Z,x3/seq(Z),[p5(x1,x2,x3)↔head(x1,x2)]
x1/seq(Z),x2/Z,x3/seq(Z),[p6(x1,x2,x3)↔tail(x1,x3)]
x1/seq(Z),x2/Z,x3/Z,x4/Z,[p4(x1,x2,x3,x4)↔plus_int(x3,x2,x4)] Example In order to construct the theorem in structured form the predicate specification must be
transformed into structured form. The initial logic specification for predicate sum/2 is the
following. x1/seq(Z), x2/Z (sumS(x1,x2) ↔ x2 =
1
#
1
1
x
i
i
x
) The logic specification of sumS(x1,x2) in structured form and its representation are following. Theorem Specification: Representation: theorem_struct(1, progr1, spec_struct1,
[all v(1):seq(int), all v(2):int, (sum(v(1):seq(int), v(2):int) <->
((eq(v(1):seq(int),nil_seq:seq(tv(1))) /\eq(v(2):int,0:int)) \/ [ex v(3):int,
ex v(4):int, ex v(5):seq(int), (eq(v(1):seq(int), seq_cons(v(4):int,
v(5):seq(int)):seq(int) ) /\ eq(v(2):int,plus(v(4):int, v(3):int)) /\
sum_s(v(5):seq(int), v(3):int) )]) )]). 3.7 An example theory and theorem Throughout this Chapter we use the correctness theorem and theory for predicate sum/2
That is, Comp(Pr) Spec A |= x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2)) The ground representation of theory is also illustrated. Representation:
progr_clause(progr1, 1,[all v(1):seq(int), all v(2):int, [sum(v(1):seq(int),v(2):int) <->
((p1(v(1):seq(int)) /\p2(v(1):seq(int), v(2):int)) \/ [ex v(3):int, ex v(4):seq(int), ex v(5):int, www.intechopen.com 171 Knowledge Representation in a Proof Checker for Logic Programs [~p1(v(1):seq(int)) /\ p3(v(1):seq(int), v(3):int,v(4):seq(int)) /\ p4(v(1):seq(int),v(3):int,
v(5):int, v(2):int) /\ sum(v(4):seq(int),v(5):int)]])]]). [~p1(v(1):seq(int)) /\ p3(v(1):seq(int), v(3):int,v(4):seq(int)) /\ p4(v(1):seq(int),v(3):int,
v(5):int, v(2):int) /\ sum(v(4):seq(int),v(5):int)]])]]). q
progr_clause(progr1, 2, [all v(6):seq(int),[p1(v(6):seq(int)) <-> empty_seq(v(6):seq(int))]]).
progr_clause(progr1, 3, [all v(7):seq(int), all v(8):int,[p2(v(7):seq(int), v(8):int) <->
neutral_add_subtr_int(v(8):int)]]).
progr_clause(progr1, 3, [all v(7):seq(int), all v(8):int,[p2(v(7):seq(int), v(8):int) <->
neutral_add_subtr_int(v(8):int)]]).
progr_clause(progr1, 4, [all v(9):seq(int), all v(10):int, all v(11):seq(int), [p3(v(9):seq(int),
v(10):int, v(11):seq(int))<-> p5(v(9):seq(int), v(10):int, v(11):seq(int)) /\ p6(v(9):seq(int),
v(10):int, v(11):seq(int))]]).
progr_clause(progr1, 4, [all v(9):seq(int), all v(10):int, all v(11):seq(int), [p3(v(9):seq(int),
v(10):int, v(11):seq(int))<-> p5(v(9):seq(int), v(10):int, v(11):seq(int)) /\ p6(v(9):seq(int),
v(10):int, v(11):seq(int))]]). q
progr_clause(progr1, 5, [all v(12):seq(int), all v(13):int, all v(14):seq(int),[p5(v(12):seq(int),
v(13):int, v(14):seq(int)) <-> head(v(12):seq(int), v(13):int)]]).
progr_clause(progr1, 5, [all v(12):seq(int), all v(13):int, all v(14):seq(int),[p5(v(12):seq(int),
v(13):int, v(14):seq(int)) <-> head(v(12):seq(int), v(13):int)]]).
progr_clause(progr1, 6, [all v(15):seq(int), all v(17):int, all v(16):seq(int),[p6(v(15):seq(int),
v(17):int, v(16):seq(int))<-> tail(v(15):seq(int), v(16):seq(int))]]).
progr_clause(progr1, 6, [all v(15):seq(int), all v(17):int, all v(16):seq(int),[p6(v(15):seq(int),
v(17):int, v(16):seq(int))<-> tail(v(15):seq(int), v(16):seq(int))]]).
progr_clause(progr1,
7,
[all
v(18):seq(int),
all
v(19):int,
all
v(20):int,
all
v(21):int,[p4(v(18):seq(int), v(19):int, v(20):int, v(21):int) <-> plus_int(v(20):int, v(19):int,
v(21):int)]]). The logic specification (Spec) is shown in Section 3.6 and its representation in ground form. The theory A of the DT operations including the specification of the DT operations is as
follows. The theory A of the DT operations including the specification of the DT operations is as
follows. Axioms Domain closure axiom for sequences Domain closure axiom for sequences x1/seq(a2),[x1= < > ( x3/a2,x4/seq(a2),[x1=x3::x4])] Its ground representation is shown in section 3.4. Its ground representation is shown in section 3.4. Uniqueness axioms for sequences Uniqueness axioms for sequences i
x1/a2,x3/seq(a2),[~[x1::x3/a2= < > ]] ii
x1/a2,x3/a2,x4/seq(a2),x5/seq(a2),[x1::x4=x3::x5 x1=x3 x4=x5] Representation:
axiom_def(2, sequences, "uniqueness i",
[all v(1):tv(1), all v(2):seq(tv(1)), [~[eq(seq_cons
(v(1):tv(1), v(2):seq(tv(1))):tv(1),nil_seq:seq(tv(1)))]]]). q
q
q
axiom_def(3,
sequences,
"uniqueness
ii",
[all
v(1):tv(1),
all
v(2):tv(1),
all v(3):seq(tv(1)), all v(4):seq(tv(1)),[eq(seq_cons(v(1):tv(1), v(3):seq(tv(1))):seq(tv(1)),
seq_cons(v(2):tv(1),
v(4):seq(tv(1))):seq(tv(1)))
->
(eq(v(1):tv(1),
v(2):tv(1))
/\
eq(v(3):seq(tv(1)), v(4):seq(tv(1))))]]). Definition of summation operation over 0 entities Definition of summation operation over 0 entities x1/seq(Z),[x1= < > Σ((i=1 to #x1 ) x1i )=0] Representation:
axiom_def(4, sequences, "summation over 0 entities", [all v(1):seq(int), [eq(v(1):seq(int),nil_seq)
-> eq(sum(1:int,len(v(1):seq(int)):int, v(1,v(3):nat):int), 0:int)]]).
axiom_def(4, sequences, "summation over 0 entities", [all v(1):seq(int), [eq(v(1):seq(int),nil_seq)
-> eq(sum(1:int,len(v(1):seq(int)):int, v(1,v(3):nat):int), 0:int)]]). Representation:
dtOp_sp(empty_seq, 1, "seq: empty", [all v(1):seq(tv(1)), [empty_seq(v(1):seq(tv(1))) <->
eq(v(1):seq(tv(1)),nil_seq:seq(tv(1)))]]). q
q
q
q
dtOp_sp(head, 2, "seq: head", [all v(1):seq(tv(1)), all v(2):tv(1),[head(v(1):seq(tv(1)), v(2):tv(1))
<->
[~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1)))
/\
[ex
v(3):seq(tv(1)),
[eq(v(1):seq
(tv(1)),seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]]). q
q
dtOp_sp(tail, 3, "seq: tail", [all v(1):seq(tv(1)), all v(2):seq(tv(1)), [tail(v(1):seq(tv(1)),
v(2):seq(tv(1))) <-> [ex v(3):tv(1),[~eq(v(1):seq(tv(1)), nil_seq:seq (tv(1))) /\ eq(v(1),
seq_cons(v(3):tv(1),v(2):seq(tv(1))):tv(1))]]]]). q
( ( )
( ) ( )
q(
( )))
( ))
)
dtOp_sp(neutral_add_subtr_int,
8,
"int:
neutral_add_subtr_int",
[all
v(1):int,
[neutral_add_subtr_int(v(1):int) <-> eq(v(1):int,0:int)]]).
dtOp_sp(plus_int,
9,"int:
plus_int",
[all
v(1):int,
all
v(2):int,
all
v(3):int,
[plus_int(v(1):int,v(2):int,v(3):int) <-> eq(v(3):int,plus(v(2):int,v(1):int))]]). Lemmas www.intechopen.com 172 Advances in Knowledge Representation x1/seq(a2),[x1 ≠ < > ↔ [x3/a2,x4/seq(a2),[x1=x3::x4/a2]]]
x1/a2,x3/seq(a2),x4/seq(a2),[x3=x1::x4(x5/N,[2≤x5≤#x3x3(x5)=x4(x5-1)])]
x1/seq(a2),x3/seq(a2),x4/a2,[x1=x4::x3#x1=#x3+1]
x1/a2,x3/seq(a2),x4/seq(a2),[x3=x1::x4/a2x1=x31/a2] Representation:
lemma_sp(1, sequences, "Non-empty sequences have at least one element",[all v(1):seq(tv(1)),
[~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1))) <-> [ex v(2):tv(1), ex v(3):seq(tv(1)), [eq(v(1):seq(tv(1)),
seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]).
lemma_sp(1, sequences, "Non-empty sequences have at least one element",[all v(1):seq(tv(1)),
[~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1))) <-> [ex v(2):tv(1), ex v(3):seq(tv(1)), [eq(v(1):seq(tv(1)),
seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]). q
q
lemma_sp(2,sequences,"if sequence s has tail t then the element si is identical to the element ti-
1",[all v(1):tv(1), all v(2):seq(tv(1)), all v(3):seq(tv(1)),[eq(v(2):seq(tv(1)), seq_cons(v(1):tv(1),
v(3):seq(tv(1))):seq(tv(1))) -> (all v(4):nat, [le(2:nat, v(4):nat) /\ le(v(4):nat, len(v(2):seq
(tv(1))):nat) -> eq(v(2, v(4):nat):tv(1), v(3, minus(v(4): nat,1:nat) ))])]]). q
lemma_sp(3, sequences, "If sequence s has tail t then the length of s is equal to the
length of t plus 1", [all v(1):seq(tv(1)), all v(2):seq(tv(1)), all v(3):tv(1), [eq(v(1):seq(tv(1)),
seq_cons(v(3):tv(1), v(2):seq(tv(1))):seq(tv(1))) -> eq(len(v(1):seq(tv(1))): nat,plus(len(v(2):
seq(tv(1))):nat,1:nat))]]). q
lemma_sp(4, sequences, "If sequence s is non-empty then its head h is identical to its first
element",
[all
v(1):tv(1),
all
v(2):seq(tv(1)),
all
v(3):seq(tv(1)),[eq(v(2):seq(tv(1)),
seq_cons(v(1):tv(1), v(3):seq(tv(1))):tv(1)) -> eq(v(1):tv(1), v(2, 1:int):tv(1))]]). Logic specifications of DT operations Logic specifications of DT operations x1/seq(a2),[empty_seq(x1)↔ x1= < > ]
x1/Z,[neutral_add_subtr_int(x1) ↔x1=0]
x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1≠ < > [ x4/seq(a2),[x1=x3::x4/a2]]]]
x1/seq(a2),x3/seq(a2),[tail(x1,x3)↔ [x4/a2,[x1≠< > x1=x4::x3/a2]]]
x1/Z,x2/Z,x3/Z,[plus_int(x1,x2,x3)x3=x2+x1] x1/seq(a2),[empty_seq(x1)↔ x1= < > ] x1/seq(a2),[empty_seq(x1)↔ x1= < > ]
x1/Z,[neutral_add_subtr_int(x1) ↔x1=0] x1/Z,[neutral_add_subtr_int(x1) ↔x1=0] x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1≠ < > [ x4/seq(a2),[x1=x3::x4/a2]]]] x1/seq(a2),x3/seq(a2),[tail(x1,x3)↔ [x4/a2,[x1≠< > x1=x4::x3/a2]]] x1/Z,x2/Z,x3/Z,[plus_int(x1,x2,x3)x3=x2+x1] 4. Schematic view of the Interaction of the main components In this section, a schematic view of the proof checker and the interaction of its main
components will be shown. In addition, the functions of its components will be discussed. An example of a proof step will illustrate the use of the KB representation in the proof task. www.intechopen.com 173 Knowledge Representation in a Proof Checker for Logic Programs user
Make necessary
selections
Knowledge
Base
‐specifications
‐axioms
‐lemmas
‐specs DT
operations
‐logic
programs
Perform Proof Step
•
Select Theory
•
Select Proof Scheme
•
Specify Theorem
1
2
3
Fig. 3. Schematic View of the Theorem Proof Checker. o
edge
Base
‐specifications
‐axioms
‐lemmas
‐specs DT
operations
‐logic
programs p
‐axioms
‐lemmas
‐specs DT
operations
‐logic
programs Make necessary
selections Perform Proof Step Fig. 3. Schematic View of the Theorem Proof Checker. 4.2 Schematic view of specification transformer Fig. 4 depicts the procedure for transforming a specification in the required structured form,
which is similar to the previous case. In this case however, the underlying theory consists of
Spec U Axioms U Lemmas. Initially, the user selects a specification, then the rest elements of
the theory are automatically selected by the system. Next, in step 2, the user has to select
specific theory elements and transformation rules. In step 3, the selected transformation rule
is performed. Step 2 and step 3 are performed iteratively until the specification is
transformed in the required structured form. user
Make necessary
selections
Knowledge
Base
-specifications
-axioms
-lemmas
-specs DT
operations
Transformation Step
Select Logic Specification and
rest elements of the theory
1
2
3
Fig. 4. Schematic View of Specification Transformer. 4.3 Illustration of a proof step
The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step”
procedure and that is why we will not present it. The schematic view of the main algorithm
for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is
assumed that the user has selected some theory elements, and a transformation rule that
should be applied to the current proof step. Select Logic Specification and
rest elements of the theory Knowledge
Base
-specifications
-axioms
-lemmas
-specs DT
operations Make necessary
selections Transformation Step Fig. 4. Schematic View of Specification Transformer. 4.1 Schematic view of the theorem proof checker The process of proving a theorem is shown in Fig. 3 and consists of three steps.
Step 1: In order to prove the correctness of a theorem the user initially has to specify the
theorem that is going to be proved and to select the theory and the proof scheme that
will be used for the proof. The theory is retrieved from the KB and it is presented to the
user for selection. It consists of a program complement, a logic specification, axioms and
lemmas. The corresponding window of the interface which allows the user to make these
selections is shown in Fig. 6. g
Step 2: After the selection the user proceeds to the actual proof of the specific theorem. In order to do that he has to select specific parts from the theorem, the theory and the
transformation rules that will be applied. The transformation rules that can be applied
are first order logic (FOL) laws, folding and unfolding.
Step 3: In this step the selected transformation is applied and the equivalent form of the
theorem is presented to the user. The user can validate the result. He is allowed to
approve or cancel the specific proof step. The last two steps are performed iteratively until the theorem is proved. The last two steps are performed iteratively until the theorem is proved. www.intechopen.com 174 Advances in Knowledge Representation 4.3 Illustration of a proof step The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step”
procedure and that is why we will not present it. The schematic view of the main algorithm
for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is
assumed that the user has selected some theory elements, and a transformation rule that
should be applied to the current proof step. The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step”
procedure and that is why we will not present it. The schematic view of the main algorithm
for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is
assumed that the user has selected some theory elements, and a transformation rule that
should be applied to the current proof step. www.intechopen.com Knowledge Representation in a Proof Checker for Logic Programs 175 Fig. 5. Schematic view of the “performProofStep” procedure. Fig. 5. Schematic view of the “performProofStep” procedure. Fig. 5. Schematic view of the “performProofStep” procedure. The function block diagram of the algorithm “performProofStep” shown in Fig. 5 will be
discussed through an example. Consider that our theorem has been transformed and its
current form is the following: x1/seq(Z),x2/Z (sums(x1,x2) ↔
(x1= <> x2=0 [x3/Z,[x4/seq(Z),false x2=x4+x3 sums(x4,x3)]])) (x1= <> x2=0 [x3/Z,[x4/seq(Z),false x2=x4+x3 sums(x4,x3)]])) The user has selected the following FOL law to be applied to the above theorem: P false ↔false P false ↔false Initially, the current theorem is converted to the corresponding ground representation by
the procedure “ConvertGr” and we get: Initially, the current theorem is converted to the corresponding ground representation by
the procedure “ConvertGr” and we get: [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<->
(eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/
[ex v(3):int,[ex v(4):int,[ex v(5):seq(int),
false/\eq(v(2):int,plus(v(4):int,v(3):int):int)/\sum_s(v(5):seq(int),v(3):int)]]])]] Then, the procedure “applyProofStep” applies the transformation rule to the current theorem
and derives the new theorem. In order to do that, this procedure constructs and asserts a set
of clauses which implement the selected transformation rule. Then, it applies this set of
clauses and derives the new theorem in ground representation. That is, [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<->
(eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/
[ex v(3):int,[ex v(4):int,[ex v(5):seq(int),
false /\ sum_s(v(5):seq(int),v(3):int)]]])]] [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<->
(eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/
[ex v(3):int,[ex v(4):int,[ex v(5):seq(int),
false /\ sum_s(v(5):seq(int),v(3):int)]]])]] The new theorem is then converted to the corresponding non-ground form in order to be
presented to the user. That is, [x1/seq(Z),[x2/Z,sums(x1,x2)
↔
(x1=<>
x2=0
[x3/Z,[x4/seq(Z),
falsesums(x4,x3)]])]] www.intechopen.com 176 Advances in Knowledge Representation 5.1 Interface illustration of the “Prove Program Correctness” task If the user selects the button “Prove Program Correctness” from the main window, the
window shown in Fig. 6 will be displayed. The aim of this window is to allow the user to
select the appropriate theory and proof scheme that he will use in his proof. In addition, the
user can either select a theorem or define a new one. After the appropriate selections, the user can proceed to the actual proof of the theorem by
selecting the button “Prove Correctness Theorem”. The window that appears next is shown in
Fig. 7. The aim of this window is to assist the user in the proof task. The theorem to be
proved and its logic specification are displayed in the corresponding position on the top-left
side of the window. This window has many functions. The user is able to choose theory
elements from the KB that will be used for the current proof step. After selection by the user
of the appropriate components for the current proof step the proper inference rule is
selected and it is applied automatically. The result of the proof step is shown to the user. Moreover, the user is able to cancel the last proof step, or to create a report with all the
details of the proof steps that have been applied so far. 5. System interface To enable users to guide this proof checker it is necessary to provide a well-designed user
interface. The design of the interface of an interactive verifier depends on the intended user. In our verifier we distinguish two kinds of users, the “basic users” and the “advanced or
experienced users”. We call “basic user” a user who is interested in proving a theorem. We call
an “advanced user” a user who in addition to proving a theorem he/she may want to
enhance the KB of the system in order to be able to deal with additional theorems. Such a
user is expected to be able to update the KB of axioms, lemmas, predicate specifications,
specifications of DT operations and programs. We will use the word “user” to mean both the
“basic user” and the “advanced user”. Both kinds of users are expected to know very well the
correctness method which is supported by our system (Marakakis, 2005). Initially, the system displays the main, top-level window as shown in Fig. 1. This window
has a button for each of its main functions. The name of each button defines its function as
well, that is, “Transform Logic Specification into Structured Form”, “Prove Program Correctness”
and “Update Knowledge Base”. The selection of each button opens a new window which has a
detailed description of the required functions for the corresponding operation. Now we will
illustrate the “Prove Program Correctness” function to better understand the whole interaction
with the user. 5.1.1 Illustration of a proof step Let’s assume that the user has selected a theorem to be proved, its corresponding theory and
a proof scheme. Therefore, he has proceeded to the verification task. For example, he likes to
prove the following theorem: Comp(Pr) Spec A |= x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1,x2)) 6. Results The results of this research work involve the development of a proof checker that can be
used efficiently by its users for the proof of correctness theorems for logic programs
constructed by our schema-based method (Marakakis, 1997). The system has been tested
and allows the verification of non-trivial logic programs. Our proof checker is highly
modular, and allows the user to focus on proof decisions rather than on the details of how to
apply each proof step, since this is done automatically by the system. The update of the KB
is supported by the proof-checker as well. The overall interface of our system is user–
friendly and facilitates the proof task. The main features of our system which make it to be an effective and useful tool for the
interactive verification of logic programs constructed by the method (Marakakis, 1997) are
the following.
The proof of the correctness theorem is guided by the logic-program construction
method (Marakakis, 1997). That is, the user has to select a proof scheme based on the
applied program schema for the construction of the top-level predicate of the logic
program whose correctness will be shown.
Proof steps can be cancelled at any stage of the proof. Therefore, a proof can move to
any previous state. any previous state.
The system supports the proof of a new theorem as part of the proof of the initial
theorem.
The system supports the proof of a new theorem as part of the proof of the initial
theorem.
The update of the theories stored in the KB of the system is supported as well.
The overall verification task including the update of the KB is performed through a
user-friendly interface.
At any stage during the verification task the user can get a detailed report of all proof
steps performed up to that point. So, he can get an overall view of the proof performed
so far. Comp(Pr) Spec A |= x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1,x2)) The user has selected the “Incremental” proof scheme which requires proof by induction on
an inductive DT. Let assume that the correctness theorem has been transformed to the
following form: www.intechopen.com www.intechopen.com 177 Knowledge Representation in a Proof Checker for Logic Programs x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z),
x1<> x1=x4::x5 x1 <> x1=x4::x5 x2=x4+x3
sum(x5,x3)]
Fig. 6. The window for selecting Theory, Theorem and Proof Scheme
Fig. 7. The window for proving a correctness theorem x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z),
x1<> x1=x4::x5 x1 <> x1=x4::x5 x2=x4+x3
sum(x5,x3)] sum(x5,x3)] Fig. 6. The window for selecting Theory, Theorem and Proof Scheme g
g
y
Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem www.intechopen.com 178 Advances in Knowledge Representation In order to proceed to the next proof step the following steps should be performed:
First, the user selects “Logic Spec. of DT_Op” and then he selects the “Head” DT
operation:
First, the user selects “Logic Spec. of DT_Op” and then he selects the “Head” DT
operation: x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < > [x4/seq(a2),[x1=x3::x4/a2]]]] x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < > [x4/seq(a2),[x1=x3::x4/a2]]]] x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < > [x4/seq(a2),[x1=x3::x4/a2]]]]
Then he selects the button “Apply Proof Step” and the result is shown in the next line of
the “Induction Step” area:
Then he selects the button “Apply Proof Step” and the result is shown in the next line of
the “Induction Step” area: x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z),
x1<> x1=x4::x5 head(x1, x4) x2=x4+x3 sum(x5,x3)] x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z),
x1<> x1=x4::x5 head(x1, x4) x2=x4+x3 sum(x5,x3)] The user continues applying proof steps until to complete the proof of the theorem. 7. Conclusions This chapter has presented our proof checker. It has been focused on the knowledge
representation layer and on its use by the main reasoning algorithms. Special importance on www.intechopen.com 179 Knowledge Representation in a Proof Checker for Logic Programs the implementation of the proof checker has been given on flexibility so the system being
developed could be enhanced with additional proof tasks. Finally, the main implementation
criteria for the knowledge representation are the support for an efficient and modular
implementation of the verifier. the implementation of the proof checker has been given on flexibility so the system being
developed could be enhanced with additional proof tasks. Finally, the main implementation
criteria for the knowledge representation are the support for an efficient and modular
implementation of the verifier. In our proof checker, a proof is guided by the selected proof scheme. The selection of a proof
scheme is related with the construction of the top-level predicate of the program that will be
verified. The user-friendly interface of our system facilitates the proof task in all stages and
the update of the KB. Its modular implementation makes our proof checker extensible and
amenable to improvements. The natural progression of our proof checker is the addition of automation. That is, we
intend to move proof decisions from the user to the system. The verifier should have the
capacity to suggest proof steps to the user. Once they are accepted by the user they will be
performed automatically. Future improvements aim to minimize the interaction with the
user and to maximize the automation of the verification task. 8. References Clarke, E. & Wing, J. (1996). Formal Methods: State of the Art and Future Directions, ACM
Computing Surveys, Vol. 28, No. 4, pp. 626-643, December, 1996. Gallagher, J. (1993). Tutorial on Specialization of Logic Programs, Proceedings of PERM’93,
the ACM Sigplan Symposium on Partial Evaluation and Semantics-Based Program
Manipulation, pp. 88-98, ACM Press, 1993. Hill, P. M. & Gallagher, J. (1998). Meta-programming in Logic Programming, Handbook of
Logic in Artificial Intelligence and Logic Programming, vol. 5, edited by D. Gabbay, C. Hogger, J. Robinson, pp. 421-497, Clarendon Press, Oxford, 1998. Hill, P. M. & Lloyd, J. W. (1994). The Gödel Programming Language, The MIT Press,
1994. Lindsay, P. (1988). A Survey of Mechanical Support for Formal Reasoning, Software
Engineering Journal, vol. 3, no. 1, pp.3-27, 1988. Lloyd, J.W. (1994). Practical Advantages of Declarative Programming. In Proceedings of the
Joint Conference on Declarative Programming, GULP-PRODE’94, 1994. Loveland, D. W. (1986). Automated Theorem Proving: Mapping Logic in AI, Proceedings of
the ACM SIGART International Symposium on Methodologies for Intelligent Systems, pp. 214-229, Knoxville, Tennessee, United States, October 22-24, 1986. Marakakis, E. (1997). Logic Program Development Based on Typed, Moded Schemata and
Data Types, PhD thesis, University of Bristol, February, 1997. Marakakis, E. (2005). Guided Correctness Proofs of Logic Programs, Proc. the 23th IASTED
International Multi-Conference on Applied Informatics, edited by M.H. Hamza, pp. 668-
673, Innsbruck, Austria, 2005. Marakakis, E. & Gallagher. J.P. (1994). Schema-Based Top-Down Design of Logic Programs
Using Abstract Data Types, LNCS 883, Proc. of 4th Int. Workshops on Logic Program
Synthesis and Transformation - Meta-Programming in Logic, pp.138-153, Pisa, Italy,
1994. www.intechopen.com 180 Advances in Knowledge Representation Advances in Knowledge Representation
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Marakakis, E. & Papadakis, N. (2009). An Interactive Verifier for Logic Programs, Proc. Of
13th IASTED International Conference on Artificial Intelligence and Soft Computing , pp.
130-137, 2009. Marakakis, E. & Papadakis, N. (2009). An Interactive Verifier for Logic Programs, Proc. Of
13th IASTED International Conference on Artificial Intelligence and Soft Computing , pp. 130-137, 2009. www.intechopen.com Advances in Knowledge Representation
Edited by Dr. Carlos Ramirez Advances in Knowledge Representation
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https://openalex.org/W4313894840 | https://www.nature.com/articles/s41598-023-27579-3.pdf | English | null | Reference range of complete blood count, Ret-He, immature reticulocyte fraction, reticulocyte production index in healthy babies aged 1–4 months | Scientific reports | 2,023 | cc-by | 4,940 | Reference range of complete
blood count, Ret‑He, immature
reticulocyte fraction, reticulocyte
production index in healthy babies
aged 1–4 months
OPEN Harapan Parlindungan Ringoringo 1*, Lina Purnamasari 2, Ari Yunanto 3,
Meitria Syahadatina 4 & Nurul Hidayah 5 Harapan Parlindungan Ringoringo 1*, Lina Purnamasari 2, Ari Yunanto 3,
Meitria Syahadatina 4 & Nurul Hidayah 5 Establishing reference ranges of the complete blood count (CBC), reticulocyte hemoglobin content
(Ret-He), immature reticulocyte fraction (IRF), and reticulocyte production index (RPI) helps
diagnose a disease related to the changes in erythrocyte indices, white blood count, platelets, and
reticulocytes, especially in babies. Therefore, the study aims to establish a reference range for CBC and
reticulocyte parameters in healthy babies aged 1–4 months. The study design was a cross-sectional
study with descriptive analysis of CBC and reticulocyte in babies aged 1–4 months. Three hundred
forty-eight babies met the inclusion criteria. This study recruited 89 babies aged 1 month, 87 babies
aged 2 months, 86 babies aged 3 months, and 86 babies aged 4 months. The P5-P95 reference range
of healthy babies for hemoglobin (Hb) aged 1 month, 2 months, 3 months, and 4 months was 9.95 to
15.45 g/dL, 9.74 to 13.42 g/dL, 9.51 to 12.40 g/dL, and 10.04 to 13.10 g/dL respectively. The P3-P97
reference range of healthy babies for Hb aged 1 month, 2 months, 3 months, and 4 months was 9.60
to 15.90 g/dL, 9.46 to 13.97 g/dL, 9.26 to 12.82 g/dL, and 10.00 to 13.33 g/dL respectively. This study
also defined reference ranges for CBC, Ret-He, IRF, and RPI. The reference range of CBC, Ret-He, IRF,
and RPI for healthy babies aged 1–4 months in this study can be used as a benchmark. All ages anemia prevalence was 22.8% globally in 2019. The prevalence was highest among children under
five years, 39.7%, with the most contributing cause being dietary iron deficiency (ID)1. Anemia is still a major
global health problem. Thereby, the early detection of anemia is crucial considering its long-term effects that
can interfere with a baby’s growth and development. Several studies have shown the impact of iron deficiency
anemia (IDA) on cognitive and behavioral deteriorations2–4. Then, early diagnosis and treatment of impending
brain dysfunction in the pre-anemic stage are necessary to prevent neurological deficits. Iron deficiency and
IDA are caused by not giving oral iron supplementation and low iron stores at birth; the baby’s growth rate is
swift, and inadequate iron intake. www.nature.com/scientificreports www.nature.com/scientificreports Discussion Establishing the lower limit of P3-P97 and P5-P95 on examining specific parameters is commonly used statisti-
cally. For example, the WHO (World Health Organization) and CDC (Centers Of Disease Control and Preven-
tion) growth charts set the lower limit of Weight-for-age, Length/height-for-age, Head circumference-for-age,
and Arm circumference-for-age at P310. Determination of the lower limit of Hb with P3-P97 and P5-P95, of
course, by considering race, ethnicity, age, gender, and altitude above sea level11. This study accommodates all
reference range limits to be used flexibly.h gl
y
The results of this study showed the reference range of CBC, reticulocyte count, Ret-He, IRF, and RPI at
P3-P97 and P5-P95. Values below the lower limit of the reference range of Hb according to age can be used as a
limit to determine if a baby has anemia. In addition, the value below the lower limit of the reference range of Ret-
He according to age can be used as a limit to determine whether a baby has ID. The baby is suffered from IDA; if
the value of Hb and Ret-He is below the lower limit of the reference range. Thus, for example, this study indicates
that the lower limit of Hb for healthy babies aged 4 months (see Tables 1 and 2) can be taken at P3 and P5, i.e.,
10.00 g/dL and 10.04 g/dL, respectively. In addition, this study indicates that the lower limit of Ret-He for healthy
babies aged 4 months (see Tables 1 and 2) can be taken at P3, and P5, i.e., 17.40 pg and 19.22 pg, respectively.hf g
g
g
y
Therefore, to determine whether a baby aged 4 months is suffering from IDA if the value of Hb and Ret-
He is below the lower limit of the reference range. Combining several parameters, Hb, MCV, MCH, RDW,
reticulocyte count, and Ret He, in conjunction with the peripheral blood smear examination, will make an IDA
diagnosis undoubtedly. The examples above can also be used for babies aged 1 month, 2 months, and 3 months
(see Tables 1 and 2).i One study showed that IDA, iron depletion and iron deficiency incidence in babies aged 0–6 months were
40.8, 28.0 and 27.0%, respectively. The incidence of IDA in babies aged 0 months, 1 month, and 2 months were
11.8, 10.9 and 11.3%, respectively. Resultsh Three hundred forty-eight healthy babies (boys 53.4%, girls 46.6%) met the inclusion criteria. Therefore, this
study recruited 89 babies aged 1 month (boys 59.6%, girls 40.4%), 87 babies aged 2 months (boys 49.4%, girls
50.6%), 86 babies aged 3 months (boys 52.3%, girls 47.7%), and 86 babies aged 4 months (52.3% boys, 47.7%
girls). P5-P95 and P3-P97 of the complete blood count, reticulocyte count, Ret-He, immature reticulocyte frac-
tion, and reticulocyte production index for healthy babies aged 1–4 months can be seen in Tables 1 and 2.h The P5-P95 reference range of healthy babies for hemoglobin (Hb) aged 1 month, 2 months, 3 months, and
4 months was 9.95 to 15.45 g/dL, 9.74 to 13.42 g/dL, 9.51 to 12.40 g/dL, and 10.04 to 13.10 g/dL respectively. The
P3-P97 reference range of healthy babies for Hb aged 1 month, 2 months, 3 months, and 4 months was 9.60 to
15.90 g/dL, 9.46 to 13.97 g/dL, 9.26 to 12.82 g/dL, and 10.00 to 13.33 g/dL respectively. www.nature.com/scientificreports/ addition, to monitor oral iron therapy, these combining parameters can be used too. For example, a lower value
than the lower limit of the Hb reference range according to age indicates a baby is anemic. addition, to monitor oral iron therapy, these combining parameters can be used too. For example, a lower value
than the lower limit of the Hb reference range according to age indicates a baby is anemic. On the other hand, other erythrocyte indices reference ranges are needed to diagnose anemia, especially
suspected IDA. The main problem is determining if a baby has IDA with a simple, cheap, and fast laboratory
test; a small amount of blood is drawn and can be done in almost any health facility. It is even better if the ID
can be detected before IDA occurs. Conventionally, ID diagnosis is based on determining biochemical parameters, such as ferritin, transferrin
saturation, and soluble transferrin receptor. Nevertheless, these biomarkers are strongly influenced by the diurnal
phase, inflammation, infection, and malignancy, and of course, they are expensive, and not every health facility
can check them. In addition, many studies have shown that Ret-He can show iron deficiency without anemia5–7. Therefore, a lower value than the lower limit of the Ret-He reference range according to age indicates that an
infant is iron deficient.h i
The clinical utility of IRF applied in various circumstances, such as monitoring anemia treatment and neonatal
transfusion needs, can be a prognostic factor in prematurity anemia and diagnosing and monitoring aplastic
anemias. Furthermore, RPI monitors bone marrow response to iron-treated anemia8. In addition, RPI can be used
as a diagnostic guide to the etiology of anemia9. Uniquely, all erythrocyte indices and reticulocyte parameters
can be seen automatically on the Sysmex XN-450 Hematology Analyzer (Sysmex Corporation, Japan).h The purpose of this study was to obtain the lower limit of the baby’s hemoglobin value related to the age so
that it can be used to declare an anemic baby or not. Moreover, establishing reference ranges of the CBC, Ret-He,
IRF, and RPI helps diagnose a disease related to the changes in erythrocyte indices, white blood count, platelets,
and reticulocytes, especially in healthy babies aged 1–4 months. Reference range of complete
blood count, Ret‑He, immature
reticulocyte fraction, reticulocyte
production index in healthy babies
aged 1–4 months
OPEN t
q
Reference range data for complete blood count (CBC), reticulocyte hemoglobin content (Ret-He), immature
reticulocyte fraction (IRF), and reticulocyte production index (RPI) for babies 1–4 months old are limited. Therefore, determination of the reference range of CBC, Ret He, IRF, and RPI in babies 1–4 months is essential
to determine whether a baby is anemic or not. Combining several parameters, Hb (hemoglobin), MCV (mean
corpuscular volume), MCH (mean corpuscular hemoglobin), RDW (red cell distribution with), reticulocyte
count, Ret He, IRF, and RPI will undoubtedly make it easier to determine if a baby has ID before IDA occurs. In 1Division of Hematology‑Oncology, Department of Child Health, Faculty of Medicine, Lambung Mangkurat
University – RSD Idaman Banjarbaru, Banjarbaru, South Kalimantan, Indonesia. 2Pediatric Resident, Department
of Child Health, Faculty of Medicine, Lambung Mangkurat University- Ulin General Hospital, Banjarmasin, South
Kalimantan, Indonesia. 3Division of Nenonatology, Department of Child Health, Faculty of Medicine, Lambung
Mangkurat University- Ulin General Hospital, Banjarmasin, South Kalimantan, Indonesia. 4Faculty of Medicine,
Reproductive Health-Maternal and Child Health-Family Planning, Lambung Mangkurat University, Banjarmasin,
South Kalimantan, Indonesia. 5Division of Neurology, Department of Child Health, Faculty of Medicine,
Lambung Mangkurat University- Ulin General Hospital, Banjarmasin, South Kalimantan, Indonesia. *email:
parlinringoringo@ulm.ac.id | https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 www.nature.com/scientificreports/ Discussion P5-P95 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular
volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell
distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution
with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils
absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte
production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. The results of this study for reference range of other erythrocyte indices, leukocyte, diff count, and platelets
can be considered a guide in diagnosing a disease relating to the changes in erythrocyte indices, white blood
count, platelets, especially in babies.l The results of this study for reference range of other erythrocyte indices, leukocyte, diff count, and platelets
can be considered a guide in diagnosing a disease relating to the changes in erythrocyte indices, white blood
count, platelets, especially in babies.l p
p
y
Immature reticulocyte fraction indicates the younger fraction of reticulocytes, reflecting erythropoietic activ-
ity. Several studies have demonstrated the clinical utility of IRF. For example, an increase in IRF within a few days
indicates recovery of bone marrow following bone marrow transplantation, erythropoiesis-stimulating agent
therapy, or chemotherapy17–19. Molina et al. consider an IRF value greater than 10% to indicate early marrow
recovery20. Chang et al. stated that increased IRF (IRF ≥ 0.23) and increased absolute reticulocyte count (ARC)
generally indicated an adequate erythroid response to anemia. Meanwhile, an IRF of 0.23 or less in patients with
anemia reflects bone marrow that is nonresponsive or under-responsive to the anemia21. Immature reticulocyte
fraction may be the first sign of hematologic recovery. It is a powerful indicator of post-chemotherapy aplasia in
children with cancer, serving as an additional parameter of impaired bone marrow function22. A low total count
with a relatively high IRF indicates a regenerating marrow, whereas reticulocytopenia with low IRF is typical of
severe aplastic anemia or renal failure. A high total count with high IRF occurs in acute hemolysis and blood loss. In contrast, a low to average total count with a high IRF occurs in dyserythropoietic and during the early response
to haematinics. It may also help decide whether macrocytic anemia is megaloblastic or nonmegaloblastic23. Mullier et al. Discussion CBC
1 Month (N = 89)
2 Months (N = 87)
3 Months (N = 86)
4 Months (N = 86)
WBC (10ˆ3/uL)
6.24–12.76
5.73–12.84
6.88–13.66
6.06–14.32
RBC (10ˆ6/uL)
3.03–4.89
3.21–4.55
3.38–4.70
3.71–5.09
HGB (g/dL)
9.95 – 15.45
9.74–13.42
9.51–12.40
10.04–13.10
HCT (%)
28.20–43.95
28.00–38.14
28.14–35.80
29.14–38.36
MCV (fL)
86.35–101.85
78.54–95.42
71.91–88.33
70.25–84.85
MCH (pg)
29.75–35.20
27.48–32.72
24.70–30.27
23.64–28.97
MCHC (g/dL)
32.25–36.90
32.78–37.00
32.84–36.27
32.07–35.50
PLT (10ˆ3/ul)
0.13–0.57
0.07–0.63
0.10 – 0.62
0.16–0.59
RDW SD (fL)
43.25–64.50
35.54–52.36
33.00–44.94
30.90–39.69
RDW CV (%)
13.05–18.30
11.94–15.54
11.54–14.93
11.50–13.96
PDW(fL)
9.50–16.97
8.43–19.12
8.62–15.94
9.23–16.42
MPV(fL)
9.30–12.47
8.90–12.67
8.80–12.06
9.09–12.31
PCT (%)
0.19–0.60
0.16–0.63
0.29–0.62
0.19–0.60
Neutrophils (Gpt/L)
0.81–3.55
0.77–4.62
1.07–3.95
0.85–4.54
Lymphocyte (Gpt/L)
3.80–7.68
3.88–8.48
4.33–9.50
4.13–10.16
Monocyte Gpt/L)
0.61–1.86
0.41–1.37
0.42–1.42
0.33–1.19
Eosinophils (Gpt/L)
0.22–1.31
0.14–0.79
0.14–1.11
0.16–1.26
Eosinophils absolut (Gpt/L)
1.45–13.64
0.93–8.96
1.13–13.05
1.12–17.47
Basophils (Gpt/L)
0.02–0.13
0.01–0.11
0.02–0.16
0.01–0.15
Basophils absolut (Gpt/L)
0.15–1.34
0.10–1.05
0.14–1.73
0.09–1.82
Reticulocyte (Tpt/L)
5.95–22.35
4.38–21.64
3.00–16.91
2.94–12.87
Reticulocyte (%)
0.47–2.06
0.92–3.11
0.63–2.90
0.56–1.78
Ret_He (pg)
21.95–28.30
20.74–26.60
17.96–29.70
19.22–29.70
IRF(%)
5.95–22.35
4.38–21.64
3.00–16.91
2.94–12.87
RPI
0.30–1.10
0.34–1.42
0.24–1.30
0.20–0.90
IPF (%)
0.60–15.80
0.54–16.58
0.60–12.56
0.74–13.20
IG (Gpt/L)
0.01–0.12
0.00–0.09
0.00–0.04
0.00–0.03 CBC
1 Month (N = 89)
2 Months (N = 87)
3 Months (N = 86)
4 Months (N = 86)
WBC (10ˆ3/uL)
6.24–12.76
5.73–12.84
6.88–13.66
6.06–14.32
RBC (10ˆ6/uL)
3.03–4.89
3.21–4.55
3.38–4.70
3.71–5.09
HGB (g/dL)
9.95 – 15.45
9.74–13.42
9.51–12.40
10.04–13.10
HCT (%)
28.20–43.95
28.00–38.14
28.14–35.80
29.14–38.36
MCV (fL)
86.35–101.85
78.54–95.42
71.91–88.33
70.25–84.85
MCH (pg)
29.75–35.20
27.48–32.72
24.70–30.27
23.64–28.97
MCHC (g/dL)
32.25–36.90
32.78–37.00
32.84–36.27
32.07–35.50
PLT (10ˆ3/ul)
0.13–0.57
0.07–0.63
0.10 – 0.62
0.16–0.59
RDW SD (fL)
43.25–64.50
35.54–52.36
33.00–44.94
30.90–39.69
RDW CV (%)
13.05–18.30
11.94–15.54
11.54–14.93
11.50–13.96
PDW(fL)
9.50–16.97
8.43–19.12
8.62–15.94
9.23–16.42
MPV(fL)
9.30–12.47
8.90–12.67
8.80–12.06
9.09–12.31
PCT (%)
0.19–0.60
0.16–0.63
0.29–0.62
0.19–0.60
Neutrophils (Gpt/L)
0.81–3.55
0.77–4.62
1.07–3.95
0.85–4.54
Lymphocyte (Gpt/L)
3.80–7.68
3.88–8.48
4.33–9.50
4.13–10.16
Monocyte Gpt/L)
0.61–1.86
0.41–1.37
0.42–1.42
0.33–1.19
Eosinophils (Gpt/L)
0.22–1.31
0.14–0.79
0.14–1.11
0.16–1.26
Eosinophils absolut (Gpt/L)
1.45–13.64
0.93–8.96
1.13–13.05
1.12–17.47
Basophils (Gpt/L)
0.02–0.13
0.01–0.11
0.02–0.16
0.01–0.15
Basophils absolut (Gpt/L)
0.15–1.34
0.10–1.05
0.14–1.73
0.09–1.82
Reticulocyte (Tpt/L)
5.95–22.35
4.38–21.64
3.00–16.91
2.94–12.87
Reticulocyte (%)
0.47–2.06
0.92–3.11
0.63–2.90
0.56–1.78
Ret_He (pg)
21.95–28.30
20.74–26.60
17.96–29.70
19.22–29.70
IRF(%)
5.95–22.35
4.38–21.64
3.00–16.91
2.94–12.87
RPI
0.30–1.10
0.34–1.42
0.24–1.30
0.20–0.90
IPF (%)
0.60–15.80
0.54–16.58
0.60–12.56
0.74–13.20
IG (Gpt/L)
0.01–0.12
0.00–0.09
0.00–0.04
0.00–0.03 Table 1. Discussion This means that the age of 0–6 months, especially 0–2 months, is critical for
a baby to suffer from an iron deficiency with or without anemia. Nevertheless, the impact will also affect the
incidence of iron deficiency at a later age. Li et al. showed that of 1,127 6-months-old infants in Beijing, the
prevalence of anemia was ~ 11.8%12. Chen et al. showed that from 509 infants aged 1–12 months, The prevalence
of ID and IDA were 3.7 and 2.7%, respectively, in babies under 6 months of age, but increased to 20.4 and 6.6%,
respectively, in babies above 6 months of age13. Salah et al. show that from 654 infants aged 9–12 months, the
prevalence of anemia and IDA was 34.6 and 32.6%, respectively14. Nazari et al. found that the prevalence of ID
and IDA in children under six years of age was 27.7 and 18.2%, respectively. Considering the high prevalence
of ID and IDA in infancy, especially at 0–6 months, iron supplementation in the form of elemental iron at a
dose of 1 mg/kg/day should be given to all babies born at term from birth15. Another study showed that Daily
iron supplementation from early life 36 h at a dose of 2 mg/kg is efficacious for improving iron status and motor
development at 6 months in babies at risk16. https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 | www.nature.com/scientificreports/ Table 1. P5-P95 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular
volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell
distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution
with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils
absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte
production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. Discussion P3-P97 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular
volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell
distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution
with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils
absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte
production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. different pediatric ages, especially in babies. Therefore, the reference value of the RPI range in this study can be
considered to assess the responsiveness of the anemia therapy given. However, according to Bracho et al., the
RPI is an inadequate tool for evaluating the bone marrow response in the presence of anemia due to differences
in hematologic values between children and adults. In addition, the absence of information on the maturation
time of reticulocytes in children25.h y
The power of this study is that it parades all reference ranges of CBC, Ret He, IRF, and RPI at P3-P97 and
P5-P95 for healthy babies aged 1–4 months. The weakness of this study is that the altitude above sea level, race,
genetics, ethnicity, and population of this study is different from other areas. Hence, it certainly affects the refer-
ence range of CBC and reticulocyte parameters. In this study, 96.5% reside at altitudes less than 100 m. Again,
however, race, genetics, and ethnicity differed from other countries. Therefore, this reference range for CBC
and reticulocyte parameters in healthy babies aged 9–11 months can be used in countries with demographic,
socioeconomic, and population structures, such as Southeast Asia, especially Indonesia. Table 2. P3-P97 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular
volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell
distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution
with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils
absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte
production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. Discussion showed that IRF, combined with reticulocyte count, may be helpful in hereditary spherocytosis
(HS) diagnosis as a high reticulocyte count characterizes HS without an equally elevated IRF. Therefore, a
reticulocytes/IRF ratio higher than 7.7 is a precondition for screening HS cases24. The IRF increases earlier than
the reticulocyte number. It helps monitor the efficacy of therapy in nutritional anemias such as megaloblastic or
IDA. Therefore, the reference value of the IRF range in this study can be considered to assess the responsiveness
of the anemia therapy given.hl y g
The reticulocyte count reflects the erythropoietic activity of bone marrow. In addition, it is valuable in diag-
nosing anemias and monitoring bone marrow response to therapy. RPI is currently used in pediatrics to assess
bone marrow responsiveness to anemia therapy given. However, considering that “conventional” RPI was devel-
oped from a study conducted in adults, it is necessary to have an RPI based on standard values adjusted for Scientific Reports | (2023) 13:423 | https://doi.org/10.1038/s41598-023-27579-3 www.nature.com/scientificreports/ CBC
1 Month (N = 89)
2 Months (N = 87)
3 Months (N = 86)
4 Months (N = 86)
WBC (10ˆ3/uL)
5.88–13.43
5.46–13.85
6.55–16.14
5.86–15.16
RBC (10ˆ6/uL)
2.92–5.09
3.08–4.62
3.08–4.78
3.54–5.15
HGB (g/dL)
9.60–15.90
9.46–13.97
9.26–12.82
10.00–13.33
HCT (%)
27.13–48.32
26.95–39.71
27.57–36.69
28.62–39.04
MCV (fL)
84.28–103.63
77.73–96.82
70.35–90.94
65.25–86.62
MCH (pg)
29.17–35.65
26.86–33.02
24.03–30.99
22.48–29.10
MCHC (g/dL)
31.67–37.29
32.49–37.50
32.02–36.38
31.92–36.04
PLT (10ˆ3/ul)
0.09–0.64
0.05–0.65
0.10–0.66
0.15–0.61
RDW SD (fL)
42.44–67.15
35.12–55.56
32.56–48.59
30.70–40.60
RDW CV (%)
12.97–18.96
11.60–16.10
11.20–17.35
11.42–14.41
PDW(fL)
8.82–17.84
8.20–22.81
8.45–16.10
8.93–17.50
MPV(fL)
8.90–12.58
8.70–13.20
8.70–12.50
8.77–12.64
PCT (%)
0.16–0.67
0.15–0.66
0.12–0.65
0.18–0.65
Neutrophils (Gpt/L)
0.74–4.08
0.66–5.34
1.00–4.97
0.77–5.08
Lymphocyte (Gpt/L)
3.30–8.12
3.46–8.95
4.11–10.42
3.48–10.73
Monocyte Gpt/L)
0.60–2.06
0.35–1.43
0.41–1.50
0.31–1.41
Eosinophils (Gpt/L)
0.19–1.50
0.12–0.84
0.11–1.17
0.15–2.17
Eosinophils absolut (Gpt/L)
1.00–14.61
0.85–9.54
1.03–15.00
0.78–27.34
Basophils (Gpt/L)
0.02–0.13
0.01–0.14
0.02–0.23
0.01–0.17
Basophils absolut (Gpt/L)
0.14–1.48
0.05–1.16
0.12–3.02
0.07–2.35
Reticulocyte (Tpt/L)
5.61–25.58
3.70–23.12
2.67–25.66
2.33–13.38
Reticulocyte (%)
0.38–2.53
0.58–3.49
0.57–3.32
0.52–1.98
Ret_He (pg)
21.74–28.56
19.85–27.24
16.78–30.24
17.40–30.22
IRF(%)
5.61–25.58
3.70–23.12
2.67–25.66
2.33–13.38
RPI
0.20–1.48
0.26–1.60
0.20–1.40
0.20–1.00
IPF (%)
0.57–18.48
0.50–20.79
0.50–17.04
0.70–14.38
IG ( Gpt/L )
0.01–0.14
0.00–0.14
0.00–0.04
0.00–0.03 Table 2. Material and methodsh Study population. The study design was a cross-sectional study with descriptive analysis of CBC and retic-
ulocyte in babies aged 1–4 months. The study was conducted at 10 Community Health Centers in Banjarbaru,
South Kalimantan, from August 2020 to August 2021. Inclusion criteria are babies born at term (gestational age
37–42 weeks) with birth weight ≥ 2500 g, babies are not twins, not taking a hematinic drug, and normal nutri-
tional status. Exclusion criteria were hematological diseases and congenital anomalies. In addition, gestational
age and birth weight had obtained from the mother’s medical record (Maternal and Child Health Book). The
doctor in charge declared the baby healthy. At the time of recruitment, the baby’s weight, length, and head cir-
cumference were measured by health personnel. Nutritional status is assessed based on body weight and length,
divided into good nutrition and undernutrition. Good nutrition if the z-score is − 2 SD to + 3 SD in this study. In contrast, undernutrition if the z-score is < − 2 SD26. All of the baby’s parents had signed the informed con-
sent. This study obtained ethical clearance from the Research Ethics Commission of the Medical Faculty of the https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 | www.nature.com/scientificreports/ University of Lambung Mangkurat No. 272/KEPK-FK ULM/EC/VIII/2020. All methods have been performed
under the relevant guidelines and regulations of the Declaration of Helsinki. Blood sampling. Every baby who meets the inclusion and exclusion criteria will be taken a blood sample of
1 ml from the median cubital vein. First, the blood sample was put in a tube with EDTA anticoagulant, homog-
enized by turning it over, and stored in a storage box. Then the blood sample was sent to the Banjarbaru Idaman
Hospital Laboratory. The Sysmex XN-450 Hematology Analyzer (Sysmex Corporation, Japan) was doing com-
plete blood count and reticulocyte examinations. Statistical analysis. All baby anthropometry measurements were analyzed by SPSS ver.25 for P3-P97 and
P5-P95. Moreover, the CBC and reticulocyte laboratory findings were analyzed by SPSS ver.25 for P3-P97 and
P5-P95. All data are presented in narrative and table. Reference range P3-P97 means that 94% of normal indi-
viduals have normal laboratory results, while the other 6% may not be sick outside the normal limits. Reference
range P5-P95 means that 90% of normal individuals have normal laboratory results, while 10% may not be sick
outside the normal limits. Data availability Research data can be provided by the Corresponding Author if needed. Received: 16 February 2022; Accepted: 4 January 2023 Received: 16 February 2022; Accepted: 4 January 2023 References 1. Gardner, W. & Kassebaum, N. Global, regional, and national prevalence of anemia and its causes in 204 countries and territories,
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23. Acknowledgements
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The authors thank Estiani for helping input the research data to SPSS ver.25. The authors did not receive any
funds or grants. Author contributions H.P.R. makes Study Design, Data Collection, Statistical Analysis, Data Interpretation, Manuscript Preparation. L.P. makes Study Design, Data Collection, Statistical Analysis, Data Interpretation, Manuscript Preparation. A.Y. makes Study Design, Data Interpretation, Manuscript Preparation MS makes Study Design, Statistical Analy-
sis, Data Interpretation, Manuscript Preparation. N.H. makes Study Design, Data Interpretation, Manuscript
Preparation. H.P.R. prepared Supplementary Tables 1–7. H.P.R. and L.P. wrote the main manuscript text. All
authors reviewed the manuscript. References Bain, B. J., Bates, I. & Laffan, M. A. Dacie and Lewis Practical Haematology (Elsevier Ltd, 2017). 24. Mullier, F. et al. Additional erythrocytic and reticulocytic parameters helpful for diagnosis of hereditary spherocytosis: Results of
a multicentre study. Ann. Hematol. 90, 759–768 (2011). a multicentre study. Ann. Hematol. 90, 759–768 (2011). y
5. Bracho, F. J. & Osorio, I. A. Evaluation of the reticulocyte production index in the pediatric population. Am. J. Clin. Pathol. 154
70–77 (2020). 26. Ariati, N. N., Wiardani, N. K., Kusumajaya, A. A. N., Supariasa, I. D. N. & Sidiartha, L. Buku saku antropometri gizi Anak PAUD
[Internet] (Inteligensia Media (Kelompok Penerbit Intrans Publishing), 2020). Scientific Reports | (2023) 13:423 | https://doi.org/10.1038/s41598-023-27579-3 www.nature.com/scientificreports/ Competing interests h p
g
The authors declare no competing interests. © The Author(s) 2023 Additional informationh Supplementary Information The online version contains supplementary material available at https://doi.org/
10.1038/s41598-023-27579-3. Correspondence and requests for materials should be addressed to H.P.R. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
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https://openalex.org/W2134872935 | https://centaur.reading.ac.uk/15707/1/2010_Dunwell_et_al_Palm.pdf | English | null | Production of haploids and doubled haploids in oil palm | BMC plant biology | 2,010 | cc-by | 15,641 | Production of haploids and doubled
haploids in oil palm Published Version Dunwell, J. M. ORCID: https://orcid.org/0000-0003-2147-665X,
Wilkinson, M. J., Nelson, S., Wening, S., Sitorus, A. C.,
Mienanti, D., Alfiko, Y., Croxford, A. E., Ford, C. S., Forster, B. P. and Caligari, P. D. S. (2010) Production of haploids and
doubled haploids in oil palm. BMC Plant Biology, 10. 218. ISSN 1471-2229 doi: https://doi.org/10.1186/1471-2229-10-
218 Available at https://centaur.reading.ac.uk/15707/ It is advisable to refer to the publisher’s version if you intend to cite from the
work. See Guidance on citing
. To link to this article DOI: http://dx.doi.org/10.1186/1471-2229-10-218 Publisher: BioMed Central All outputs in CentAUR are protected by Intellectual Property Rights law,
including copyright law. Copyright and IPR is retained by the creators or other
copyright holders. Terms and conditions for use of this material are defined in
the End User Agreement
. www.reading.ac.uk/centaur * Correspondence: j.m.dunwell@reading.ac.uk; jjw@aber.ac.uk
† Contributed equally
1School of Biological Sciences, University of Reading, Whiteknights, Reading,
RG6 6AS, UK
2Institute of Biological, Environmental and Rural Sciences, Aberystwyth
University, Aberystwyth, SY23 3DA, UK
Full list of author information is available at the end of the article Abstract Background: Oil palm is the world’s most productive oil-food crop despite yielding well below its theoretical
maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of
such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1
generation. Results: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and
doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived
further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and
expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop
female inflorescences. Conclusions: This study has generated genetically diverse H/DH palms from which parental clones can be selected
in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in
productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse
rainforest. Desire for a more generic H/DH production system to
improve agricultural yields is increasing as population
growth, climate change, biofuel demand and other land-
use pressures intensify. Clearly, in any species the
production of F1 varieties depends not only on the pro-
duction of homozygous lines to act as parents, but also
it requires an efficient method to intercross the parents. This latter procedure is relatively simple in species with
an outcrossing breeding system, like maize or oil palm,
compared with those with an inbreeding system like rice
or wheat. Production of F1 hybrids has been achieved
successfully in this category of crops (for example
hybrid rice in China) but often requires a male sterility
system. Production of haploids and doubled haploids in
oil palm Jim M Dunwell1*†, Mike J Wilkinson2*†, Stephen Nelson3, Sri Wening4, Andrew C Sitorus4, Devi Mienanti4,
Yuzer Alfiko4, Adam E Croxford2, Caroline S Ford2, Brian P Forster5, Peter DS Caligari3,5,6 © 2010 Dunwell et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited. Central Archive at the University of Reading
Reading’s research outputs online Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Open Access Background Success of early F1 hybrid maize varieties exemplifies the
advantages of heterosis [1]. The use of doubled haploids
as parents for F1 variety production fully exploits this
phenomenon and has enabled substantial yield improve-
ments in several crops [2,3]. This strategy was outlined
with the first DH crop variety [4] and has led to H/DH
production systems being described for >250 species [5]. However, few of these protocols generate the large num-
bers of Hs/DHs needed for commercial breeding, with
just three methods (androgenesis, wide crossing, gyno-
genesis [6]) routinely adopted for H/DH production in
only 30 species [5]. The most important of these meth-
ods in widespread use in commercial breeding is the
generation of haploids in maize via pollination with a
haploid inducing line such as a ‘Stock 6’ derivative. Annually, oil palm (Elaeis guineensis) yields eight to
ten times more oil per hectare than rapeseed or soybean
[7,8] and in 2008 generated 38.9 million tonnes of oil
worldwide [9]. The area assigned to the crop expanded
~1.7 fold between 1997 (8.7 M ha) and 2007 (14.6 M
ha) [9] with further increases forecast. Over this same
period global production of palm oil increased ~2.2 fold
from 18 to 38.9 Mt y-1. Thus, yield increases have been Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 2 of 25 characteristics of H/DH (slow growth, altered flowering
phenology, smaller stomata and smaller organs [5])
could be used for diagnosis but are difficult to score
qualitatively on a large scale and require plants of a rea-
sonable size. An alternative strategy is to seek undefined
atypical phenotypic features that may arise from reduced
cell size and/or the hemizygous state of haploid indivi-
duals (homozygous for DHs) and that are manifest at
the seedling stage when high-throughput visual assess-
ment is more plausible. A more directed approach is
also possible. Spontaneous H/DH seedlings are often
associated with aberrant germination features, such as
twin embryos from the same carpel [20], providing a
defined feature for phenotypic selection. Here, we com-
bined a large-scale visual survey for undefined atypical
palm seedling phenotypes coupled with active selection
for seeds with twin embryos to assemble a sub-popula-
tion of seedlings enriched for H/DHs. achieved predominantly by expansion of cultivated area
and not through yield enhancement. Background This trend raises
concerns over the ecological impact of felling rainforest
to accommodate oil palm cultivation [10,11] and has sti-
mulated debate over strategies to limit further agricul-
tural expansion [12-14]. One option explored here is to
use market forces to help address the problem. If F1
varieties could increase yields sufficiently to exceed
demand, commodity prices would fall. This would dis-
courage clear felling and simultaneously incentivise early
replacement of existing plantations with high-yielding
varieties. Feasibility of the approach clearly relies on the
ability to gain marked improvements in yield. Current
yields of oil palm (generally 4-10.5 t ha-1) [15,16] are
much lower than the most conservative estimates of the
crop’s potential (17 t ha-1 [14] to 60 t ha-1 [16]). Indeed,
yields per hectare in the two largest producer countries
(Indonesia and Malaysia) have remained static for 30
years [9]. It should be noted, however, that in both
these countries there are examples of selected varieties
with much higher yields, with the highest yields from
commercial breeding trials already exceeding 10 t ha-1. Results markers
used
Ploidy
50-Mix5-7
11260406301
9
x
50-03060367C
07280501801
15
x
50-03060260C-2
07280501901
15
x
53-03080954C-2
09270500101
10
x
53-03090761C-5
09280504501
10
x
BATCH 51;03060318C;1
060728_0010_01_a 15
x
BATCH 53;03090761C;5
060728_0018_01_a 15
x
0623/172;05095508C;1
060728_0021_01_a 15
x
BATCH 50;03060260C;2
060728_0027_01_a 15
x
0611/32;05050248C;1
060728_0032_01_a 15
x
0611/16;05050228C;1
060728_0034_01_a 15
x
BATCH 53;03080954C;2
060728_0035_01_a 15
x
06 412;04059061B;3
060728_0050_01_a 14
2x
0628/152;05100720C;1
060729_0021_01_a 15
x
0628/185;05100351C;1
060729_0063_01_a 15
x
BATCH 51;03060626C;1
060729_0127_02_a 15
x
BATCH 67;0409034MC;2
060729_0130_02_a 14
2x
BATCH 67;0409034MC;4
060729_0131_02_a 15
2x
BATCH
67;0409034MC;15
060729_0132_02_a 15
2x
BATCH 65;0409034MC;7
060729_0134_02_a 15
2x
BATCH
65;0409034MC;35
060729_0138_02_a 15
2x
BATCH
65;0409034MC;56
060729_0139_02_a 15
2x
BATCH
65;0409034MC;50
060729_0141_02_a 15
2x
BATCH
65;0409034MC;47
060729_0142_02_a 15
2x
0628/53;05090595C;1
060731_0043_01_a 15
x
0627/125;05090717C;2
060731_0065_01_a 15
x
0627/12;05080220C;1
060731_0080_01_a 15
x
0627/6;05080095C;1
060731_0086_01_a 14
x
0631/
Normal;05039033B;31
060731_0265_01_a 14
x
64-0409021MC-34
02130604301
15
2x
64-0410040MC-1
02130604801
15
2x
51-03060626C
02130605301
15
x
64-0410040MC-20
02140600401
15
2x
64-0410040MC-16
02140600801
15
2x
65-0409021MC-2
02140601001
15
2x
06 412B-04059061B-3
02170605501
15
2x
06 412B-04129091B
02170605801
15
2x
0550-15/05010827C
02200602401
15
x
0550-17/05010442C-1
02200602601
15
x
0550-23/05020059C
02200603101
15
x
0550-33/05020568C
02200603401
15
x
0550-36/05020420C-2
02200603701
15
x
0550-40/05010880C
02200607501
14
x had twin embryos. More than 2,000 of these seedlings
(including all those with twin embryos) were trans-
ferred to the nursery prior to further screening. Although Hs could be identified relatively easily on the
basis of their reduced genome size, we initially wished
to target the more difficult, but more valuable DHs to
circumvent the need for chromosome doubling. For
the second level screen, we exploited the fact that Hs
and DHs would be either hemi- or homozygous across
all loci; thus individuals exhibiting heterozygosity at
any locus could be discarded. Applying this logic, we
performed a sequential screen using 9-15 microsatellite
markers (Table 1) on all individuals and found 117
seedlings that exhibited a single allele across all loci
(Table 2). These individuals were retained as candidate
H/DH, and subsequent flow cytometry of leaf samples
identified 83 as H, and 34 as diploid (Table 2). The
haploid status of six palms was further confirmed by
cytological examination of intact cells from root
squashes. Each contained the expected 16 chromo-
somes (Figure 2). A larger-scale survey for heterozygosity was then per-
formed using 97 additional microsatellites (Table 3) to
confirm absolute hemizygosity of Hs and identify ‘false’
candidate DHs showing any heterozygosity. Results Over two years, we performed two large-scale screens
for morphological ‘off-types’ among oil palm seedlings
generated by the Bah Lias Research Station, Indonesia. The first screen utilised 10,900,000 seedlings from a
wide range of crosses and identified 3,854 morphologi-
cal ‘off-types’ (H/DH candidates), of which 53 had twin
embryos and 3,801 were phenotypically abnormal (Fig-
ure 1). The second screen of approximately 10,000,000
seedlings from commercial seed production activities
and approximately 1,000,000 seedlings from breeding
experiments generated 5,704 H/DH candidates, of
which 5,601 were phenotypically abnormal and 103 To date, a H/DH-derived F1 breeding approach has
been precluded by the repeated failure to secure H/DHs
via anther or microspore culture [17] and successful
generation of H/DHs in oil palm is unreported in the
literature. The report of a spontaneous H in the related
coconut palm [18] and in other species [19] nevertheless
gave hope that spontaneous Hs may also occur in oil
palm. However, the characteristically rare occurrence of
spontaneous H/DHs necessitates development of an
effective high-throughput screening system. Phenotypic Figure 1 Seed germination morphology for H/DH identification. a: normal; b: abnormal; c: twin embryo. Figure 1 Seed germination morphology for H/DH identification. a: normal; b: abnormal; c: twin embryo. Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 3 of 25 Table 2 Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both
morphologically atypical and homozygous for the
markers listed in Table 1
Candidate
DNA sample
code
No. Results markers
used
Ploidy
50-Mix5-7
11260406301
9
x
50-03060367C
07280501801
15
x
50-03060260C-2
07280501901
15
x
53-03080954C-2
09270500101
10
x
53-03090761C-5
09280504501
10
x
BATCH 51;03060318C;1
060728_0010_01_a 15
x
BATCH 53;03090761C;5
060728_0018_01_a 15
x
0623/172;05095508C;1
060728_0021_01_a 15
x
BATCH 50;03060260C;2
060728_0027_01_a 15
x
0611/32;05050248C;1
060728_0032_01_a 15
x
0611/16;05050228C;1
060728_0034_01_a 15
x
BATCH 53;03080954C;2
060728_0035_01_a 15
x
06 412;04059061B;3
060728_0050_01_a 14
2x
0628/152;05100720C;1
060729_0021_01_a 15
x
0628/185;05100351C;1
060729_0063_01_a 15
x
BATCH 51;03060626C;1
060729_0127_02_a 15
x
BATCH 67;0409034MC;2
060729_0130_02_a 14
2x
BATCH 67;0409034MC;4
060729_0131_02_a 15
2x
BATCH
67;0409034MC;15
060729_0132_02_a 15
2x
BATCH 65;0409034MC;7
060729_0134_02_a 15
2x
BATCH
65;0409034MC;35
060729_0138_02_a 15
2x
BATCH
65;0409034MC;56
060729_0139_02_a 15
2x
BATCH
65;0409034MC;50
060729_0141_02_a 15
2x
BATCH
65;0409034MC;47
060729_0142_02_a 15
2x
0628/53;05090595C;1
060731_0043_01_a 15
x
0627/125;05090717C;2
060731_0065_01_a 15
x
0627/12;05080220C;1
060731_0080_01_a 15
x
0627/6;05080095C;1
060731_0086_01_a 14
x
0631/
Normal;05039033B;31
060731_0265_01_a 14
x
64-0409021MC-34
02130604301
15
2x
64-0410040MC-1
02130604801
15
2x
51-03060626C
02130605301
15
x
64-0410040MC-20
02140600401
15
2x
64-0410040MC-16
02140600801
15
2x
65-0409021MC-2
02140601001
15
2x
06 412B-04059061B-3
02170605501
15
2x
06 412B-04129091B
02170605801
15
2x
0550-15/05010827C
02200602401
15
x
0550-17/05010442C-1
02200602601
15
x
0550-23/05020059C
02200603101
15
x
0550-33/05020568C
02200603401
15
x
0550-36/05020420C-2
02200603701
15
x n 2,000 of these seedlings
in embryos) were trans-
r to further screening. ed relatively easily on the
e size, we initially wished
ut more valuable DHs to
omosome doubling. For
xploited the fact that Hs
mi- or homozygous across
ibiting heterozygosity at
. Applying this logic, we
using 9-15 microsatellite
dividuals and found 117
ngle allele across all loci
were retained as candidate
cytometry of leaf samples
s diploid (Table 2). The
was further confirmed by
intact cells from root
he expected 16 chromo-
erozygosity was then per-
icrosatellites (Table 3) to
y of Hs and identify ‘false’
eterozygosity. All Hs pro-
les across all microsatel-
d heterozygosity via locus
ed. All diploids were het-
d so discarded. However,
9582C) identified from a
homozygous across all 36
airs used to identify
s H candidates in the
Reverse primer (5’-3’)
TCAAAATTAAGAAAGTATGC
CGCGTGAAAGATATGAATCAAC
GGATGTATGCTTTACCTCCGAAT
CTCCTTTTCCCCATCACAGA
ATTCTGAAAGGAGGGGGAAA
TGCCTCTGGTTGTTAGTCTGG
T TGGCAATCAGCACACATTCT
TGTGGTCTCCTGAGGAAGATG
CCCCTTTTGCTTCCCTATTT
CCAGAATCATCAGACTCGGACAG
TTCAACATACCGTCTGTA
GGCACCAAACACAGTAA
AGAACCACCGGAGTTAC
TTTTCTCCATAGTCCGTTAC
TGGCTGGCTTCGGTCTTAG
[27]. Table 2 Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both
morphologically atypical and homozygous for the
markers listed in Table 1
Candidate
DNA sample
code
No. Markers 10-15 obtained from Billotte et al. [27]. Results All Hs pro-
duced single-allele peak profiles across all microsatel-
lites, thereby discounting fixed heterozygosity via locus
duplication for all markers used. All diploids were het-
erozygous at several loci and so discarded. However,
one diploid (0644-219/05049582C) identified from a
later screen (see below) was homozygous across all 36 Table 1 Microsatellite primer pairs used to identify
homozygous DH or hemizygous H candidates in the
initial molecular screen
No. Forward primer (5’-3’)
Reverse primer (5’-3’)
1
GAGATTACAAAGTCCAAACC
TCAAAATTAAGAAAGTATGC
2
ACGCATGCAGCTAGCTTTTC
CGCGTGAAAGATATGAATCAAC
3
CACGCACGCAGTTTATTCTT
GGATGTATGCTTTACCTCCGAAT
4
CCCCTTTTGCTTCCCTATTT
CTCCTTTTCCCCATCACAGA
5
GACACAAGCAAAAACAAAAGCA
ATTCTGAAAGGAGGGGGAAA
6
ATATGTGTGGGTGTGCGTGT
TGCCTCTGGTTGTTAGTCTGG
7
TCTCTCTCTCTCTCTCTATGTGTGTGT TGGCAATCAGCACACATTCT
8
GCAGCTCTTTCCACACCTCT
TGTGGTCTCCTGAGGAAGATG
9
TTTTCCCCATCACAGAATTG
CCCCTTTTGCTTCCCTATTT
10
TAGCCGCACTCCCACGAAGC
CCAGAATCATCAGACTCGGACAG
11
AGCTCTCATGCAAGTAAC
TTCAACATACCGTCTGTA
12
CCTTCAAGCAAAGATACC
GGCACCAAACACAGTAA
13
GTAGCTTGAACCTGAAA
AGAACCACCGGAGTTAC
14
GCTCGTTTTTGTTTAGGTGA
TTTTCTCCATAGTCCGTTAC
15
CCTCGGGTTATCCTTTTTACC
TGGCTGGCTTCGGTCTTAG
Markers 10-15 obtained from Billotte et al. [27]. Table 1 Microsatellite primer pairs used to identify
homozygous DH or hemizygous H candidates in the
initial molecular screen Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 4 of 25 Table 2: Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both morpholo-
gically atypical and homozygous for the markers listed
in Table 1 (Continued)
0551-36/05020511C
02200607601
15
x
0551-32/05020361C-1
02210600401
15
x
0552-4/05010836C-2
02210600901
15
x
0552-38/05020501C
02210603101
14
x
0552-39/05020415C
02210603201
15
x
0552-31/05020858C
02210603701
15
x
0552-91/05020375C
02210603901
15
x
0552-111/05020626C
02210607201
15
x
0552-128/05020558C-1
02210607701
15
x
0601-35/05020946C
02210608201
15
x
0601-42/05030201C-6
02210609501
15
x
0601-51/05030224C-2
02220600201
15
x
0607-21/05040317C-3
02220601801
14
x
0606-32/05040240C
02220606201
13
x
0601-77/05020961C
02230600701
15
x
0601-62/05030147C
02230601401
15
x
0601-54/05030462C
02230601901
15
x
0551-21/05020271C-1
02200605801
14
x
0601-9/05020843C-2
02230603101
15
x
0602-17/05020631C-1
02230605501
15
x
0607-111/05040970C-1
03010600201
15
x
0607-81/05040578C-1
03010600501
15
x
0607-73/05040573C-1
03010605101
15
x
0607-89/05040748C-3
03010605501
15
x
0607-102/05050016C-2
03010606601
15
x
0608-15/05040519C-3
03010606901
15
x
0608-45/05041003C-1
03150603401
15
x
0610-60/05041024C-2
03150604401
15
x
0610-124/05055039C-1
03150604601
15
x
0609-54/05050089C-2
03150604701
15
x
0610-41/05050352C-1
03150606701
15
x
0609-58/05050255C-1
03220600201
15
x
0610-82/05050099C-2
03220601401
15
x
0610-77/05050353C-1
03220602701
15
x
0610-121/05055090C-1
03220603301
15
x
0610-81/05050099C-1
03220605901
15
x
0609-100/05055311C-1
03290600301
15
x
0610-11/05040938C-1
03290601101
15
x
0610-68/05050376C-3
03290602001
15
x
0610-58/05050344C-1
03290602201
15
x
0610-73/05050594C-3
03290603301
15
x
0611-84/05050714C-4
03290605001
15
x
0611-70/05050223C-1
03290606701
15
x
0611-73/05050351C-1
03290608001
15
x
0610-67/05050376C-2
04050600501
15
x
0610-40/05050102C-2
04050600901
15
x
0611-99/05050544C-1
04050602601
15
x
0611-110/05055011C-1
04050603601
15
x
0612-2/05050017C-1
04050609101
15
x mapped loci found to be heterozygous in the maternal
parent (palm number BL013/12-06). Results Taking account of
linkage between mapped markers, the probability of
such an individual occurring by chance following selfing
Figure 2 Chromosome spread of a haploid root cell from oil
palm containing 16 C-metaphase chromosomes
Table 2: Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both morpholo-
gically atypical and homozygous for the markers listed
in Table 1 (Continued)
0551-36/05020511C
02200607601
15
x
0551-32/05020361C-1
02210600401
15
x
0552-4/05010836C-2
02210600901
15
x
0552-38/05020501C
02210603101
14
x
0552-39/05020415C
02210603201
15
x
0552-31/05020858C
02210603701
15
x
0552-91/05020375C
02210603901
15
x
0552-111/05020626C
02210607201
15
x
0552-128/05020558C-1
02210607701
15
x
0601-35/05020946C
02210608201
15
x
0601-42/05030201C-6
02210609501
15
x
0601-51/05030224C-2
02220600201
15
x
0607-21/05040317C-3
02220601801
14
x
0606-32/05040240C
02220606201
13
x
0601-77/05020961C
02230600701
15
x
0601-62/05030147C
02230601401
15
x
0601-54/05030462C
02230601901
15
x
0551-21/05020271C-1
02200605801
14
x
0601-9/05020843C-2
02230603101
15
x
0602-17/05020631C-1
02230605501
15
x
0607-111/05040970C-1
03010600201
15
x
0607-81/05040578C-1
03010600501
15
x
0607-73/05040573C-1
03010605101
15
x
0607-89/05040748C-3
03010605501
15
x
0607-102/05050016C-2
03010606601
15
x
0608-15/05040519C-3
03010606901
15
x
0608-45/05041003C-1
03150603401
15
x
0610-60/05041024C-2
03150604401
15
x
0610-124/05055039C-1
03150604601
15
x
0609-54/05050089C-2
03150604701
15
x
0610-41/05050352C-1
03150606701
15
x
0609-58/05050255C-1
03220600201
15
x
0610-82/05050099C-2
03220601401
15
x
0610-77/05050353C-1
03220602701
15
x
0610-121/05055090C-1
03220603301
15
x
0610-81/05050099C-1
03220605901
15
x
0609-100/05055311C-1
03290600301
15
x
0610-11/05040938C-1
03290601101
15
x
0610-68/05050376C-3
03290602001
15
x
0610-58/05050344C-1
03290602201
15
x
0610-73/05050594C-3
03290603301
15
x
0611-84/05050714C-4
03290605001
15
x
0611-70/05050223C-1
03290606701
15
x
0611-73/05050351C-1
03290608001
15
x
0610-67/05050376C-2
04050600501
15
x
0610-40/05050102C-2
04050600901
15
x
0611-99/05050544C-1
04050602601
15
x
0611-110/05055011C-1
04050603601
15
x
0612-2/05050017C-1
04050609101
15
x
Table 2: Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both morpholo-
gically atypical and homozygous for the markers listed
in Table 1 (Continued)
0612-70/05050530C-1
04050609201
15
x
0612-76/05050512C-1
04050610301
15
x
0611-109/05055144C-1
04120600101
15
x
0611-31/05050220C-1
04120600601
15
x
0611-38/05050284C-4
04120600901
15
x
0611-40/05050171C-1
04120601101
14
x
0612-80/05050713C-1
04120603101
15
x
65-0409034 MC-66
060829_0001_02_a 15
2x
65-0409034 MC-68
060829_0002_02_a 15
2x
65-0409034 MC-72
060829_0003_02_a 14
2x
65-0409034 MC-111
060829_0005_02_a 15
2x
65-0409034 MC-94
060829_0011_02_a 14
2x
65-0409034 MC-120
060829_0012_02_a 15
2x
65-0409034 MC-144
060829_0013_02_a 15
2x
65-0409034 MC-133
060829_0015_02_a 15
2x
65-0409034 MC-187
060829_0020_02_a 15
2x
65-0409034 MC-193
060829_0021_02_a 14
2x
65-0409034 MC-199
060829_0023_02_a 15
2x
65-0409034 MC-135
060829_0025_02_a 15
2x
65-0409034 MC-114
060829_0026_02_a 13
2x
65-0409034 MC-147
060829_0027_02_a 15
2x
65-0409034 MC-36 B
060829_0030_02_a 15
2x
65-0409034 MC-39 A
060829_0031_02_a 15
2x
65-0409034 MC-73 A
060829_0034_02_a 15
2x
65-0409034 MC-71 A
060829_0035_02_a 14
2x
Note: in this initial round, no DH was found. Results The DH (0644-219/05049582C)
was detected in a subsequent batch. Table 2: Results of ploidy analysis by flow cytometry of
117 candidate H/DH palms identified as both morpholo-
gically atypical and homozygous for the markers listed
in Table 1 (Continued) Note: in this initial round, no DH was found. The DH (0644-219/05049582C)
was detected in a subsequent batch. Note: in this initial round, no DH was found. The DH (0644-219/05049582C)
was detected in a subsequent batch. mapped loci found to be heterozygous in the maternal
parent (palm number BL013/12-06). Taking account of
linkage between mapped markers, the probability of
such an individual occurring by chance following selfing mapped loci found to be heterozygous in the maternal
parent (palm number BL013/12-06). Taking account of
linkage between mapped markers, the probability of
such an individual occurring by chance following selfing Figure 2 Chromosome spread of a haploid root cell from oil
palm containing 16 C-metaphase chromosomes. Figure 2 Chromosome spread of a haploid root cell from oil
palm containing 16 C-metaphase chromosomes. Page 5 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Table 3 Microsatellite markers (described by Billotte et al. [27]) used for a larger-
and homozygosity of DH candidates previously identified by the morphological s
markers) and flow cytometry screen
No. Forward primer (5’-3’)
Reverse pr
16
GACCTTTGTCAGCATACTTGGTGTG
GCAGGCCT
17
ATGCATGTGATTTTATTAGGTGAGA
CGACCCTCA
18
AAGCTAGCGACCTATGATTTTAGA
AAACAAGT
19
CCCACCACCCCTAGCTTCTC
ACCCCGGT
20
AGAGAGAGAGAGTGCGTATG
GTCCCTGTG
21
GGGTAGCAAACCTTGTATTA
ACTTCCATT
22
CGAGGCCCAAAAACATTCAC
GGTCCCGA
23
TTGCGGCCCATCGTAATC
TCCCTGCAG
24
AGGGAATTGGAAGAAAAGAAAG
TCCTGAGCT
25
AGCAAGAGCAAGAGCAGAACT
CTTGGGGG
26
TAGCCATGCCGCCACCACTT
CAATCCATT
27
CTTACCCCGCCTCCTCTCCT
CGAAATGC
28
CCTTATATCGCACGGGTTCC
TTCTTGGGG
29
GCAAGATGCAATGGAGTTCA
CAAACCGC
30
GCAAAATTCAAAGAAAACTTA
CTGACAGTG
31
CGTTCATCCCACCACCTTTC
GCTGCGAG
32
GAATGTGGCTGTAAATGCTGAGTG
AAGCCGCA
33
ACATTCCCTCTATTATTCTCAC
GTTTTGTTTG
34
AAGCCAACTTCACAGATATGTTGAT
ATGAGCCTA
35
AGTGAGGTATGGTTGATTAGGA
TATTGATAG
36
CTCCGATGGTCAAGTCAGA
AAATGGGG
37
GCCGTTCAAGTCAATTAGAC
TTTGGGAGC
38
TGCTTCTTGTCCTTGATACA
CCACGTCTA
39
CACCACATGAAGCAAGCAGT
CCTACCACA
40
TTTTATTTTCCCTCTCTTTTGA
ATTGCGTCT
41
CATATGGCGCACAGGCAC
GCAATACA
42
AGTTGGTTTGCTGATTTG
TGTTGCTTC
43
GCTGAAGATGAAATTGATGTA
TTCAGGTCC
44
ATGACCTAAAAATAAAATCTCAT
ACAGATCA
45
GGTGCAAGAGAGGAGGAATG
TTTGGTAGT
46
GTTTGGCTTTGGACATG
TCCATCACA
47
TGTTTTGTTTCGTGCATGTG
GGCTGACA
48
CGGTTTTGTCGCATCTATG
GTCGTCAGG
49
CAATCATTGGCGAGAGA
CGTCACCTT
50
GAGCATGACGCAAACAAAGG
GCAACATG
51
TCCAAGTAGCAAATGATGAC
TGCCCTGAA
52
GAAGGGGCATTGGATTT
TACCTATTA
53
AACACTCCAGAAGCCAGGTC
GGTTTAGGT
54
GATCCCAATGGTAAAGACT
AAGCCTCA
55
TGTGGTTTGAGGCATCTTCT
GCCCACCA
56
TAGCCGCACTCCCACGAAGC
CCAGAATC
57
TCAAAGAGCCGCACAACAAG
ACTTTGCTG
58
GGGGATGAGTTTGTTTGTTC
CCTGCTTGG
59
TCTAATGCTCCCAAGGTACA
GGCTTGGTC
60
AGCTCTCATGCAAGTAAC
TTCAACATA
61
TCCTCACTGCTCCTCTAATC
ACTCCCTAT
62
AGGGAGGCGAACGAGAAACA
CGACTGCTG
63
CTACGGACTCACACCTATAT
ATGGTTCAT
64
GTGAGCGATTGAGGGGTGTG
GGGGCTTG Table 3 Microsatellite markers (described by Billotte et al. Results [27]) used for a larger-scale survey for hemizygosity of Hs
and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15
markers) and flow cytometry screen
No. Forward primer (5’-3’)
Reverse primer (5’-3’)
16
GACCTTTGTCAGCATACTTGGTGTG
GCAGGCCTGAAATCCCAAAT
17
ATGCATGTGATTTTATTAGGTGAGA
CGACCCTCAGTCAATCAGTAAG
18
AAGCTAGCGACCTATGATTTTAGA
AAACAAGTAATGTGCATAACCTTTC
19
CCCACCACCCCTAGCTTCTC
ACCCCGGTCCAAATAAAATC
20
AGAGAGAGAGAGTGCGTATG
GTCCCTGTGGCTGCTGTTTC
21
GGGTAGCAAACCTTGTATTA
ACTTCCATTGTCTCATTATTCT
22
CGAGGCCCAAAAACATTCAC
GGTCCCGATCCCGTCTACTG
23
TTGCGGCCCATCGTAATC
TCCCTGCAGTGTCCCTCTTT
24
AGGGAATTGGAAGAAAAGAAAG
TCCTGAGCTGGGGTGGTC
25
AGCAAGAGCAAGAGCAGAACT
CTTGGGGGCTTCGCTATC
26
TAGCCATGCCGCCACCACTT
CAATCCATTAGCGTGCCCTTCT
27
CTTACCCCGCCTCCTCTCCT
CGAAATGCCCTTCCTTTACACTA
28
CCTTATATCGCACGGGTTCC
TTCTTGGGGTCTCGCTACGG
29
GCAAGATGCAATGGAGTTCA
CAAACCGCAGCAAGTCAGA
30
GCAAAATTCAAAGAAAACTTA
CTGACAGTGCAGAAAATGTTATAGT
31
CGTTCATCCCACCACCTTTC
GCTGCGAGGCCACTGATAC
32
GAATGTGGCTGTAAATGCTGAGTG
AAGCCGCATGGACAACTCTAGTAA
33
ACATTCCCTCTATTATTCTCAC
GTTTTGTTTGGTATGCTTGT
34
AAGCCAACTTCACAGATATGTTGAT
ATGAGCCTAACAAAGCACATTCTAA
35
AGTGAGGTATGGTTGATTAGGA
TATTGATAGCATTTGGGATTAG
36
CTCCGATGGTCAAGTCAGA
AAATGGGGAAGGCAATAGTG
37
GCCGTTCAAGTCAATTAGAC
TTTGGGAGCAAGCATTATCA
38
TGCTTCTTGTCCTTGATACA
CCACGTCTACGAAATGATAA
39
CACCACATGAAGCAAGCAGT
CCTACCACAACCCCAGTCTC
40
TTTTATTTTCCCTCTCTTTTGA
ATTGCGTCTCTTTCCATTGA
41
CATATGGCGCACAGGCAC
GCAATACAAGAGCACCCAAAT
42
AGTTGGTTTGCTGATTTG
TGTTGCTTCTTTGATTTTC
43
GCTGAAGATGAAATTGATGTA
TTCAGGTCCACTTTCATTTA
44
ATGACCTAAAAATAAAATCTCAT
ACAGATCATGCTTGCTCACA
45
GGTGCAAGAGAGGAGGAATG
TTTGGTAGTCGGGCGTTTTA
46
GTTTGGCTTTGGACATG
TCCATCACAGGAGGTATAG
47
TGTTTTGTTTCGTGCATGTG
GGCTGACATGCAACACTAAC
48
CGGTTTTGTCGCATCTATG
GTCGTCAGGGAACAACAGT
49
CAATCATTGGCGAGAGA
CGTCACCTTTCAGGATATG
50
GAGCATGACGCAAACAAAGG
GCAACATGTTTGATGCATTAATAGTC
51
TCCAAGTAGCAAATGATGAC
TGCCCTGAAACCCTTGA
52
GAAGGGGCATTGGATTT
TACCTATTACAGCGAGAGTG
53
AACACTCCAGAAGCCAGGTC
GGTTTAGGTATTGGAACTGATAGAC
54
GATCCCAATGGTAAAGACT
AAGCCTCAAAAGAAGACC
55
TGTGGTTTGAGGCATCTTCT
GCCCACCAAAAGAAAGTAGT
56
TAGCCGCACTCCCACGAAGC
CCAGAATCATCAGACTCGGACAG
57
TCAAAGAGCCGCACAACAAG
ACTTTGCTGCTTGGTGACTTA
58
GGGGATGAGTTTGTTTGTTC
CCTGCTTGGCGAGATGA
59
TCTAATGCTCCCAAGGTACA
GGCTTGGTCCACGATCTT
60
AGCTCTCATGCAAGTAAC
TTCAACATACCGTCTGTA
61
TCCTCACTGCTCCTCTAATC
ACTCCCTATGGACCTTAGTC Table 3 Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs
and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15
k
)
d fl
t
t Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 6 of 25 Table 3: Microsatellite markers (described by Billotte et al. Results [27]) used for a larger-scale survey for hemizygosity of Hs
and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15
markers) and flow cytometry screen (Continued)
65
AGGGCAAGTCATGTTTC
TATAAGGGCGAGGTATT
66
GAAGCCTGAGACCGCATAGA
TTCGGTGATGAAGATTGAAG
67
TTTCTTATGGCAATCACACG
GGAGGGCAGGAACAAAAAGT
68
GTTTATCATTTTGGGGTCAG
CGGTGTCCCTCAGGATGTA
69
CATGCACGTAAAGAAAGTGT
CCAAATGCACCCTAAGA
70
AATCCAAGTGGCCTACAG
CATGGCTTTGCTCAGTCA
71
TGTAGGTGGTGGTTAGG
TGTCAGACCCACCATTA
72
AGCAAGACACCATGTAGTC
GACACGTGGGATCTAGAC
73
AAAAGCCGATAGTGGGAACA
ATGCTGAGAGGTGGAAAATAGAG
74
GTCCATGTGCATAAGAGAG
CTCTTGGCATTTCAGATAC
75
AGCCAATGAAGGATAAAGG
CAAGCTAAAACCCCTAATC
76
CAATTCCAGCGTCACTATAG
AGTGGCAGTGGAAAAACAGT
77
GGGCTTTCATTTTCCACTAT
GCTCAACCTCATCCACAC
78
GACAGCTCGTGATGTAGA
GTTCTTGGCCGCTATAT
79
ACTTGTAAACCCTCTTCTCA
GTTTCATTACTTGGCTTCTG
80
CCTTCAAGCAAAGATACC
GGCACCAAACACAGTAA
81
CCACTGCTTCAAATTTACTAG
GCGTCCAAAACATAAATCAC
82
GGGAGAGGAAAAAATAGAG
CCTCCCTGAGACTGAGAAG
83
AGCAGGGCAAGAGCAATACT
TTCAGCAGCAGGAAACATC
84
GCCTATCCCCTGAACTATCT
TGCACATACCAGCAACAGAG
85
CATCAGAGCCTTCAAACTAC
AGCCTGAATTGCCTCTC
86
ATTCATTGCCATTCCCTTCA
TTGTCCCCTCTGTTCACTCA
87
ATTGCAGAGATGATGAGAAG
GAGATGCTGACAATGGTAGA
88
TCTCCCAAATCACTAGAC
ATCTGCAAGGCATATTC
89
ACGTTTTGGCAACTCTC
ACTCCCCTCTTTGACAT
90
TCCACTCTGGCAACTCC
AAGGATGGGCTTTGTAGT
91
TTTAGAGGACAAGGAGATAAG
CGACCGTGTCAAGAGTG
92
AGCAAAATGGCAAAGGAGAG
GGTGTGTGCTATGGAAGATCATAGT
93
GTAGCTTGAACCTGAAA
AGAACCACCGGAGTTAC
94
AAGCCACCAGGATCATC
GTCATTGCCACCTCTAACT
95
TTACTTGCTAAGCTCTCTAGC
TGGCTGTTTAATCTGTCTG
96
TCTATATTTGGTTGGCTTGA
ACTCATTTCAATCTCAGTGTC
97
TGCTACGTGCTGAAATA
ATTTCAGGTTCGCTTCA
98
CCTCCACTTCTCTTCATCTT
CTTCCTCAAGCTCAAACAAT
99
GATGTTGCCGCTGTTTG
CATCCCATTTCCCTCTT
100
ATGCTCCACCAAGTTTA
CACATCCTAGCATCATTG
101
AAGCAATATAGGTTCAGTTC
TCATTTTCTAATTCCAAACAAG
102
GCTCGTTTTTGTTTAGGTGA
TTTTCTCCATAGTCCGTTAC
103
CAGCACACAAATGACAT
CACCTTTCCTTTTTGTC
104
CCTATTCCTTACCTTTCTGT
GACTTACTATCTTGGCTCAC
105
CCTTGCATTCCACTATT
AGTTCTCAAGCCTCACA
106
CCTCCTTTGGAATTATG
GTGTTTGATGGGACATACA
107
ATTGGAGAGCACTTGGATAG
TTCTCTTCCTTCTCACTTGT Table 3: Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs
and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15
markers) and flow cytometry screen (Continued) Table 3: Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs
and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15
markers) and flow cytometry screen (Continued) Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Page 7 of 25 Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids;
green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild
material. Microsatellite data in Table 7. Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids;
green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild
material. Microsatellite data in Table 7. Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids;
green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild
material. Microsatellite data in Table 7. was 8.72 × 10-8 (see Methods). This palm was therefore
deemed a spontaneous DH. Results selection proving substantially more effective than
screening for twin embryos. This result suggests that
our method could be used to secure large numbers of
Hs but is less able to isolate DHs at useful frequencies. This finding, when coupled with the routine nature of H These initial screens collectively revealed 83 sponta-
neous Hs but no DHs (although one DH was discovered
subsequently), with the undirected phenotypic ‘off-type’ Figure 4 Selection of haploid oil palm plants growing in a nursery. Figure 4 Selection of haploid oil palm plants growing in a nursery. Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 8 of 25 chromosome doubling in other crops [21], suggested the
most promising route for commercial DH production
lay in the isolation of Hs followed by somatic doubling. In subsequent screening of abnormal seedlings, high-
throughput flow cytometry therefore replaced molecular
analysis for candidate H identification. Haploid identity
was then supported using at least 15 microsatellite mar-
kers. Plants identified as diploid by flow cytometry con-
tinued to be screened for DHs as above. Using this
amended screening procedure, we have identified over
1,100 H palms from approximately 60 million seedlings
(to July 2009). Figure 5 Doubled haploid palm. To have maximum utility this H/DH material should
encompass as much genetic diversity from within the
breeding germplasm as possible. A Principal Coordi-
nates Analysis performed on H profiles using 28 micro-
satellite loci showed the first two axes accounted for
58% of the detected variation. While most Hs had a
strong affinity to commercial duras, Hs have also been
generated from pisifera types and overall variability
amongst Hs encompassed that seen for the entire com-
mercial palm material (Figure 3). Effort then focussed on the creation of DHs from this
rich germplasm of H genotypes (Figure 4). The most
direct route to obtain DHs is to use chemical applica-
tion to induce chromosome doubling. We applied a
range of treatments to 50 H seedlings and screened
leaves of the recovered material for evidence of chromo-
some doubling. Flow cytometry revealed that 48 seed-
lings contained substantial diploid sectors in their
leaves; one palm was 100% doubled after exposure to10
mM colchicine (Figure 5) and 100 ppm GA3. To date,
16 H genotypes have produced pollen. This finding
demonstrates scope for securing fertile gametes from
diploid inflorescences or inflorescence sectors for DH or
F1 production. Results Indeed, seed set using pollen from DH
material has now been achieved (data not shown). Whilst further optimization work is required, our results
when combined with experience in other crops [21] sug-
gest routine production of fertile DH oil palm lines will
be a relatively simple task. Figure 5 Doubled haploid palm. Figure 5 Doubled haploid palm. In the case of oil palm, the efficacy of our H screening
combined with the demonstrated ability to create DH
palms, opens the way for the development of 100% true-
breeding parental clones for F1 variety breeding. There-
after, it is hoped that the potential genetic gain available
from oil palm F1 hybrids will match that in other crops. If such a gain is achieved it could be beneficial in several
ways. First, high-yielding F1 palms are likely to acceler-
ate replacement of palms in existing plantations and
cause a step-increase in production. Secondly, this
breeding strategy provides greater flexibility for breeders
to respond rapidly to emergent threats (e.g. climate
change). Thirdly, using palm oil and its associated
wastes for energy generation [7] could substantially
reduce carbon-based emissions currently associated with
the palm oil lifecycle [23]. Fourthly, DH oil palms could
be exploited in combination with transgenic techniques
that are now available for this crop [24]. Looking for-
ward, the clear challenge is to maintain and improve oil
palm productivity in the face of a changing climate Discussion and Conclusions The simple high-throughput phenotypic-genotypic seed-
ling selection system used here provides a fourth practi-
cal approach to supplement androgenesis, wide crossing
and gynogenesis [6] and has potential for many crops
where H/DH production remains elusive. The prospect
of adopting a similar untargeted approach more widely
seems both plausible and attractive, and may be possible
without experienced operators, especially as sophisti-
cated phenomic screening systems [22] become more
accessible. Page 9 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Abnormal seedlings
124,094
1st molecular screening
111,320
Flow cytometry
25,235
Haploid
1,123
Diploid
24,027
Doubled
haploid
4
2nd
molecular
screening
11,897
Alive
858
Dead
265
Germinated seeds
95,265,687
Morphological screening
Molecular screening
Flow Cytometry
50 haploids produced per month
Figure 6 Summary of stages for identification of haploid and doubled haploid palm. Germinated seeds
95,265,687 Flow cytometry
25,235 Haploid
1,123 ure 6 Summary of stages for identification of haploid and doubled haploid palm. crops recalcitrant to in vitro based H/DH systems. This
methodology, in particular the application of high-
throughput flow cytometry, has recently been applied
successfully to two other tropical crops, namely rubber
(Hevea brasiliensis L.) and cocoa (Theobroma cacao L.)
(Nasution et al. unpublished). crops recalcitrant to in vitro based H/DH systems. This
methodology, in particular the application of high-
throughput flow cytometry, has recently been applied
successfully to two other tropical crops, namely rubber
(Hevea brasiliensis L.) and cocoa (Theobroma cacao L.)
(Nasution et al. unpublished). sufficient to keep pace with growing demand [25]. How-
ever, it is important to point out that breeding is simply
one stage in a long process from plantation to the even-
tual processed product and the economic realities of
this international industry will finally determine the
impact of any novel technology on the global agricul-
tural system for this crop. Methods The provision here of a system for haploid-based F1
hybrid breeding in oil palm represents the first techno-
logical breakthrough likely to lead to step improvements
in yield for this crop, and can also be applied to other Hs and DHs were identified using three methods: a mor-
phological screen; homozygosity/hemizygosity assessment;
and ploidy level measurement. Initial screens emphasized Figure 7 PCR amplicons generated by microsatellite marker 10 fractionated in 2% w/v agarose. Lanes 1-11 & 12-20: candidate H/DH
palm plants; lane L: HyperladderI (Bioline, UK); lane 21: heterozygote control; lane 22: homozygote control. Candidates in lanes 1, 3, 4, 7, 8, 10,
11, 13, 16, 17, 19, 20 were deemed heterozygous and discarded. Figure 7 PCR amplicons generated by microsatellite marker 10 fractionated in 2% w/v agarose. Lanes 1-11 & 12-20: candidate H/DH
palm plants; lane L: HyperladderI (Bioline, UK); lane 21: heterozygote control; lane 22: homozygote control. Candidates in lanes 1, 3, 4, 7, 8, 10,
11, 13, 16, 17, 19, 20 were deemed heterozygous and discarded. Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 10 of 25 Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C)
No
Marker
Forward Primer (5’-3’)
Reverse Primer (5’-3’)
1
VS1
GAGATTACAAAGTCCAAACC
TCAAAATTAAGAAAGTATGC
2
OPSSR 3
ACGCATGCAGCTAGCTTTTC
CGCGTGAAAGATATGAATCAAC
3
OPSSR 7
CACGCACGCAGTTTATTCTT
GGATGTATGCTTTACCTCCGAAT
4
OPSSR 8
CCCCTTTTGCTTCCCTATTT
CTCCTTTTCCCCATCACAGA
5
OPSSR 9
GACACAAGCAAAAACAAAAGCA
ATTCTGAAAGGAGGGGGAAA
6
OPSSR 14
ATATGTGTGGGTGTGCGTGT
TGCCTCTGGTTGTTAGTCTGG
7
OPSSR 19
TCTCTCTCTCTCTCTCTATGTGTGTGT
TGGCAATCAGCACACATTCT
8
OPSSR 29
GCAGCTCTTTCCACACCTCT
TGTGGTCTCCTGAGGAAGATG
9
OPSSR 30
TTTTCCCCATCACAGAATTG
CCCCTTTTGCTTCCCTATTT
10
OPSSR32
GAACAAAACGGGAAGAAGCA
CCTCAAATGGGAGAAACCAG
11
mEgUWA07
CGGATAGAGGCAGCAAGACT
CTCGGGTTGTTTAACCCATT
12
mEgUWA44
TTGAGACGTCGTTCCTTTCC
AGCGGAGACCCAATAATCCT
13
mEgUWA50
CCTGCAACTGCAAATGAGAC
TCCAGACACAAACTACACACACC
14
mEgCIR0037
Published by Billotte et al. [27]
15
mEgCIR0055
Published by Billotte et al. [27]
16
mEgCIR0059
Published by Billotte et al. [27]
17
mEgCIR0067
Published by Billotte et al. [28]
18
mEgCIR0074
Published by Billotte et al. [27]
19
mEgCIR0146
Published by Billotte et al. [27]
20
mEgCIR0163
Published by Billotte et al. [27]
21
mEgCIR0173
Published by Billotte et al. [27]
22
mEgCIR0177
Published by Billotte et al. [27]
23
mEgCIR0192
Published by Billotte et al. [27]
24
mEgCIR0195
Published by Billotte et al. [27]
25
mEgCIR0243
Published by Billotte et al. [27]
26
mEgCIR0246
Published by Billotte et al. [27]
27
mEgCIR0257
Published by Billotte et al. [27]
28
mEgCIR0268
Published by Billotte et al. [27]
29
mEgCIR0328
Published by Billotte et al. Methods [27]
30
mEgCIR0359
Published by Billotte et al. [27]
31
mEgCIR0366
Published by Billotte et al. [27]
32
mEgCIR0369
Published by Billotte et al. [27]
33
mEgCIR0380
Published by Billotte et al. [27]
34
mEgCIR0399
Published by Billotte et al. [27]
35
mEgCIR0408
Published by Billotte et al. [27]
36
mEgCIR0409
Published by Billotte et al. [27]
37
mEgCIR0425
Published by Billotte et al. [27]
38
mEgCIR0433
Published by Billotte et al. [27]
39
mEgCIR0439
Published by Billotte et al. [27]
40
mEgCIR0445
Published by Billotte et al. [27]
41
mEgCIR0446
Published by Billotte et al. [27]
42
mEgCIR0465
Published by Billotte et al. [27]
43
mEgCIR0521
Published by Billotte et al. [27]
44
mEgCIR0551
Published by Billotte et al. [27]
45
mEgCIR0555
Published by Billotte et al. [27]
46
mEgCIR0588
Published by Billotte et al. [27]
47
mEgCIR0772
Published by Billotte et al. [27]
48
mEgCIR0773
Published by Billotte et al. [27]
49
mEgCIR0774
Published by Billotte et al. [27]
50
mEgCIR0775
Published by Billotte et al. [27] Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm
candidate palm (0644-219/05049582C) Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 11 of 25 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal paren
candidate palm (0644-219/05049582C) (Continued)
51
mEgCIR0778
Published by Billotte et al. [27
52
mEgCIR0779
Published by Billotte et al. [27
53
mEgCIR0781
Published by Billotte et al. [27
54
mEgCIR0786
Published by Billotte et al. [27
55
mEgCIR0787
Published by Billotte et al. [27
56
mEgCIR0788
Published by Billotte et al. [27
57
mEgCIR0790
Published by Billotte et al. [27
58
mEgCIR0793
Published by Billotte et al. [27
59
mEgCIR0800
Published by Billotte et al. [27
60
mEgCIR0801
Published by Billotte et al. [27
61
mEgCIR0802
Published by Billotte et al. [27
62
mEgCIR0803
Published by Billotte et al. [27
63
mEgCIR0804
Published by Billotte et al. [27
64
mEgCIR0825
Published by Billotte et al. Methods [27
65
mEgCIR0827
Published by Billotte et al. [27
66
mEgCIR0844
Published by Billotte et al. [27
67
mEgCIR0874
Published by Billotte et al. [27
68
mEgCIR0878
Published by Billotte et al. [27
69
mEgCIR0882
Published by Billotte et al. [27
70
mEgCIR0886
Published by Billotte et al. [27
71
mEgCIR0894
Published by Billotte et al. [27
72
mEgCIR0905
Published by Billotte et al. [27
73
mEgCIR0906
Published by Billotte et al. [27
74
mEgCIR0910
Published by Billotte et al. [27
75
mEgCIR0912
Published by Billotte et al. [27
76
mEgCIR1729
Published by Billotte et al. [27
77
mEgCIR1740
Published by Billotte et al. [27
78
mEgCIR1753
Published by Billotte et al. [27
79
mEgCIR1773
Published by Billotte et al. [27
80
mEgCIR1917
Published by Billotte et al. [27
81
mEgCIR1977
Published by Billotte et al. [27
82
mEgCIR1996
Published by Billotte et al. [27
83
mEgCIR2110
Published by Billotte et al. [27
84
mEgCIR2144
Published by Billotte et al. [27
85
mEgCIR2149
Published by Billotte et al. [27
86
mEgCIR2188
Published by Billotte et al. [27
87
mEgCIR2212
Published by Billotte et al. [27
88
mEgCIR2215
Published by Billotte et al. [27
89
mEgCIR2380
Published by Billotte et al. [27
90
mEgCIR2387
Published by Billotte et al. [27
91
mEgCIR2414
Published by Billotte et al. [27
92
mEgCIR2417
Published by Billotte et al. [27
93
mEgCIR2422
Published by Billotte et al. [27
94
mEgCIR2423
Published by Billotte et al. [27
95
mEgCIR2427
Published by Billotte et al. [27
96
mEgCIR2436
Published by Billotte et al. [27
97
mEgCIR2440
Published by Billotte et al. [27
98
mEgCIR2492
Published by Billotte et al. [27
99
mEgCIR2518
Published by Billotte et al. [27
100
mEgCIR2525
Published by Billotte et al. [27
101
mEgCIR2569
Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
-219/05049582C) (Continued) Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
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Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. Methods [27 Table 4: Microsatellite markers used to screen for heterozygosity
candidate palm (0644-219/05049582C) (Continued)
51
mEgCIR0778
52
mEgCIR0779
53
mEgCIR0781
54
mEgCIR0786
55
mEgCIR0787
56
mEgCIR0788
57
mEgCIR0790
58
mEgCIR0793
59
mEgCIR0800
60
mEgCIR0801
61
mEgCIR0802
62
mEgCIR0803
63
mEgCIR0804
64
mEgCIR0825
65
mEgCIR0827
66
mEgCIR0844
67
mEgCIR0874
68
mEgCIR0878
69
mEgCIR0882
70
mEgCIR0886
71
mEgCIR0894
72
mEgCIR0905
73
mEgCIR0906
74
mEgCIR0910
75
mEgCIR0912
76
mEgCIR1729
77
mEgCIR1740
78
mEgCIR1753
79
mEgCIR1773
80
mEgCIR1917
81
mEgCIR1977
82
mEgCIR1996
83
mEgCIR2110
84
mEgCIR2144
85
mEgCIR2149
86
mEgCIR2188
87
mEgCIR2212
88
mEgCIR2215
89
mEgCIR2380
90
mEgCIR2387
91
mEgCIR2414
92
mEgCIR2417
93
mEgCIR2422
94
mEgCIR2423
95
mEgCIR2427
96
mEgCIR2436
97
mEgCIR2440
98
mEgCIR2492
99
mEgCIR2518
100
mEgCIR2525 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27] 51
mEgCIR0778
52
mEgCIR0779
53
mEgCIR0781
54
mEgCIR0786
55
mEgCIR0787
56
mEgCIR0788
57
mEgCIR0790
58
mEgCIR0793
59
mEgCIR0800
60
mEgCIR0801
61
mEgCIR0802
62
mEgCIR0803
63
mEgCIR0804
64
mEgCIR0825
65
mEgCIR0827
66
mEgCIR0844
67
mEgCIR0874
68
mEgCIR0878
69
mEgCIR0882
70
mEgCIR0886
71
mEgCIR0894
72
mEgCIR0905
73
mEgCIR0906
74
mEgCIR0910
75
mEgCIR0912
76
mEgCIR1729
77
mEgCIR1740
78
mEgCIR1753
79
mEgCIR1773
80
mEgCIR1917
81
mEgCIR1977
82
mEgCIR1996
83
mEgCIR2110
84
mEgCIR2144
85
mEgCIR2149
86
mEgCIR2188
87
mEgCIR2212
88
mEgCIR2215
89
mEgCIR2380
90
mEgCIR2387
91
mEgCIR2414
92
mEgCIR2417
93
mEgCIR2422
94
mEgCIR2423
95
mEgCIR2427
96
mEgCIR2436
97
mEgCIR2440
98
mEgCIR2492
99
mEgCIR2518
100
mEgCIR2525
101
mEgCIR2569 Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
-219/05049582C) (Continued) Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 12 of 25 Table 4: Microsatellite markers used to screen for heterozygosity
candidate palm (0644-219/05049582C) (Continued)
102
mEgCIR2575
103
mEgCIR2577
104
mEgCIR2590
105
mEgCIR2595
106
mEgCIR2600
107
mEgCIR2621
108
mEgCIR2628
109
mEgCIR2763
110
mEgCIR2813
111
mEgCIR2860
112
mEgCIR2887
113
mEgCIR2893
114
mEgCIR3040
115
mEgCIR3111
116
mEgCIR3160
117
mEgCIR3194
118
mEgCIR3213
119
mEgCIR3232
120
mEgCIR3295
121
mEgCIR3296
122
mEgCIR3297
123
mEgCIR3298
124
mEgCIR3300
125
mEgCIR3301
126
mEgCIR3305
127
mEgCIR3307
128
mEgCIR3310
129
mEgCIR3311
130
mEgCIR3316
131
mEgCIR3321
132
mEgCIR3328
133
mEgCIR3350
134
mEgCIR3384
135
mEgCIR3389
136
mEgCIR3399
137
mEgCIR3400
138
mEgCIR3402
139
mEgCIR3427
140
mEgCIR3428
141
mEgCIR3433
142
mEgCIR3439
143
mEgCIR3477
144
mEgCIR3519
145
mEgCIR3526
146
mEgCIR3533
147
mEgCIR3534
148
mEgCIR3535
149
mEgCIR3538
150
mEgCIR3543
151
mEgCIR3544
152
mEgCIR3546 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27] 102
mEgCIR2575
103
mEgCIR2577
104
mEgCIR2590
105
mEgCIR2595
106
mEgCIR2600
107
mEgCIR2621
108
mEgCIR2628
109
mEgCIR2763
110
mEgCIR2813
111
mEgCIR2860
112
mEgCIR2887
113
mEgCIR2893
114
mEgCIR3040
115
mEgCIR3111
116
mEgCIR3160
117
mEgCIR3194
118
mEgCIR3213
119
mEgCIR3232
120
mEgCIR3295
121
mEgCIR3296
122
mEgCIR3297
123
mEgCIR3298
124
mEgCIR3300
125
mEgCIR3301
126
mEgCIR3305
127
mEgCIR3307
128
mEgCIR3310
129
mEgCIR3311
130
mEgCIR3316
131
mEgCIR3321
132
mEgCIR3328
133
mEgCIR3350
134
mEgCIR3384
135
mEgCIR3389
136
mEgCIR3399
137
mEgCIR3400
138
mEgCIR3402
139
mEgCIR3427
140
mEgCIR3428
141
mEgCIR3433
142
mEgCIR3439
143
mEgCIR3477
144
mEgCIR3519
145
mEgCIR3526
146
mEgCIR3533
147
mEgCIR3534
148
mEgCIR3535
149
mEgCIR3538
150
mEgCIR3543
151
mEgCIR3544
152
mEgCIR3546 Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
-219/05049582C) (Continued) ndidate palm (0644 219/05049582C) (Continued)
153
mEgCIR3555
Published by Billotte et al. [27
154
mEgCIR3557
Published by Billotte et al. [27
155
mEgCIR3563
Published by Billotte et al. [27
156
mEgCIR3567
Published by Billotte et al. [27
157
mEgCIR3569
Published by Billotte et al. [27
158
mEgCIR3574
Published by Billotte et al. [27
159
mEgCIR3587
Published by Billotte et al. [27
160
mEgCIR3590
Published by Billotte et al. [27
161
mEgCIR3592
Published by Billotte et al. [27
162
mEgCIR3593
Published by Billotte et al. [27
163
mEgCIR3607
Published by Billotte et al. [27
164
mEgCIR3622
Published by Billotte et al. [27
165
mEgCIR3633
Published by Billotte et al. [27
166
mEgCIR3639
Published by Billotte et al. [27
167
mEgCIR3643
Published by Billotte et al. [27
168
mEgCIR3649
Published by Billotte et al. [27
169
mEgCIR3653
Published by Billotte et al. [27
170
mEgCIR3655
Published by Billotte et al. [27
171
mEgCIR3663
Published by Billotte et al. [27
172
mEgCIR3668
Published by Billotte et al. [27
173
mEgCIR3672
Published by Billotte et al. [27
174
mEgCIR3683
Published by Billotte et al. [27
175
mEgCIR3684
Published by Billotte et al. [27
176
mEgCIR3691
Published by Billotte et al. [27
177
mEgCIR3693
Published by Billotte et al. [27
178
mEgCIR3696
Published by Billotte et al. [27
179
mEgCIR3698
Published by Billotte et al. [27
180
mEgCIR3705
Published by Billotte et al. [27
181
mEgCIR3711
Published by Billotte et al. [27
182
mEgCIR3716
Published by Billotte et al. [27
183
mEgCIR3718
Published by Billotte et al. [27
184
mEgCIR3722
Published by Billotte et al. [27
185
mEgCIR3727
Published by Billotte et al. [27
186
mEgCIR3728
Published by Billotte et al. [27
187
mEgCIR3732
Published by Billotte et al. [27
188
mEgCIR3737
Published by Billotte et al. [27
189
mEgCIR3739
Published by Billotte et al. [27
190
mEgCIR3745
Published by Billotte et al. [27
191
mEgCIR3747
Published by Billotte et al. [27
192
mEgCIR3750
Published by Billotte et al. [27
193
mEgCIR3755
Published by Billotte et al. [27
194
mEgCIR3766
Published by Billotte et al. [27
195
mEgCIR3769
Published by Billotte et al. [27
196
mEgCIR3775
Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27
197
mEgCIR3782
Published by Billotte et al. [27
198
mEgCIR3785
Published by Billotte et al. [27
199
mEgCIR3787
Published by Billotte et al. [27
200
mEgCIR3788
Published by Billotte et al. [27
201
mEgCIR3792
Published by Billotte et al. [27
202
mEgCIR3807
Published by Billotte et al. [27
203
mEgCIR3808
Published by Billotte et al. [27 Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 13 of 25 Table 4: Microsatellite markers used to screen for heterozygosity
candidate palm (0644-219/05049582C) (Continued)
153
mEgCIR3555
154
mEgCIR3557
155
mEgCIR3563
156
mEgCIR3567
157
mEgCIR3569
158
mEgCIR3574
159
mEgCIR3587
160
mEgCIR3590
161
mEgCIR3592
162
mEgCIR3593
163
mEgCIR3607
164
mEgCIR3622
165
mEgCIR3633
166
mEgCIR3639
167
mEgCIR3643
168
mEgCIR3649
169
mEgCIR3653
170
mEgCIR3655
171
mEgCIR3663
172
mEgCIR3668
173
mEgCIR3672
174
mEgCIR3683
175
mEgCIR3684
176
mEgCIR3691
177
mEgCIR3693
178
mEgCIR3696
179
mEgCIR3698
180
mEgCIR3705
181
mEgCIR3711
182
mEgCIR3716
183
mEgCIR3718
184
mEgCIR3722
185
mEgCIR3727
186
mEgCIR3728
187
mEgCIR3732
188
mEgCIR3737
189
mEgCIR3739
190
mEgCIR3745
191
mEgCIR3747
192
mEgCIR3750
193
mEgCIR3755
194
mEgCIR3766
195
mEgCIR3769
196
mEgCIR3775
197
mEgCIR3782
198
mEgCIR3785
199
mEgCIR3787
200
mEgCIR3788
201
mEgCIR3792
202
mEgCIR3807
203
mEgCIR3808 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27] 153
mEgCIR3555
154
mEgCIR3557
155
mEgCIR3563
156
mEgCIR3567
157
mEgCIR3569
158
mEgCIR3574
159
mEgCIR3587
160
mEgCIR3590
161
mEgCIR3592
162
mEgCIR3593
163
mEgCIR3607
164
mEgCIR3622
165
mEgCIR3633
166
mEgCIR3639
167
mEgCIR3643
168
mEgCIR3649
169
mEgCIR3653
170
mEgCIR3655
171
mEgCIR3663
172
mEgCIR3668
173
mEgCIR3672
174
mEgCIR3683
175
mEgCIR3684
176
mEgCIR3691
177
mEgCIR3693
178
mEgCIR3696
179
mEgCIR3698
180
mEgCIR3705
181
mEgCIR3711
182
mEgCIR3716
183
mEgCIR3718
184
mEgCIR3722
185
mEgCIR3727
186
mEgCIR3728
187
mEgCIR3732
188
mEgCIR3737
189
mEgCIR3739
190
mEgCIR3745
191
mEgCIR3747
192
mEgCIR3750
193
mEgCIR3755
194
mEgCIR3766
195
mEgCIR3769
196
mEgCIR3775
197
mEgCIR3782
198
mEgCIR3785
199
mEgCIR3787
200
mEgCIR3788
201
mEgCIR3792
202
mEgCIR3807
203
mEgCIR3808 Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
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Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27]
Published by Billotte et al. Molecular pre-screen to exclude heterozygotes Molecular pre-screen to exclude heterozygotes
DNA was isolated from leaf tissue using DNeasy 96
Plant Kit (Qiagen, UK). Initial heterozygosity screens
used 15 microsatellites (Table 1) yielding alleles readily
distinguished by agarose gel electrophoresis (Figure 7). 10 μl PCR mixes comprised 1.0 μl 10× NH4 buffer (Bio-
line), 0.3 μl MgCl2 (10 mM), 0.4 μl dNTPs (10 mM), 0.2
μl each primer (10 mM), 1-5 ng DNA and 1U Taq poly-
merase (Bioline). Thermocycling conditions: 2 min at
94°C followed by 35 cycles of 94°C for 30 s, 52-58°C for
30 s and 72°C for 45 s, with a final extension of 72°C
for 7 min. Candidates presenting two allelic bands after
fractionation by (2-3% w/v metaphor) agarose gel elec-
trophoresis were discarded. DH candidate 0644-219/05049582C was found to be
homozygous across all 48 loci that were heterozygous in
its maternal parent. Of these 48 loci, 36 have been
mapped by Billotte et al. [27] (Table 5). We first consid-
ered the probability of obtaining the observed homozyg-
osity levels via independent assortment using only the
unlinked markers from this group. For unlinked loci,
the probability of homozygous offspring arising by inde-
pendent assortment is 0.5 per locus. Given that hetero-
zygous loci were secured from 14 of the 16 linkage
groups, with the addition of a further unlinked (unas-
signed) marker, the probability of these markers all
becoming
homozygous
by
chance
is
therefore:
P = 0.515 = 0.000030517578125. DH candidate verification To verify DH candidate 0644-219/05049582C we
screened 212 microsatellites (Table 4) for heterozygosity
in the maternal parent (BL013/12-06). 10 μl PCR mixes
comprising: 5 μl BioMix™(Bioline, UK), 0.05 μl forward
primer plus M13 adaptor (10 μM), 0.2 μl labelled M13
(-29) (10 μM) (Sigma Genosys, UK), 0.2 μl reverse primer
(10 μM) and 5-10 ng DNA were subjected to: 2 min at
94°C, followed by 35 cycles of 30 s at 94°C, 30 s at 52°C,
45 s at 72°C, with a final extension of 72°C for 7 min. Amplicons were surveyed for heterozygosity by high-
resolution melt (HRM) analysis according to Croxford et
al. [26] using the candidate as the reference comparator. Samples with amplicons variable between the maternal
parent and candidate DH were fractionated by capillary
electrophoresis as above. 48 markers identified as hetero-
zygous in the maternal parent (Table 5) were applied to
the DH candidate to assess homozygosity. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) [27]
Published by Billotte et al. [27]
Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 14 of 25 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued)
204
mEgCIR3809
Published by Billotte et al. [27]
205
mEgCIR3813
Published by Billotte et al. [27]
206
mEgCIR3819
Published by Billotte et al. [27]
207
mEgCIR3825
Published by Billotte et al. [27]
208
mEgCIR3826
Published by Billotte et al. [27]
209
mEgCIR3828
Published by Billotte et al. [27]
210
mEgCIR3847
Published by Billotte et al. [27]
211
mEgCIR3850
Published by Billotte et al. [27]
212
mEgCIR3869
Published by Billotte et al. [27] e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
-219/05049582C) (Continued) identification of candidate DHs where seedling morphol-
ogy screening was followed by homozygosity/hemizygosity
assessment using microsatellites. H/DHs were then distin-
guished by flow cytometry and DHs subjected to an exten-
sive homozygosity screen (Figure 6). Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH
candidate palm (0644-219/05049582C) (Continued) As spontaneous DH
frequency was low, later screens emphasized H recovery
where the morphological screen was followed by flow
cytometry; homozygosity of candidate Hs was thereafter
confirmed with microsatellites. identification of candidate DHs where seedling morphol-
ogy screening was followed by homozygosity/hemizygosity
assessment using microsatellites. H/DHs were then distin-
guished by flow cytometry and DHs subjected to an exten-
sive homozygosity screen (Figure 6). As spontaneous DH
frequency was low, later screens emphasized H recovery
where the morphological screen was followed by flow
cytometry; homozygosity of candidate Hs was thereafter
confirmed with microsatellites. microsatellites (Table 3) with 150 seedlings of normal phe-
notype and 24 heterozygous tenera palms as controls. PCR
conditions were as described above and resultant products
were fractionated on an ABI3730XL capillary sequencer
(Applied Biosystems, USA) by Macrogen Inc (Korea). Allele size was determined (Genemapper v4.0) against a
GS400HD standard. Individuals with two alleles at any
locus were discarded. Seed morphological screen For seed storage, mesocarps were removed from freshly
harvested seed, and seeds air-dried at ambient tempera-
ture (24 h). Seeds were thereafter stored at 25°C with
15-18% moisture content. To induce germination, stored
seeds were re-hydrated over 3 d to 18-20% moisture
content, followed by 38-40°C incubation (40-60 d). Seeds were then re-hydrated for a further 5 d to >22%
moisture content, and air-dried at ambient temperature
(4 h). Seeds were germinated at ambient temperature
(7 d to 3 months after treatment) and examined for aty-
pical germination morphology (Figure 1). Extended molecular screen 62
55
88
95
87
LG6
9
LG7
93
LG8
52
LG1
×
×
×
×
× (
)
×
(
)
× (
)
×
0 0
0
0
0
0
0
0
(
)
×
×
×
× (
)
× (
)
×
(
)
×
. . . . . . . 93
94
87
83
LG12
5
LG14
5
LG15
6
LG16
(
)
=
×
−
0
0
. . . 51
8 72
1
8 Confirmation of Hs by chromosome squashes Harvested roots were pre-treated in iced water (24 h),
then fixed in 3:1 v/v alcohol: glacial acetic acid at 4°C
(24 h). They were then rinsed in water, softened in 1N
HCl (20 min), rinsed in water (2 min) and stained in
saturated aceto-orcein (1 min). The root tip was then
squashed, mounted onto a glass slide, and examined
using a compound photomicroscope. Extended molecular screen Candidate DHs and some Hs were subjected to an exten-
sive assay for heterozygosity using 97 fluorescently-labelled Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 15 of 25 Table 5 Markers shown to be heterozygous in the
maternal parent (palm BL013/12-06) and homozygous in
the DH candidate (0644-219/05049582C)
No
Marker
Linkage Group
1
mEgCIR0268
1
2
mEgCIR0874
1
3
mEgCIR3847
1
4
mEgCIR2149
2
5
mEgCIR2518
3
6
mEgCIR0425
3
7
mEgCIR3544
3
8
mEgCIR3716
4
9
mEgCIR1917
4
10
mEgCIR3535
4
11
mEgCIR3310
4
12
mEgCIR3705
4
13
mEgCIR3477
4
14
mEgCIR0059
4
15
mEgCIR3557
4
16
mEgCIR2813
5
17
mEgCIR3543
6
18
mEgCIR0195
6
19
mEgCIR0894
7
20
mEgCIR0905b
7
21
mEgCIR0774
8
22
mEgCIR2440
8
23
mEgCIR0825
10
24
mEgCIR3826
10
25
mEgCIR0788
10
26
mEgCIR2628
10
27
mEgCIR0146
10
28
mEgCIR0878
11
29
mEgCIR1773
12
30
mEgCIR3311
12
31
mEgCIR0779
14
32
mEgCIR0588
14
33
mEgCIR3737
15
34
mEgCIR3850
15
35
mEgCIR3639
16
36
mEgCIR0905a
16
37
mEgCIR3739
unlinked
38
mEgCIR3160
unmapped
39
mEgCIR3360
unmapped
40
mEgCIR0801
unmapped
41
mEgCIR2577
unmapped
42
OPSSR14
unmapped
43
OPSSR30
unmapped
44
OPSSR32
unmapped
45
mEgUWA44
unmapped
46
mEgUWA50
unmapped
47
mEgUWA07
unmapped
48
VS1
unmapped
Linkage group assigned according to Billotte et al. [27]. Table 5 Markers shown to be heterozygous in the
maternal parent (palm BL013/12-06) and homozygous in
the DH candidate (0644-219/05049582C) This figure was further reduced by the inclusion of the
remaining 21 markers that had been assigned a map
position [27]. Here, linkage was accommodated by mul-
tiplying by 1-(distance in cM/100). Thus the inclusion
of a new marker 10 cM from an existing marker would
mean multiplying the cumulative total by 1- (10/100) =
1-0.1 = 0.9 (rather than 0.5 for an unlinked marker). This reduced the probability as follows: P =
×
0 0000 0
. ,
3 517578125
extra markers from Linkage Group 1 LG11
92
92
extra
markers from LG3
81
93
LG4
86
(
)
×
×
×
× (
)
×
0
0
0
0
0
. . (
)
. . . 00
0
0
0
0
0
0
0
. . . . . . . . Flow Cytometry
l
d Newly matured leaflets or radicles from candidate H/DH
palms were subjected to flow cytometry according to
Anumaganathan & Earle [29] to establish ploidy level. Commercial tenera palms were included as diploid con-
trols. For high-throughput mass screening, tissue samples
were bulked at a rate of five individual tissue samples per
bulk. Bulked samples (about 0.5 cm2 for radicles and 1
cm2 for leaf material (per each individual) were sliced by
chopping with a sharp clean razor-blade (20-30 chops),
in a plastic 9 cm diameter Petri dish containing 1.5 ml of
cold (5°C) CyStain® UV Ploidy solution (Partec, Germany)
modified by addition of 6.48 mM dithiothreitol (DTT)
and 1% (v/v) polyvinylpyrrolidone (PVP-40) (Sigma-
Aldrich, USA). The addition of DTT and PVP-40 were
found to reduce background counts (’noise’) in output
histograms of particle fluorescence in the analyte. Linkage group assigned according to Billotte et al. [27]. Principal Coordinates Analysis The genetic affinity of 270 Hs was compared with 95
representative diploids (Table 6) using 28 microsatel-
lites (Table 7) by Principal Coordinates Analysis
(PCoA). The PCoA was constructed using GenAlEx v6
[30]. Genetic distance option ‘codominant-genotypic’
was applied, where pairwise, individual-by-individual
(N × N) genetic distances are calculated for codomi-
nant data. For a single-locus analysis, with i-th, j-th, k-
th and l-th different alleles, a set of squared distances
is defined as d2(ii, ii) = 0, d2(ij, ij) = 0, d2(ii, ij) = 1, d2
(ij, ik) = 1, d2(ij, kl) = 2, d2(ii, jk) = 3, and d2(ii, jj) =
4. The algorithm used in GenAlEx is based on Orloci Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 16 of 25 able 6 Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
nalysis
No
Label no in PCO
Sample name in PCO
Palm Id
Ploidy level
1
1
haploid
05020271_0001
x
2
2
haploid
05050099_0001
x
3
3
haploid
05050099_0002
x
4
4
haploid
05020961_0001
x
5
5
haploid
05020511_0001
x
6
6
haploid
05020946_0001
x
7
8
haploid
05030147_0001
x
8
9
haploid
05030462_0001
x
9
10
haploid
05020420_0002
x
10
11
haploid
05020361_0001
x
11
12
haploid
05030060_0001
x
12
13
haploid
05020558_0001
x
13
14
haploid
05020631_0001
x
14
15
haploid
05040748_0003
x
15
16
haploid
05030308_0001
x
16
18
haploid
05080318_0003
x
17
19
haploid
06020186_0001
x
18
20
haploid
05110212_0001
x
19
21
haploid
05120555_0001
x
20
22
haploid
06011022_0001
x
21
23
haploid
05020059_0001
x
22
24
haploid
06020320_0004
x
23
25
haploid
06020571_0004
x
24
26
haploid
06020381_0001
x
25
27
haploid
05060119_0001
x
26
28
haploid
05090172_0001
x
27
30
haploid
05100321_0001
x
28
31
haploid
06010670_0006
x
29
32
haploid
06010842_0004
x
30
33
haploid
05050228_0001
x
31
34
haploid
05110260_0001
x
32
35
haploid
05110260_0002
x
33
36
haploid
05110162_0001
x
34
37
haploid
05101030_0001
x
35
38
haploid
05040273_0001
x
36
39
haploid
05110003_0001
x
37
40
haploid
05120002_0001
x
38
41
haploid
05080095_0001
x
39
43
haploid
06110122_0002
x
40
44
haploid
05110716_0001
x
41
45
haploid
05010836_0001
x
42
46
haploid
05120155_0001
x
43
47
haploid
05110875_0001
x
44
48
haploid
05070553_0001
x
45
49
haploid
05070466_0001
x
46
50
haploid
06010650_0001
x codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 17 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
nalysis (Continued)
47
51
haploid
05110718_0001
x
48
52
haploid
05110496_0001
x
49
53
haploid
06010107_0001
x
50
54
haploid
05120429_0002
x
51
55
haploid
06010953_0001
x
52
56
haploid
05030686_0001
x
53
57
haploid
05060107_0001
x
54
58
haploid
05030791_0001
x
55
59
haploid
05080585_0001
x
56
60
haploid
05020375_0001
x
57
61
haploid
05121048_0001
x
58
62
haploid
05055090_0001
x
59
63
haploid
05121004_0002
x
60
64
haploid
06030064_0001
x
61
65
haploid
05121061_0004
x
62
66
haploid
05060276_0001
x
63
67
haploid
05100988_0001
x
64
68
haploid
05060315_0001
x
65
69
haploid
06030324_0003
x
66
70
haploid
05080506_0001
x
67
71
haploid
06010813_0001
x
68
72
haploid
05110881_0001
x
69
73
haploid
05100717_0001
x
70
74
haploid
06020169_0009
x
71
75
haploid
05110134_0001
x
72
76
haploid
05030196_0001
x
73
77
haploid
05050220_0001
x
74
78
haploid
06011195_0001
x
75
79
haploid
05120725_0001
x
76
80
haploid
05100510_0001
x
77
81
haploid
05060624_0001
x
78
82
haploid
05060712_0001
x
79
83
haploid
05030150_0001
x
80
84
haploid
06030180_0001
x
81
85
haploid
06020915_0001
x
82
86
haploid
05101150_0003
x
83
87
haploid
05101152_0001
x
84
88
haploid
05020415_0001
x
85
89
haploid
05040029_0002
x
86
90
haploid
05040035_0003
x
87
91
haploid
06020573_0001
x
88
93
haploid
05121112_0008
x
89
94
haploid
05090078_0001
x
90
95
haploid
05060495_0001
x
91
96
haploid
05070484_0001
x
92
97
haploid
06020455_0001
x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 18 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
93
98
haploid
05075185_0001
x
94
99
haploid
05090522_0004
x
95
100
haploid
06020625_0002
x
96
101
haploid
05100812_0002
x
97
102
haploid
05100862_0001
x
98
103
haploid
05030224_0002
x
99
104
haploid
05040439_0001
x
100
105
haploid
05040317_0003
x
101
106
haploid
05080030_0001
x
102
107
haploid
05070703_0003
x
103
108
haploid
05080485_0001
x
104
109
haploid
05110470_0002
x
105
110
haploid
05100423_0001
x
106
111
haploid
05110423_0001
x
107
112
haploid
05080362_0003
x
108
113
haploid
05110625_0001
x
109
114
haploid
05120719_0001
x
110
115
haploid
05121073_0002
x
111
116
haploid
06050726_0002
x
112
117
haploid
06060063_0001
x
113
119
haploid
06121220_0001
x
114
120
haploid
06080516_0001
x
115
121
haploid
06090505_0002
x
116
122
haploid
06090407_0004
x
117
123
haploid
06051133_0002
x
118
124
haploid
06060740_0031
x
119
125
haploid
06060740_0077
x
120
126
haploid
06060740_0090
x
121
127
haploid
06120178_0001
x
122
128
haploid
06090960_0003
x
123
129
haploid
06090657_0001
x
124
130
haploid
06120377_0001
x
125
131
haploid
06070208_0001
x
126
132
haploid
07010308_0001
x
127
133
haploid
06121125_0001
x
128
134
haploid
06121125_0002 A
x
129
135
haploid
06121125_0002 B
x
130
136
haploid
06019052_0005
x
131
137
haploid
06129197_0001
x
132
138
haploid
06079077_0001
x
133
139
haploid
07019130_0003
x
134
140
haploid
06075474_0001
x
135
141
haploid
06075474_0003
x
136
142
haploid
06075544_0001
x
137
143
haploid
06045801_0001
x
138
144
haploid
06065285_0001
x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 19 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
139
145
haploid
06081027_0001
x
140
146
haploid
06090264_0001
x
141
147
haploid
06090264_0002
x
142
148
haploid
06070430_0001
x
143
149
haploid
06090861_0001
x
144
150
haploid
06051245_0001
x
145
151
haploid
06070716_0001
x
146
152
haploid
06051468_0001
x
147
153
haploid
06075617_0001
x
148
154
haploid
06040273_0001
x
149
155
haploid
06080584_0001
x
150
156
haploid
06070825_0001
x
151
158
haploid
06110390_0015
x
152
159
haploid
06031385_0001
x
153
160
haploid
06045657_0001
x
154
161
haploid
06110204_0008
x
155
162
haploid
06050161_0001
x
156
163
haploid
06071068_0010
x
157
164
haploid
06100785_0002
x
158
165
haploid
06010987_0028
x
159
166
haploid
07010166_0001
x
160
167
haploid
06100730_0001
x
161
168
haploid
06080681_0001
x
162
169
haploid
06080532_0005
x
163
170
haploid
06040024_0001
x
164
172
haploid
06080217_0010
x
165
173
haploid
06120975_0001
x
166
174
haploid
06070581_0002
x
167
175
haploid
06060477_0001
x
168
176
haploid
06120852_0001
x
169
177
haploid
06091392_0001
x
170
178
haploid
06060344_0001
x
171
179
haploid
06090211_0001
x
172
180
haploid
06100858_0001
x
173
181
haploid
06080272_0007
x
174
182
haploid
06050493_0004
x
175
183
haploid
06101033_0002
x
176
184
haploid
06081043_0001
x
177
185
haploid
07011057_0001
x
178
186
haploid
06070921_0001
x
179
187
haploid
06111210_0002
x
180
188
haploid
06121495_0001
x
181
189
haploid
06110610_0001
x
182
190
haploid
06090772_0001
x
183
191
haploid
06090318_0002
x
184
192
haploid
06121313_0001
x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 20 of 25 Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
185
193
haploid
06085027_0001
x
186
194
haploid
06090109_0001
x
187
195
haploid
06080157_0001
x
188
196
haploid
06121316_0001
x
189
197
haploid
06110900_0001
x
190
198
haploid
06070228_0002
x
191
199
haploid
06101174_0001
x
192
200
haploid
06060805_0001
x
193
201
haploid
06085063_0001
x
194
202
haploid
06101037_0001
x
195
203
haploid
06110444_0002
x
196
204
haploid
06101487_0001
x
197
205
haploid
06100937_0001
x
198
206
haploid
06090820_0002
x
199
207
haploid
06070039_0001
x
200
208
haploid
06070772_0001
x
201
209
haploid
07011408_0001
x
202
210
haploid
07011408_0002
x
203
211
haploid
06100319_0001
x
204
212
haploid
06070468_0001
x
205
213
haploid
06121385_0002
x
206
214
haploid
06100537_0001
x
207
215
haploid
06120726_0001
x
208
216
haploid
06070883_0001
x
209
217
haploid
06040041_0001
x
210
218
haploid
06100263_0001
x
211
219
haploid
06040043_0009
x
212
220
haploid
06101232_0001
x
213
221
haploid
06060189_0003
x
214
222
haploid
06091275_0002
x
215
223
haploid
06060097_0001
x
216
224
haploid
06100873_0001
x
217
225
haploid
06050038_0001
x
218
226
haploid
06100025_0001
x
219
227
haploid
06100940_0002
x
220
228
haploid
06040800_0001
x
221
229
haploid
06071007_0002
x
222
230
haploid
06020043_0026
x
223
231
haploid
06060811_0153
x
224
232
haploid
06080751_0001
x
225
233
haploid
06050178_0068
x
226
234
haploid
06040287_0001
x
227
236
haploid
06101496_0001
x
228
237
haploid
06040643_0001
x
229
238
haploid
06045788_0003
x
230
239
haploid
06050326_0001
x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 21 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
231
240
haploid
06080649_0002
x
232
241
haploid
06080649_0003
x
233
242
haploid
06080601_0001
x
234
243
haploid
06101247_0001
x
235
244
haploid
06111271_0001
x
236
245
haploid
06090337_0001
x
237
246
haploid
06050125_0002
x
238
247
haploid
06050331_0001
x
239
248
haploid
06060728_0002
x
240
249
haploid
06080109_0001
x
241
250
haploid
06101048_0001
x
242
251
haploid
06051077_0001
x
243
253
haploid
06041067_0003
x
244
254
haploid
06040302_0002
x
245
255
haploid
06110121_0001
x
246
256
haploid
06090845_0001
x
247
257
haploid
06060375_0001
x
248
258
haploid
06070494_0001
x
249
259
haploid
06040938_0003
x
250
260
haploid
06081010_0001
x
251
261
haploid
06070415_0003
x
252
263
haploid
07010776_0001
x
253
264
haploid
06120890_0001
x
254
265
haploid
06120316_0001
x
255
266
haploid
06121413_0001
x
256
267
haploid
06090247_0001
x
257
268
haploid
06090247_0002
x
258
269
haploid
06090801_0001
x
259
270
haploid
06041160_0002
x
260
271
haploid
06031248_0001
x
261
272
haploid
07010075_0001
x
262
273
haploid
07011039_0001
x
263
274
haploid
06041232_0001
x
264
275
haploid
06101271_0002
x
265
276
haploid
06060506_0001
x
266
277
haploid
06080566_0001
x
267
278
haploid
06060124_0001
x
268
279
haploid
07020168_0001
x
269
281
haploid
06090909_0002
x
270
282
haploid
06080869_0001
x
271
1
commercial pisifera
BL605/39-04
2x
272
2
commercial pisifera
BL607/91-10
2x
273
3
commercial pisifera
BL612/84-05
2x
274
4
commercial pisifera
BL1120/75-07
2x
275
5
commercial pisifera
BL143/04-10
2x
276
6
commercial pisifera
BL147/21-05
2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 22 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
277
7
commercial pisifera
BL148/05-08
2x
278
8
commercial pisifera
BL158/A2-13
2x
279
1
commercial tenera
BL10452/207-02
2x
280
2
commercial tenera
BL10323/104-06
2x
281
3
commercial tenera
BL1177/184-09
2x
282
1
commercial dura
BL10887/08-22
2x
283
2
commercial dura
BL10885/08-27
2x
284
3
commercial dura
BL1221/51-14
2x
285
4
commercial dura
BL1222/32-02
2x
286
5
commercial dura
BL1224/14-19
2x
287
6
commercial dura
BL1231/02-01
2x
288
7
commercial dura
BL1235/14-01
2x
289
8
commercial dura
BL1125/03-02
2x
290
9
commercial dura
BL1124/17-09
2x
291
10
commercial dura
BL1136/01-02
2x
292
11
commercial dura
BL10868/12-10
2x
293
12
commercial dura
BL10868/12-11
2x
294
13
commercial dura
BL10868/12-13
2x
295
14
commercial dura
BL10879/08-06
2x
296
15
commercial dura
BL10879/08-07
2x
297
16
commercial dura
BL10879/08-09
2x
298
17
commercial dura
BL10883/04-06
2x
299
18
commercial dura
BL10883/04-08
2x
300
19
commercial dura
BL10883/04-09
2x
301
20
commercial dura
BL10883/05-06
2x
302
21
commercial dura
BL10891/04-23
2x
303
22
commercial dura
BL10891/04-24
2x
304
23
commercial dura
BL10891/05-22
2x
305
24
commercial dura
BL10891/05-23
2x
306
25
commercial dura
BL10873/52-18
2x
307
26
commercial dura
BL10873/52-19
2x
308
27
commercial dura
BL10873/52-21
2x
309
28
commercial dura
BL10873/53-19
2x
310
29
commercial dura
BL1229/48-15
2x
311
30
commercial dura
BL1230/42-15
2x
312
31
commercial dura
A1122/04-01
2x
313
32
commercial dura
A1122/12-05
2x
314
33
commercial dura
A1122/12-08
2x
315
34
commercial dura
A1122/36-02
2x
316
35
commercial dura
A1123/01-02
2x
317
36
commercial dura
A1123/01-06
2x
318
37
commercial dura
A1123/01-07
2x
319
38
commercial dura
A1123/01-12
2x
320
39
commercial dura
A1130/02-02
2x
321
40
commercial dura
A1130/02-06
2x
322
41
commercial dura
A1130/02-10
2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 23 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued)
323
42
commercial dura
A1130/02-16
2x
324
43
commercial dura
A1127/08-16
2x
325
44
commercial dura
A1127/08-06
2x
326
45
commercial dura
A1127/05-11
2x
327
46
commercial dura
A1127/05-03
2x
328
47
commercial dura
B1134/35-09
2x
329
48
commercial dura
B1133/07-10
2x
330
49
commercial dura
B1136/21-11
2x
331
50
commercial dura
B1136/21-12
2x
332
51
commercial dura
C1128/07-14
2x
333
52
commercial dura
C1121/13-08
2x
334
53
commercial dura
BL11508/111-1
2x
335
54
commercial dura
BL11396/11-21
2x
336
1
Ghana wild
K31-1/GHANA/1-1
2x
337
2
Ghana wild
K31-1/GHANA/41-498
2x
338
3
Ghana wild
K31-1/GHANA/39-875
2x
339
4
Ghana wild
K31-1/GHANA/31-430
2x
340
5
Ghana wild
K31-1/GHANA/26-629
2x
341
6
Ghana wild
K31-1/GHANA/24-1164
2x
342
7
Ghana wild
K31-1/GHANA/56-1185
2x
343
8
Ghana wild
K31-1/GHANA/29-1087
2x
344
9
Ghana wild
K31-1/GHANA/38-1193
2x
345
10
Ghana wild
K31-1/GHANA/43-994
2x
346
11
Ghana wild
K31-1/GHANA/8-1100
2x
347
12
Ghana wild
K31-1/GHANA/11-1192
2x
348
13
Ghana wild
K31-1/GHANA/35-1190
2x
349
14
Ghana wild
K31-1/GHANA/3-46
2x
350
15
Ghana wild
K31-1/GHANA/5-102
2x
351
16
Ghana wild
K31-1/GHANA/7-121
2x
352
17
Ghana wild
K31-1/GHANA/12-239
2x
353
18
Ghana wild
K31-1/GHANA/14-350
2x
354
19
Ghana wild
K31-1/GHANA/18-368
2x
355
20
Ghana wild
K31-1/GHANA/19-245
2x
356
21
Ghana wild
K31-1/GHANA/21-1180
2x
357
22
Ghana wild
K31-1/GHANA/32-1141
2x
358
23
Ghana wild
K31-1/GHANA/37-1124
2x
359
24
Ghana wild
K31-1/GHANA/45-448
2x
360
25
Ghana wild
K31-1/GHANA/47-1175
2x
361
26
Ghana wild
K31-1/GHANA/50-1037
2x
362
27
Ghana wild
K31-1/GHANA/52-547
2x
363
28
Ghana wild
K31-1/GHANA/53-1167
2x
364
29
Ghana wild
K31-1/GHANA/54-1196
2x
365
30
Ghana wild
K31-1/GHANA/57-1153
2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates
Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the
Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Page 24 of 25 Table 7 Primer pairs used in the Principal Coordinates Analysis to compare the genetic diversity and affinities of Hs
compared with a representative sample of commercial and wild diploid palms (listed in Table 6)
No Primer
Forward (5’-3’)
Reverse (5’-3’)
1
1996
CACTGGGGTCATCTTCATCT
TCGTTCTCTTTCCTTTTGTC
2
2215
GAACTTGGCGTGTAACT
TGGTAGGTCTATTTGAGAGT
3
2427
GAAGGGGCATTGGATTT
CAGGTGACCAAGTGTAAT
4
2569
TAGCCGCACTCCCACGAAGC
CCAGAATCATCAGACTCGGACAG
5
2595
TCAAAGAGCCGCACAACAAG
ACTTTGCTGCTTGGTGACTTA
6
2600
GGGGATGAGTTTGTTTGTTC
GGCAACATGAAGGTAAG
7
3282
GTAACAGCATCCACACTAAC
GCAGGACAGGAGTAATGAGT
8
3298
GACTACCGTATTGCGTTCAG
TTTATCAGGAGTTTTTGTTTGAGAG
9
3311
AATCCAAGTGGCCTACAG
TCCCTACAATAGCCATCTC
10
3321
CAAGGAGGAGCAGGTGAG
TACGGCCTCGGTTCTACAC
11
3399
AGCCAATGAAGGATAAAGG
CCACTTAGAGGTAAAACAACAG
12
3400
CAATTCCAGCGTFAFTATAG
AGTGGCAGTGGAAAAACAGT
13
3433
GGTTCAATGGCATACAT
ACTCCCCTCTTTGACAT
14
3538
TCAAGCCACATCCTAACTAC
CTCATAGCCTTTGTTGTGT
15
3544
AGCAGGGCAAGAGCAATACT
TTCAGCAGCAGGAAACATC
16
3546
GCCTATCCCCTGAACTATCT
TGCACATACCAGCAACAGAG
17
3574
AGAGACCCTATTTGCTTGAT
GACAAAGAGCTTGTCACAC
18
3711
GTCTCATGTGGCTACCTCTC
GCTAGGTGAAAAATAAAGTT
19
3819
CCTCCTTTGGAATTATG
GTGTTTGATGGGACATACA
20
219
TTTGCTCGGCGGATACAT
GGAGGGCAGGAACAAAAAGT
21
257
GCAGCTAGTCACCTGAAC
GACGAGACTGGAAAGATG
22
782
CGTTCATCCCACCACCTTTC
GCTGCGAGGCCACTGATAC
23
783
GAATGTGGCTGTAAATGCTGAGTG
AAGCCGCATGGACAACTCTAGTAA
24
882
TTGATCTTAGACATAACATACTGTA
AAAGCGCGTAATCTCATAGT
25
894
TGCTTCTTGTCCTTGATACA
CCACGTCTACGAAATGATAA
26
3213
GCTCTTTGTATTTCCTGGTTC
AGCAGCAAACCCTACTAACT
27
3691
GCATCATTGGACTATCATACC
TTGTGAACCAGGGAACTATC
28
vs1
GAGATTACAAAGTCCAAACC
TCAAAATTAAGAAAGTATGC
All primers except VS1 were taken from Billotte et al. [27]. Table 7 Primer pairs used in the Principal Coordinates Analysis to compare the genetic diversity
compared with a representative sample of commercial and wild diploid palms (listed in Table 6) All primers except VS1 were taken from Billotte et al. [27]. [31] using distance matrix with standardization (by
dividing the distance inputs by the square root of n-1). Here, Hs were treated as the DHs they were assumed
to generate; thus genotypes were homozygous not
hemizygous. weekly intervals. The resultant pollen (0.03 g) was
applied to a targeted section of the female inflorescence
of a diploid dura palm. The inflorescence was then
bagged to prevent inadvertent wind pollination. In addition, some untreated H plants contained up to
30% fully stained pollen using Fluorescein diacetate
(FDA) that was presumed to be viable. Pollen from
these plants and from palms with apparently inviable
pollen (unstained) was applied to targeted sections of a
female inflorescence of diploid dura palms in the same
way as above. Colchicine treatment Roots of confirmed haploid seedlings were washed and
immersed in 2.5, 5.0, 7.5, or 10 mM aqueous colchicine
for 5 h. Seedlings were then rinsed with water and
planted (2:1:1 v/v compost, sand and soil). g
This work was funded by Sumatra Bioscience as part of their R&D
programme in oil palm. The authors are grateful for the assistance of all staff
of the Breeding Department and Seed Production Unit at Bah Lias Research
Station, Indonesia. Author details
1 20. Germana MA: Haploids and doubled haploids in fruit trees. In Advances in
Haploid Production in Higher Plants. Edited by: Touraev A, Forster BP, Jain
SM. The Netherlands: Springer-Verlag; 2009:241-263. 1School of Biological Sciences, University of Reading, Whiteknights, Reading,
RG6 6AS, UK. 2Institute of Biological, Environmental and Rural Sciences,
Aberystwyth University, Aberystwyth, SY23 3DA, UK. 3Sumatra Bioscience Pte
Ltd, 8 Eu Tong Sen Street, #16-94/95 The Central, 059818, Singapore. 4PT
Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia. 5BioHybrids International Ltd, Earley, Reading, RG6 5FY, UK. 6Instituto de
Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca,
Chile. 1School of Biological Sciences, University of Reading, Whiteknights, Reading,
RG6 6AS, UK. 2Institute of Biological, Environmental and Rural Sciences, 21. Lim W, Earle ED: Enhanced recovery of doubled haploid lines from
parthenogenetic plants of melon. Plant Cell Tiss Org 2009, 98:351-356. 22. Finkel E: With ‘phenomics,’ plant scientists hope to shift plant breeding
into overdrive. Science 2009, 325:380-381. 23. Reijnders L, Huijbregts MAJ: Palm oil and the emission of carbon-based
greenhouse gases. J Clean Product 2008, 16:477-482. 24. Parveez GKA: Biolistic mediated production of transgenic oil palm. Method Mol Biol 2009, 477:301-320. Received: 2 June 2010 Accepted: 7 October 2010
Published: 7 October 2010 29. Arumuganathan K, Earle ED: Estimation of nuclear DNA content of plants
by flow cytometry. Plant Mol Biol Rep 1991, 9:221-231. Acknowledgements
h
k
f
d d A developing male inflorescence of a confirmed H at the
PMC stage was treated with 2.5 mM colchicine via
injection into the spathe. This treatment was repeated at This work was funded by Sumatra Bioscience as part of their R&D
programme in oil palm. The authors are grateful for the assistance of all staff
of the Breeding Department and Seed Production Unit at Bah Lias Research
Station, Indonesia. Page 25 of 25 Page 25 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218
http://www.biomedcentral.com/1471-2229/10/218 Authors’ contributions JMD, PDSC, SN and MJW conceived the project. SN, BPF and ACS supervised
the phenotypic screen and flow cytometry. MJW supervised the molecular
analysis conducted by SW, AEC, CSF and YA, and the cytology conducted by
DM. JMD and MJW wrote the manuscript and all authors discussed the
results and commented on the manuscript. 25. Persson UM, Azar C: Preserving the world’s tropical forests - a price on
carbon may not do. Environ Sci Technol 2010, 44:210-215. JMD, PDSC, SN and MJW conceived the project. SN, BPF and ACS supervised
the phenotypic screen and flow cytometry. MJW supervised the molecular
analysis conducted by SW, AEC, CSF and YA, and the cytology conducted by 26. Croxford AE, Rogers T, Caligari PDS, Wilkinson MJ: High-resolution melt
analysis to identify and map sequence-tagged site anchor points onto
linkage maps: a white lupin (Lupinus albus) map as an exemplar. New
Phytol 2008, 180:594-607. y
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Singh R, Herran A, Asmady H, Billot C, Amblard P, Durand-Gasselin T,
Courtois B, Asmono D, Cheah SC, Rohde W, Ritter E, Charrier A:
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Submit your manuscript at
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and take full advantage of:
• Convenient online submission
• Thorough peer review
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• Immediate publication on acceptance
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Submit your manuscript at
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https://openalex.org/W2084351461 | https://europepmc.org/articles/pmc3833032?pdf=render | English | null | Transplantation of Autologous Minced Bladder Mucosa for a One-Step Reconstruction of a Tissue Engineered Bladder Conduit | BioMed research international | 2,013 | cc-by | 6,994 | Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1
Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2 1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet,
Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden
2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden
3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital,
171 76 Stockholm, Sweden 1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet,
Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden
2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden
3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital,
171 76 Stockholm, Sweden orrespondence should be addressed to Magdalena Fossum; magdalena.fossum@ki.se Received 29 April 2013; Revised 12 August 2013; Accepted 18 September 2013 Received 29 April 2013; Revised 12 August 2013; Accepted 18 September 2013 Academic Editor: Esmaiel Jabbari Academic Editor: Esmaiel Jabbari Copyright © 2013 Gisela Reinfeldt Engberg et al. This is an open access article distributed under the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Surgical intervention is sometimes needed to create a conduit from the abdominal wall to the bladder for self-catheterization. We
developed a method for tissue engineering a conduit for bladder emptying without in vitro cell culturing as a one-step procedure. In
a porcine animal model bladder, wall tissue was excised and the mucosa was minced to small particles. The particles were attached to
a tube in a 1 : 3 expansion rate with fibrin glue and transplanted back by attaching the tube to the bladder and through the abdominal
wall. Sham served as controls. After 4-5 weeks, conduits were assessed in respect to macroscopic and microscopic appearance in
6 pigs. Two pigs underwent radiology before termination. Gross examination revealed a patent conduit with an opening to the
bladder. Histology and immunostaining showed a multilayered transitional uroepithelium in all cases. Up to 89% of the luminal
surface area was neoepithelialized but with a loose attachment to the submucosa. No epithelium was found in control animals. CT imaging revealed a patent channel that could be used for filling and emptying the bladder. Animals that experienced surgical
complications did not form conduits. Hindawi Publishing Corporation
BioMed Research International
Volume 2013, Article ID 212734, 10 pages
http://dx.doi.org/10.1155/2013/212734 Hindawi Publishing Corporation
BioMed Research International
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http://dx.doi.org/10.1155/2013/212734 Hindawi Publishing Corporation
BioMed Research International
Volume 2013, Article ID 212734, 10 pages
http://dx.doi.org/10.1155/2013/212734 Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1
Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2 Minced autologous bladder mucosa can be transplanted around a tubular mold to create a
conduit to the urinary bladder without in vitro culturing. Research Article
Transplantation of Autologous Minced Bladder
Mucosa for a One-Step Reconstruction of a Tissue Engineered
Bladder Conduit Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1
Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2
1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet,
Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden
2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden
3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital,
171 76 Stockholm, Sweden 2. Materials and Methods Eleven 15–25 kg (11-12 weeks old) female Yorkshire-Swedish
Country Pigs (Vallrum, Sala, Sweden) were initially used in
this study. The protocol was pre-approved by the Stockholm
County Committee on Animals and all procedures con-
formed to the regulations for animal use, as well as relevant
federal statutes.h 2.2. Mincing the Bladder Mucosa and the Preparation of Tubes. The excised bladder wall was washed in Dulbecco’s modified
Eagle medium (Sigma-Aldrich, Steinheim, Germany) twice,
and the detrusor muscle was removed mechanically with
curved scissors for dissection (Figures 1(e) and 1(f)). The
mucosal tissue was stretched on a cutting board and thickness
was measured with a caliper to approximately 0,2 mm and
appropriate amount of bladder mucosa was removed. As
we aimed for a 3-fold expansion rate for regeneration of a
confluent mucosa in vivo, we estimated the area of the inner
surface of the conduit by calculating the outer surface of
the tubular mold (18 Fr) (Figure 2(b)). Five cm2 was therefore
separated for use in the study (remaining bladder tissue was
used for other studies). Immediately prior to transplantation,
the graft was minced with a mincing device that has been
developed for this purpose [12, 13] (Figure 2(a)). Briefly, the
device cuts with 30 rotating cutting disks placed with 0.8 mm
distance from each other. By running the device twice over
the tissue in perpendicular directions, small square particles
measuring approximately 0.2 × 0.8 × 0.8 mm in size were
formed (Figure 1(g)). The pigs were stalled in pairs in every box except for a few
hours postoperatively when they were kept single until they
regained full normal activity. They had full supply of fresh
water and were fed according to standard protocols at the
animal institution where they were stalled. Heat lamps were
used and the ground was covered with straw for rooting and
toys for enrichment. Protocols were held to ensure normal urination pre-
and postoperatively. Dressings and wounds were checked
at least twice daily postoperatively to ensure early action if
signs of infection, hernias, or other unpredictable events. Animals were euthanized at study endpoint up to 5 weeks
posttransplantation. 2.1. Surgical Procedures. After a 12-hour fasting, an intra-
muscular injection of azaperone 2 mg/kg (Stresnil, Janssen-
Cilag, Pharma, Austria) was administered as premedica-
tion. 1. Introduction and it can serve as a conduit for catheterization of the
bladder [3, 4]. Drawbacks with using intestinal tissue for
reconstructive urology include the need for laparotomy and
high risk of mucus and stone formations as well as infections
[5]. If the use of appendix is contraindicated, removal of distal
small intestine can lead to secondary malabsorption of bile
acids that induce diarrhea and malabsorption of liposoluble
vitamins leading to malnutrition [6, 7]. Autologous tissue from the urinary system for tissue engi-
neering would be an appealing approach for tissue recon-
struction in pediatric urology. Conditions with lack of
bladder tissue as well as low compliance and high pressure
bladders, often need surgical intervention with an abdominal
conduit for self-catheterization and/or a bladder augmenting
approach, to reduce the risk of secondary renal failure.t For tissue engineering, the algorithm for clinical studies
in the urinary pathway and for skin replacements has so far
mostly included in vitro cell culturing for tissue expansion
[8–11]. This procedure is however time consuming, demands
high standard laboratory facilities, and is associated with high
costs and will demand highly specialized centers. To date, reconstructions in the urinary pathway often use
autologous intestinal tissue. Primarily, the appendix is used
for self-catheterization of the bladder [1]. If nonexisting, or
if the appendix is preferred for the creation of a stoma for
antegrade enemas [2], the small intestine can be reconfigured 2 BioMed Research International 2 applications of chlorhexidine (Klorhexidin 5%, Fresenius
Kabi, Sweden). The urinary bladder was catheterized using a
10-French silicone catheter, emptied and then filled with ster-
ile saline solution (approximately 8 mL/kg of body weight). After exposure of the bladder by midline incision below the
umbilicus, a lenticular area of the bladder dome measuring
12 cm longitudinally and 9 cm transversally (approximately a
forth of the total bladder surface area) was marked, removed,
and partly used in this study (Figures 1(c) and 1(d)). In previous studies, we transplanted small particles of
skin or urothelium by attaching the minced tissue to three-
dimensional tubular molds into the subcutaneous tissue in
pigs [12, 13]. 1. Introduction After withdrawing the mold, a continuous
epithelium in the luminal surface of subcutaneous tunnels
was formed already after 2 weeks.h t
The objective of the present study was to reconstruct such
a three-dimensional conduit through the abdominal wall into
the bladder in a large animal experimental model in order to
catheterize the bladder through the canal. For postoperative analgesia, buprenorphine 45 micro-
grams/kg (Temgesic, RB Pharmaceuticals, Great Britain) was
administered by intramuscular injections in single doses. For
infection prophylaxis, an intra-operative dose of trimetoprim
4 mg/kg and sulfonamide 20 mg/kg (Tribrissen vet, Intervet,
Sweden) was administered by intramuscular injection and
followed by injections twice daily for three days and then once
daily for 5 days (total of 9 days). 2. Materials and Methods A combination of tiletamine hypochloride 2,5 mg/kg,
zolazepam hypochloride 2,5 mg/kg (Zoletil, Virbac, France),
and medetomidine 25 micrograms/kg (Domitor, Orion
Pharma, Sweden) was then administered for induction
of anesthesia together with atropine 25 micrograms/kg
(Atropin, Mylan Inc, Canonsburg, PA) as intramuscular
injections. Analgesic treatment was initiated peroperatively
by administrating buprenorphine 45 micrograms/kg (Tem-
gesic, RB Pharmaceuticals, Great Britain), carprofen 3 mg/kg
(Rimadyl, Orion Pharma, Sweden) intravenously and by
local injection of lidocaine (Xylocaine, AstraZeneca, Sweden)
before skin incisions. 18 Fr latex catheters covered with a silicone elastomer
(Bard Foley Catheter, C.A. Bard Inc, Covington, GA) were
cut into 10 cm long tubes. Each end was closed with a 3-
cm long segment of 16 Fr latex catheters sutured with 4-
0 nylon (Ethilon, Ethicon, Johnson & Johnson, Sweden) at
right angles (stopping end) in order to secure the tubes
into the bladder and to lower the risk of movement in the
subcutaneous tissue (Figures 1(a) and 1(b)). To minimize
the risk of infection during take of the transplants, the
conduit was blocked until sedation for radiology studies and
termination. Phenobarbiturate 15 mg/kg (Pentobarbital, APL, Sweden)
was given prior endotracheal intubation and general anes-
thesia was maintained with 0, 8–2% isoflurane (Isoflurane,
Baxter, Deerfield, IL). Glucose 25 mg/mL (Baxter, Deerfield,
IL) was administered intravenously and body temperature,
saturation, blood pressure, and pulse were monitored during
the whole procedure. 2.3. Transplantation. The 8 cm long outer surface (14.5 cm2)
of the tube was covered with two thin layers of the sealer pro-
tein concentrate (fibrinogen) from a two-component tissue
sealant (Tisseel VH, Baxter, Westlake village, CA). Immedi-
ately after the second application, the thrombin component
was added and particles of minced bladder mucosa were
applied evenly and randomly orientated. Two pigs underwent With the pig turned to a supine position, the abdominal
skin was cleaned with chlorhexidine gluconate (Hibiscrub
40 mg/mL, Regent Medical, England) and with successive 3 3 BioMed Research International ed Research International
(a)
(b)
(c)
(d)
(e)
(f)
(g)
∗
(h)
e 1: (a) Cartoon demonstrating a cross-section of the pig urinary bladder and abdominal wall with a tube place
inary bladder, through the abdominal muscle wall and to the cutaneous tissue. (b) Tube used for transplant
sa showing stopping ends used to hold the tube still. (c) The pig urinary bladder exposed through the surgica
er wall being removed. 2. Materials and Methods (b) Formula for calculating area of implanted mold and expected inner area of conduit. (c) Cross-section of conduit on slide with
marking of inner surface with epithelial lining. No magnification. (a) L = 80mm
D = 7mm
D × 𝜋× L = area
(b) (b) (a) (c) (c) Figure 2: (a) Side view of mincing device and insert demonstrating frontal aspect of central part of device with 30 parallel rotating cutting
discs. (b) Formula for calculating area of implanted mold and expected inner area of conduit. (c) Cross-section of conduit on slide with
marking of inner surface with epithelial lining. No magnification. For radiological assessment of the conduit, reconstruc-
tion algorithm called Xper-CT, where the flat detector C-arm
can perform volume acquisitions through back projection
computed tomography (CT) reconstructions with a 0.5 mm
slice thickness, was used [14]. Image stacks were then trans-
ferred to a working station, postprocessed and analyzed in
Osirix v 4.1.1 software (Open Source, OsiriX Foundation,
Geneva, Switzerland). 3D surface rendering was used for
gross anatomical illustration after examining CT stacks in
axial, frontal, and sagittal planes. To illustrate the entire
tract including the intact conduit, 3D curved multiplanar
reconstructions (MPR) were performed as illustrated in the
figure (Figure 3(d)). Animals were euthanized after radiolog-
ical assessments. Johnson, Sweden) (Figures 1(a) and 1(h)). Thereafter, the wall
of the urinary bladder and the abdomen were repaired. The
subcutaneous tissue was closed in two layers with absorbable
braided sutures (Polysorb, Tyco Healthcare, Mansfield, MA)
and the skin with interrupted 3-0 nylon sutures (Ethilon,
Ethicon, Johnson & Johnson, Sweden). 2.4. Catheterization and Radiological Assessment of 3D Con-
duit. At 4 and 5 weeks after transplantation, two pigs (one
each week) were sedated with sodium pentothal (Pentobarbi-
talnatrium vet. 60 mg/mL, APL, Sweden) and fentanyl (Fen-
tanyl vet. 50 𝜇g/mL, Braun, Germany) and placed in scanning
equipment for angiography (XD20, Philips Medical System,
Netherlands). In order to analyze the conduit for filling,
emptying, and radiology, the transversal end of the tube, lying
in the subcutaneous fat, was localized, skin was incised, and
the end was cut off with scissors (Figures 1(a), 1(b), and 1(h)). The remaining tube was pushed into the bladder and the
conduit was assessed from the newly created opening in the
skin. An 8 Fr tube could be inserted through the conduit for
filling and emptying the bladder. 2. Materials and Methods The detrusor muscle has been marked for easy identification and for measuring of tissu
ation of bladder mucosa from the detrusor. (f) Bladder mucosa mounted to the left and separated detrusor
les of bladder mucosa. (h) Tube with minced particles being placed in the surgical wound. In the top one, the
tive bladder (upper arrow). Middle part of tube is resting on the abdominal muscle (asterix) and in the outer e
r arrow). (a) (b) (a) (b) (d) (c) (d) (c) (e) (f) (f) (e) (g) ∗
(h) (g) (h) Figure 1: (a) Cartoon demonstrating a cross-section of the pig urinary bladder and abdominal wall with a tube placed to form a conduit from
the urinary bladder, through the abdominal muscle wall and to the cutaneous tissue. (b) Tube used for transplantation of minced bladder
mucosa showing stopping ends used to hold the tube still. (c) The pig urinary bladder exposed through the surgical wound. (d) Part of the
bladder wall being removed. The detrusor muscle has been marked for easy identification and for measuring of tissue biopsy. (e) Mechanical
separation of bladder mucosa from the detrusor. (f) Bladder mucosa mounted to the left and separated detrusor to the right. (g) Minced
particles of bladder mucosa. (h) Tube with minced particles being placed in the surgical wound. In the top one, the end is coming out from
the native bladder (upper arrow). Middle part of tube is resting on the abdominal muscle (asterix) and in the outer end placed under the skin
(lower arrow). sham procedure with same size excision of bladder tissue and
thereafter implantation of the same type of tubing covered
with fibrin glue but without minced particles. inside). The tube was placed tangential through the abdom-
inal wall, thus penetrating the abdominal rectus muscle and
the oblique muscles before placement of the other end in the
subcutaneous tissue, immediately under the skin, and sutured
with 4-0 nylon to stay in place (Ethilon, Ethicon, Johnson & i
Each tube was placed in the bladder with a purse string
suture around the end of the tube (3 cm right angle part 4 BioMed Research International (a)
L = 80mm
D = 7mm
D × 𝜋× L = area
(b)
(c)
Figure 2: (a) Side view of mincing device and insert demonstrating frontal aspect of central part of device with 30 parallel rotating cutting
discs. 3. Results the basal lamina, connective tissue, and mucus, according to
standard protocols.h All pigs tolerated the excision and removal of bladder tissue
(approximately 1/4 of bladder) and voided shortly after
surgery and none developed postoperative fever or signs
of strain or pain when voiding. The first four animals
were affected by midline hernia. Two had to be euthanized
due to incarceration of the small intestine 2 and 4 days
postoperatively. The surgical technique was changed for the
next animals so that bladder conduit was placed from the
side of the dome, to the left of the midline, through the rectus
muscles, and not through the midline incision. One pig was
euthanized the second day postoperatively due to signs of
pain. Autopsy showed a perforated ulceration of the ventricle. The two surviving animals with midline hernia ful filled the
study protocol and were euthanized four weeks after trans-
plantation. In these subjects, the midline hernia including
small intestines was encountered by the tube, no conduit
had been formed and no epithelium could be detected in
the surrounding tissue on histological examination. By these
means, a total of five animals were excluded due to surgical
complications. The tissue specimens were evaluated by immunostaining
with primary antibodies against various cytokeratins (1 : 300)
(pancytokeratins 1–7, 10, 13–16 and 19, DakoCytomation, Cat#
M0821, clone: MNF 116, Denmark) and uroplakin III (1 : 400)
(Fitzgerald Industries, Clone AU1, CatRDI-PRO610108, Con-
cord, MA). Biotinylated secondary antibodies were detected
by using ABC-HRP kit (Vectastain Elite ABC kit, Vector
Labs, UK) and all sections were developed employing 3,3-
diaminobenzidine (DAB) (Sigma Chemical Co., St. Louis,
MO) substrate according to standard routine and manufac-
turer instructions. Mayer’s hematoxylin solution was used for
counter staining. 2.6. Measurements of Neo-Epithelialization. Mean, standard
deviation, and full range were used to evaluate planimetric
data from tissue sections. All measurements were performed
under 100x magnification in a light microscope (Axioscope 2
MOT Zeiss microscope) using a built in ruler. We calculated
the mean epithelialized area of 5 serial sections for each
biopsy specimen at four different levels of each conduit;
at the junction to the bladder (0 cm), 3 (in the abdominal
muscle), 5 (between muscle and subcutaneous fat), and 8 cm
(in the subcutaneous fat) from the junction. The percentage
was calculated for each level by linear measurement of the
epithelium in relation to the total inner luminal surface
(18 Fr) (Figures 2(b)-2(c)). 2. Materials and Methods Intravenous contrast agent,
iohexol (Omnipaque 240 mg/mL, GE Healthcare, Sweden)
and diuretics furosemide (Furix 10 mg/mL, Takeda Pharma,
Sweden) were given in order to visualize the urinary excretory
pathway including the kidneys, ureters, the urinary bladder,
and the conduit. 2.5. Histological Examination. At 4 (6 animals) and 5 (2
animals) weeks posttransplantation, a lethal dose of sodium
thiopental (Sodium Pentothal, Abbott Laboratories, North
Chicago, IL) was administrated for termination. Tissue spec-
imens including the whole conduit, from the subcutaneous
tissue to the bladder were excised and fixed in 10% formalin
solution prior to dehydration, embedding in paraffin and
slicing into 5 𝜇m-thick sections. Slides were stained with
haematoxylin-eosin (H&E) for routine histology, van Gieson
for evaluation of collagen and other connective tissue, and
periodic acid shift (PAS) for staining of carbohydrates in BioMed Research International 5 (a) (a)
(b)
(c)
(d)
(e)
(E)
(F)
(G)
(f)
(g)
Figure 3: In order to visualize the anatomical properties of the conduit an XD20 imaging system was used. (a) 3D reconstruction showing the
gross anatomical conditions. (b) The concomitant side projection. (c) A 0.5 mm thick CT reconstructed slice is shown. In order to illustrate
the conduits passage to the bladder, a MultiPlanar (MP) reconstruction was performed through the CT stack illustrated in (d). Arrows in (d)
indicate orthogonal projections along the MP reconstruction. In (e), (f), and (g) showing orthogonal projections along the MP reconstruction
illustrating functioning ureters filling the bladder and intact conduit. (d)
(e)
(E)
(F)
(G)
(f)
(g) (d)
(E)
(F)
(G) (e) (b) (a) (e) (f) (b) (c) (f) (g) (d) (a) (c) (g) Figure 3: In order to visualize the anatomical properties of the conduit an XD20 imaging system was used. (a) 3D reconstruction showing the
gross anatomical conditions. (b) The concomitant side projection. (c) A 0.5 mm thick CT reconstructed slice is shown. In order to illustrate
the conduits passage to the bladder, a MultiPlanar (MP) reconstruction was performed through the CT stack illustrated in (d). Arrows in (d)
indicate orthogonal projections along the MP reconstruction. In (e), (f), and (g) showing orthogonal projections along the MP reconstruction
illustrating functioning ureters filling the bladder and intact conduit. 3. Results Two of the animals were sedated and the 18 French latex
tubes did not adhere to the adjacent tissue and could easily
be pushed into the bladder (not removed through the skin
due to the stopping end). The remaining conduit was easy to
catheterize using 8 Fr catheters and lidocaine anesthetic gel
(2% Xylocaine gel, AstraZeneca, Sweden) for lubrication. Xper-CT reconstructions clearly showed an intact con-
duit with contrast agent passage into the bladder both in the 6 BioMed Research International 6 (a)
(b)
Figure 4: Macroscopic appearance at removal of conduit. (a) Looking from inside the bladder that has been cut open. Inner opening to
conduit is exposed. (b) Macroscopic appearance of transsection of conduit with catheter still in place in the lumen. (a) (b) (a) (b) Figure 4: Macroscopic appearance at removal of conduit. (a) Looking from inside the bladder that has been cut open. Inner opening to
conduit is exposed. (b) Macroscopic appearance of transsection of conduit with catheter still in place in the lumen. bladder. At three and five centimeters from the junction, only
transplanted conduits revealed epithelium (61, 22, 38, and
17%). At five centimeters, only half presented with epithelium
(0, 0, 89, and 44%). From the most lateral part of the conduit,
surrounded by subcutaneous fat, only traces of urothelial
cells could be found in transplanted specimens. Conduit
from control specimens had no epithelial lining in any tissue
sections except at the junction to the bladder (Figures 6(e)–
6(h)). CT stacks reconstructed in three planes and in 3D surface
rendered volumes (Figure 3). To illustrate the entire tract
including the intact conduit 3D curved MPR, reconstructions
were performed as illustrated in the figure (Figure 3(d)). This
reconstruction clearly shows that the conduit is allowing fluid
passage without leakage (Figures 3(a) and 3(b)). The bladder
could be completely emptied by insertion of the catheter (not
shown). Gross examination of the bladder revealed a scar in the
frontal midline with no signs of inflammation. When opening
the bladder, the mucosa had a normal appearance and the
opening into the conduit revealed an orifice placed on the
left side of the bladder dome with a normal mucosal lining
(Figure 4(a)). 4. Discussion In this porcine, large animal study, we have created catheter-
izable conduits by placing autologous urinary tissue around
a three-dimensional mold (a tube) into the urinary bladder. The surgical technique is easy and fast forward and after
removal of the mold, the conduit could be used for filling and
emptying of the bladder. Advantages with the porcine model
include a good-sized bladder for tissue harvesting and good
tolerance for reduction of its size. No complications occurred
in respect to infection. Histological assessments were obtained at 4 (4 samples
including one control) and 5 weeks (2 samples including
one control) after transplantation (Table 1). Routine histology
of full thickness biopsies of the wall of the constructed
conduit demonstrated a continuous epithelium covering the
inner surface of the conduit in all cases except controls
(Figure 5(a)). Morphology revealed a transitional cell epithe-
lium up to 4 or 5 cell layers thick. Submucosal tissue revealed
signs of inflammation with infiltration of mononucleated
cells and less mature extracellular matrix in comparison
to bladder biopsies (Figures 5(b) and 5(c)). PAS reaction
revealed a supporting basal lamina underlying the neoepithe-
lium (Figure 5(d)). We could document a patent conduit by administrating
intravenous contrast and diuretics and performing 3D recon-
structions of computed tomography images [14]. Kidneys
excreted contrast and ureters and bladder were filled and then
emptied through the tissue engineered bladder conduit. The
use of 3D curved MPR was in accordance with CT urography
guidelines used for high-definition visualization of an entire
urinary tract albeit the use of angiographic equipment as
primary imaging modality is not standard [15]. However, the
Xper-CT algorithms give a high enough resolution to clearly
provide an unambiguous image of the continuity of the open
channel.h Immunostaining of cytokeratins and uroplakin showed
that the cells covering the inner lumen were of uroepithelial
origin (Figures 5(e) and 5(f)). Histology at 4 and 5 weeks
after transplantation revealed up to 90% uroepithelial lining
but the area with epithelium varied between samples, and
regenerated mucosa was more loosely adhering than in native
bladder mucosa (Figures 6(a)–6(d)). The two specimens that
were subjected to catheterization before histology revealed
loose epithelium in the lumen. 3. Results Gross appearance of conduit revealed that the
tube used for transplantation was lying loose inside the
conduit and that the wall surrounding had an even inner
tubular shape with a glossy surface under some nonadhering
debris (Figure 4(b)). 4. Discussion All samples (including con-
trols) showed some urothelial cells at the junction to the The rationale for transplanting small parts of minced
tissue for epithelial cells expansion by using the patients
own body as a bioreactor has been discussed in previous
publications [12, 13, 16]. For this study, we used a similar
expansion rate as described before for creating epithelium
around tubular molds (approximately 1 : 3 expansion), how-
ever, under optimal conditions in a full-thickness wound BioMed Research International 7 Table 1: Table summarizing results from the analyses of conduits at different distances from the bladder junction. Animals numbered 1–4 were
transplanted with minced urothelial particles, and animals 1 and 4 underwent radiological assessment before termination. At the junction,
(0 cm) part of the native bladder was included in the biopsy. Biopsies from conduit running through the abdominal muscle (3 cm) reveal
a median urothelial lining of 6 mm, SD 2.5 mm (33 ± 13%). Biopsy at the boarder between abdominal muscle and subcutaneous fat (5 cm)
demonstrates a median urothelial lining of 6 mm, SD 6 mm (33 ± 33%). Table 1: Table summarizing results from the analyses of conduits at different distances from the bladder junction. Animals numbered 1–4 were
transplanted with minced urothelial particles, and animals 1 and 4 underwent radiological assessment before termination. At the junction,
(0 cm) part of the native bladder was included in the biopsy. Biopsies from conduit running through the abdominal muscle (3 cm) reveal
a median urothelial lining of 6 mm, SD 2.5 mm (33 ± 13%). Biopsy at the boarder between abdominal muscle and subcutaneous fat (5 cm)
demonstrates a median urothelial lining of 6 mm, SD 6 mm (33 ± 33%). Pig
Weeks after transplantation
0 cm
(mm)
3 cm
(mm)
3 cm
(%)
5 cm
(mm)
5 cm
(%)
8 cm
(mm)
Inner lumen
(mm)
1
X-ray
4
18
11
61
+
+
+
18
2
4
18
4
22
+
+
+
18
3
4
18
6
33
17
89
+
18
4
X-ray
5
18
3
17
8
44
+
18
5
Control
4
16
0
0
0
0
0
18
6
Control
5
16
0
0
0
0
0
18
All transplanted conduits demonstrated some urothelial cells at the most distal part of the conduit but none in controls. 4. Discussion Marking with (+) indicates the presence
of urothelial cells but not as confluent epithelium at the inner luminal surface. All transplanted conduits demonstrated some urothelial cells at the most distal part of the conduit but none in controls. Marking with (+) indicates the presence
of urothelial cells but not as confluent epithelium at the inner luminal surface. 25𝜇M
(a)
100 𝜇M
(b)
100 𝜇M
(c)
50𝜇M
(d)
100 𝜇M
(e)
50𝜇M
(f)
Figure 5: Microscopic analyses of tissue sections from conduit and from native bladder. (a) Wall of conduit covered with epithelium
toward lumen after 4 weeks and submucosal capillaries (∗) (H&E). (b) Staining of submucosal tissue from conduitwall (Van Gieson). (c)
Staining of submucosal tissue from native pig bladder wall (Van Gieson). (d) Basal membrane under the epithelial cells (arrows) (PAS). (e)
Immunostaining of cytokeratins (MNF116) in epithelial lining of conduit wall. (f) Immunostaining of Uroplakin III in epithelial lining of
conduit wall. 100 𝜇M
(c) 100 𝜇M
(b) 25𝜇M
(a) (c) (b) (a) 50𝜇M
(d) 50𝜇M
(f) 100 𝜇M
(e) (f) (d) (e) Figure 5: Microscopic analyses of tissue sections from conduit and from native bladder. (a) Wall of conduit covered with epithelium
toward lumen after 4 weeks and submucosal capillaries (∗) (H&E). (b) Staining of submucosal tissue from conduitwall (Van Gieson). (c)
Staining of submucosal tissue from native pig bladder wall (Van Gieson). (d) Basal membrane under the epithelial cells (arrows) (PAS). (e)
Immunostaining of cytokeratins (MNF116) in epithelial lining of conduit wall. (f) Immunostaining of Uroplakin III in epithelial lining of
conduit wall. healing model, a 100-fold expansion rate was successful after
only 14 days [17]. This indicates that further improvements
of the healing conditions in our experimental model could
result in successful take and regeneration also with smaller
amounts of tissue at initiation. glycosaminoglycans normally residing on the surface of the
bladder mucosa [18]. Until now, we have not tried removing
this mucous layer before mincing and transplantation. Histology at 4 and 5 weeks posttransplantation demon-
strated a multilayered transitional uroepithelium along the
inside of the newly formed conduit (Figure 5). The histol-
ogy revealed that during this time period, the transplanted
minced autologous urothelial transplants had reorganized
from a random placement on the mold to a well-organized,
continuous layer of mature epithelium facing the lumen and
without adherence to the mold [13]. 4. Discussion The basal membrane Due to the mincing device, particle size was basically
uniform although for urothelium, it is sometimes hard to
get 100% dissociation between the particles in comparison
to minced skin epithelium. Sometimes 2–5 mucosa particles
attach to each other even though they had been mechan-
ically separated, the reason for this is probably the sticky 8 BioMed Research International 8 (a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Figure 6: H and E staining of cross-sections from different parts of a conduit. (a)–(d): transplanted conduit. (e)–(h): sham operated control. (a) and (e) at junction between bladder and conduit. (b) and (f) 3 cm from junction. (c) and (g) 5 cm from junction. (d) and (h) 8 cm from
junction. (a) (d) (b) (c) (c) (d) (a) (b) (h) (f) (e) (g) (f) (g) (h) (e) Figure 6: H and E staining of cross-sections from different parts of a conduit. (a)–(d): transplanted conduit. (e)–(h): sham operated control. (a) and (e) at junction between bladder and conduit. (b) and (f) 3 cm from junction. (c) and (g) 5 cm from junction. (d) and (h) 8 cm from
junction. of the neo-epithelium covered the newly created channel. At the same time, tissue had expanded by division of cells
from the transplanted tissue, most probably from the edges
of the minced transplants according to the theory of Meek
[19]. Histology from control animals showed no epithelium,
which excludes that urothelium derived by migration from
the bladder.fi be an acceptable material for implantation, in particular not
in the group of patients that could potentially benefit from its
application, we need to further study alternative materials in
the molds before clinical application. Also, with longer time
of exposure, 4-5 weeks, latex might have had a negative effect
on the newly formed epithelium. We also found that only half of the amount of conduits
demonstrated urothelium at 5 cm from the bladder junction
and only traces of urothelial cells were found at 8 cm (Table 1). One reason for this could be that the fatty tissue surrounding
this part of the conduit had lower vascularization and poorer
conditions for take of transplant than the medial part that
passed through the abdominal muscles. The most lateral part
might also be more susceptible for trauma by outer pressure
to the skin as well as friction due to movements of the skin. 4. Discussion In this porcine in vivo study, we encountered difficulties
that influenced the outcome negatively. Differences in pig
anatomy, compared to human, include the intraperitoneal
position of the urinary bladder. The animals had a risk of
developing incarcerated intestinal midline hernias and the
four animals that experienced this also had undesirable out-
comes (two early terminations and two negative results). In
this matter, we experienced a learning curve and by creating
the conduit in a paramedian location through the abdominal
rectus muscle, this problem was solved. Additionally, one pig
was terminated due to acute peptic ulcer of unclear etiology. At the end of the study, a total of six conduits could be
analyzed including two sham operated controls.f Histology of the two conduits that had been exposed
to radiological examinations and catheterizations revealed
urothelium in the lumen that had detached from the surface. The mechanical trauma from expelling the inner tube and
insertion of a catheter most probably eroded the surface. This suggests that the neoepithelium is not strong enough
for longstanding duration. In studies of transplanted cul-
tured skin epithelium for treatment of severe burn injuries,
the subepithelial tissue of the dermis seems imperative for
good mechanical strength, stability, and to reduce the risk
of peeling off and infection [21]. This might be a factor
for bad attachment of the urothelium also in our cases. Although some submucosal tissue from the lamina propria
is transplanted within the minced tissue, the regenerative
properties of the cells and structures are not the same as for
epithelium and thereby the supporting mechanical structures
might not be strong enough in our study model. Differences in body physiology including the resting and
natural standing positions of the pig in combination with
a fast increase in body weight (20 to 60 kg in 4 weeks)
might also exert high-mechanical stress on the conduit [20]. The changes in histological appearance with inflammatory
submucosal infiltration and loosely attached epithelium com-
pared to native urothelium might be due to these factors. In this study, we chose latex covered with a thin silicon
elastomer to form the mold for guided tissue regeneration. The rationale for this was that previous studies showed a
more favorable outcome in respect to neoepithelialization
when compared to silicone molds [12]. After ten days in
vivo, latex tubes demonstrated a significantly larger area
of neoepithelialization in comparison to the silicon tube
counterparts. References l
Although we found that minced urothelium expands and
regenerates and that submucosal capillary networks develop
that support epithelial nutrition, further improvements need
to be undertaken in order for the newly formed tissue to
withstand catheterizations several times a day. Most likely
lack of appropriate lamina propria and a reduced amount
of anchoring filaments and normal junctions between basal
cells and the submucosa is the key problem for mechanical
durability as the conduit runs through muscular and fatty
tissue of the abdominal wall in analogy to problems related
to transplanted cultured skin [22]. One mode of action
might be to add minced bladder submucosal tissue with the
minced bladder mucosa. We also hypothesize that a collagen
carrier could support further submucosal tissue regeneration
[23]. Preliminary studies have shown that a collagen-PCL
hybrid construct does support migration, reorganization,
and expansion of minced bladder mucosa in vitro and this
could be next step for addressing this problem and further
improving the method [24]. [1] P. Mitrofanoff, “Trans-appendix continent vesicostomy in treat-
ment of neurogenic bladder in children,” Chirurgie Pediatrique,
vol. 21, no. 4, pp. 297–305, 1980 (French). [2] P. S. Malone, P. G. Ransley, and E. M. Kiely, “Preliminary report:
the antegrade continence enema,” The Lancet, vol. 336, no. 8725,
pp. 1217–1218, 1990. [3] J. A. Leslie, A. M. Dussinger, and K. K. Meldrum, “Creation
of continence mechanisms (Mitrofanoff) without appendix: the
Monti and spiral Monti procedures,” Urologic Oncology, vol. 25,
no. 2, pp. 148–153, 2007. [4] I. D. Sugarman, P. S. Malone, T. R. Terry, and M. A. Koyle,
“Transversely tubularized ileal segments for the Mitrofanoff
or Malone antegrade colonie enema procedures: the Monti
principle,” British Journal of Urology, vol. 81, no. 2, pp. 253–256,
1998. [5] M. Gibbons, “Urinary problems after formation of a Mitrofanoff
stoma,” Professional Nurse, vol. 10, no. 4, pp. 221–224, 1995. [6] J. Fitchner, “Follow-up after urinary diversion,” Urologia Inter-
nationalis, vol. 63, pp. 40–45, 1999. [7] B. A. Vanderbrink, M. P. Cain, S. King et al., “Is oral vitamin
B12 therapy effective for vitamin B12 deficiency in patients with
prior ileocystoplasty?” Journal of Urology, vol. 184, supplement
4, pp. 1781–1785, 2010. In future studies, we would add a supportive matrix
that could promote submucosal tissue regeneration and
strengthen the anchorage of the neo-epithelial to the under-
lying tissue [16]. In a human setting, one of the advantages
would be an extraperitoneal placement. 4. Discussion As a proof of principle, we therefore chose latex
in this animal model. However, as latex is not considered to In our previous studies using minced epithelium in the
subcutaneous tissue, we also noted a tendency of loosening
of the epithelial lining with time in vivo [12, 13]. Due to
these findings, we hypothesized that contact with the bladder BioMed Research International 9 Swedish Brain Foundation, the Swedish Research council,
and Karolinska Institutet, supported this work. Swedish Brain Foundation, the Swedish Research council,
and Karolinska Institutet, supported this work. Swedish Brain Foundation, the Swedish Research council,
and Karolinska Institutet, supported this work. cavity and filling of urine would overcome the problem of
placing a foreign body (the tube) in a blind cavity. However, as
we still experience histological results with loosely adhering
epithelium, we conclude that this mode of action was not
enough for reducing the inflammatory reaction. References Postoperatively, the
patient would not be resting on the transplanted area and
neither would a significant change of body weight be expected
during the course of a month. [8] M. Fossum and A. Nordenskj¨old, “Tissue-engineered trans-
plants for the treatment of severe hypospadias,” Hormone
Research in Pædiatrics, vol. 73, no. 2, pp. 148–152, 2010. [9] A. Raya-Rivera, D. R. Esquiliano, J. J. Yoo, E. Lopez-Bayghen,
S. Soker, and A. Atala, “Tissue-engineered autologous urethras
for patients who need reconstruction: an observational study,”
The Lancet, vol. 377, no. 9772, pp. 1175–1182, 2011. In conclusion, we demonstrate that it is possible to create
conduits to the urinary bladder by randomly transplanting
small particles of autologous urothelial tissue on a tubular
mold placed in a surgically created canal through the abdom-
inal wall. The method is easy to perform and the transplanted
tissue specimens have capacity to expand around the mold
without requiring any ex vivo cell culturing. Further studies
are needed in order to evaluate the mechanical strength of the
neo-epithelium in the newly formed conduits, in particular
after injury that may occur when catheterizing the stoma. With further success, this could be of value for a large group
of patients needing bladder emptying by catheterization
through an abdominal stoma. [10] A. Atala, S. B. Bauer, S. Soker, J. J. Yoo, and A. B. Retik,
“Tissue-engineered autologous bladders for patients needing
cystoplasty,” The Lancet, vol. 367, no. 9518, pp. 1241–1246, 2006. [11] L. Mart´ınez-Santamar´ıa, S. Guerrero-Aspizua, and M. del R´ıo,
“Skin bioengineering: preclinical and clinical applications,”
Actas Dermo-Sifiliogr´aficas, vol. 103, no. 1, pp. 5–11, 2012. [12] M. Fossum, B. Zuhaili, T. Hirsch et al., “Minced skin for tissue
engineering of epithelialized subcutaneous tunnels,” Tissue
Engineering A, vol. 15, no. 8, pp. 2085–2092, 2009. [13] M. Fossum, B. Zuhaili, J. Bergmann, M. Spielmann, T. Hirsch,
and E. Eriksson, “Minced urothelium to create epithelialized
subcutaneous conduits,” Journal of Urology, vol. 184, no. 2, pp. 757–761, 2010. Conflict of Interests [14] M. S¨oderman, D. Babic, S. Holmin, and T. Andersson, “Brain
imaging with a flat detector C-arm: technique and clinical
interest of XperCT,” Neuroradiology, vol. 50, no. 10, pp. 863–868,
2008. No financial conflict of interests exists for any of the authors. Acknowledgments [15] A. J. Molen, N. C. Cowan, U. G. Mueller-Lisse, C. C. A. Nolte-
Ernsting, S. Takahashi, and R. H. Cohan, “CT urography:
definition, indications and techniques. A guideline for clinical
practice,” European Radiology, vol. 18, no. 1, pp. 4–17, 2008. The authors thank Professor Elof Eriksson, Harvard Med-
ical School, for the kind provision of the mincing device. Grants from the Swedish Society for Medical Research, the
Promobilia Foundation, the Crown Princess Lovisa Founda-
tion, the Freemason Foundation for Children’s Welfare, the
Solstickan Foundation, the Swedish Society of Medicine, the [16] T. Svensj¨o, B. Pomahac, F. Yao, J. Slama, N. Wasif, and E. Eriks-
son, “Autologous skin transplantation: comparison of minced
skin to other techniques,” Journal of Surgical Research, vol. 103,
no. 1, pp. 19–29, 2002. BioMed Research International 10 [17] F. Hackl, J. Bergmann, S. R. Granter et al., “Epidermal regen-
eration by micrograft transplantation with immediate 100-fold
expansion,” Plastic and Reconstructive Surgery, vol. 129, no. 3,
pp. 443e–452e, 2012. [18] J. C. Nickel and J. Cornish, “Ultrastructural study of an
antibody-stabilized bladder surface: a new perspective on the
elusive glycosaminoglycan layer,” World Journal of Urology, vol. 12, no. 1, pp. 11–14, 1994. [19] C. P. Meek, “Successful microdermagrafting using the Meek-
Wall microdermatome,” The American Journal of Surgery, vol. 96, no. 4, pp. 557–558, 1958. [20] P. Geutjes, L. Roelofs, H. Hoogenkamp et al., “Tissue engineered
tubular construct for urinary diversion in a preclinical porcine
model,” The Journal of Urology, vol. 188, no. 2, pp. 653–660, 2012. [21] M. Meuli and M. Raghunath, “Tops and flops using cultured
epithelial autografts in children,” Pediatric Surgery Interna-
tional, vol. 12, no. 7, pp. 471–477, 1997. [22] M. Raghunath and M. Meuli, “Cultured epithelial autografts:
diving from surgery into matrix biology,” Pediatric Surgery
International, vol. 12, no. 7, pp. 478–483, 1997. [23] J. L. Pariente, B. S. Kim, and A. Atala, “In vitro biocompatibility
assessment of naturally derived and synthetic biomaterials
using normal human urothelial cells,” Journal of Biomedical
Materials Research, vol. 55, no. 1, pp. 33–39, 2001. [24] F. Ajalloueian, S. Zeiai, R. Rojas, M. Fossum, and J. Hilborn,
“One-stage tissue engineering of bladder wall patches for an
easy-to-use approach at the surgical table,” Tissue Engineering
C, vol. 19, no. 9, pp. 688–696, 2013. |
https://openalex.org/W4236839136 | https://repository.helmholtz-hzi.de/bitstream/10033/622732/1/Baltz%20et%20al.pdf | English | null | Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2019” | Journal of industrial microbiology and biotechnology/Journal of industrial microbiology & biotechnology | 2,019 | cc-by | 541 | Introduction to the special issue: “Natural Product Discovery
and Development in the Genomic Era: 2019” Published online: 7 February 2019
© Society for Industrial Microbiology and Biotechnology 2019 Republic, Denmark, Germany, Italy, Netherlands, Spain,
Switzerland, and United Kingdom). The Honorary Co-chairs
for the meeting were Professors Heinz Floss and Christopher
Walsh. This Special Issue is dedicated to Professors Floss
and Walsh for their outstanding contributions to the under-
standing of the fundamental enzymology of natural product
biosynthesis in microorganisms that has helped establish the
basis for current advances on genome mining and combina-
torial biosynthesis for drug discovery. Their contributions
are described in more detail in the accompanying Dedication
prepared by Rolf Müller and Gerry Wright. This special issue of the Journal of Industrial Microbiol-
ogy and Biotechnology contains reviews, original articles,
and perspectives describing recent scientific advances in
natural product discovery and development. The volume
is composed primarily of information presented at the 2nd
International Conference on “Natural Product Discovery
and Development in the Genomic Era” held in Clearwater,
Florida, in January of 2018. The conference was co-spon-
sored by the Society for Industrial Microbiology (SIMB),
the Korean Society for Microbiology and Biotechnology
(KMB), and the Society for Actinomycetes Japan (SAJ),
and was attended by 175 scientists from North America
(USA and Canada), South America (Brazil and Chile),
Asia (Japan, South Korea, and China), and Europe (Czech Publisher’s Note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. * Richard H. Baltz
rbaltz923@gmail.com rbaltz923@gmail.com
1
CognoGen Biotechnology Consulting, 7636 Andora Drive,
Sarasota, FL 34238, USA
2
Graduate School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113‑0033, Japan
3
Department of Biological Engineering, Inha University,
Incheon 402‑751, Korea
4
Helmholtz Institute for Pharmaceutical Research Saarland
(HIPS), Helmholtz Centre for Infection Research
and Department of Pharmacy, Saarland University, Saarland
University Campus, Building E8.1, 66123 Saarbrücken,
Germany
5
Department of Pharmaceutical Sciences, College
of Pharmacy, University of Kentucky, 789 S. Introduction to the special issue: "Natural Product
Discovery and Development in the Genomic Era: 2019". Item Type
Editorial
Authors
Baltz, Richard H; Abe, Ikuro; Kim, Eung-Soo; Müller, Rolf; Van
Lanen, Steven G; Wright, Gerry
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J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):249. doi: 10.1007/
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https://doi.org/10.1007/s10295-019-02138-w EDITORIAL EDITORIAL EDITORIAL Introduction to the special issue: “Natural Product Discovery
and Development in the Genomic Era: 2019” Limestone
Street, Lexington, KY 40536, USA
6
Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton, ON L8N 3Z5, Canada 1
CognoGen Biotechnology Consulting, 7636 Andora Drive,
Sarasota, FL 34238, USA 2
Graduate School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113‑0033, Japan 3
Department of Biological Engineering, Inha University,
Incheon 402‑751, Korea 4
Helmholtz Institute for Pharmaceutical Research Saarland
(HIPS), Helmholtz Centre for Infection Research
and Department of Pharmacy, Saarland University, Saarland
University Campus, Building E8.1, 66123 Saarbrücken,
Germany 5
Department of Pharmaceutical Sciences, College
of Pharmacy, University of Kentucky, 789 S. Limestone
Street, Lexington, KY 40536, USA 6
Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton, ON L8N 3Z5, Canada :(0123456789)
1 3 :(0123
1 |
https://openalex.org/W2957315691 | https://run.unl.pt/bitstream/10362/96250/1/Metabolic_signatures_of_germination_triggered_by_kinetin_in_Medicago_truncatula.pdf | English | null | Metabolic signatures of germination triggered by kinetin in Medicago truncatula | Scientific reports | 2,019 | cc-by | 11,211 | Metabolic signatures of
germination triggered by kinetin
in Medicago truncatula Received: 11 March 2019
Accepted: 1 July 2019
Published: xx xx xxxx Susana Araújo 1, Andrea Pagano2, Daniele Dondi3, Simone Lazzaroni3, Eduardo Pinela
Anca Macovei2 & Alma Balestrazzi2 In the present work, non-targeted metabolomics was used to investigate the seed response to
kinetin, a phytohormone with potential roles in seed germination, still poorly explored. The aim of
this study was to elucidate the metabolic signatures of germination triggered by kinetin and explore
changes in metabolome to identify novel vigor/stress hallmarks in Medicago truncatula. Exposure to
0.5 mM kinetin accelerated seed germination but impaired seedling growth. Metabolite composition
was investigated in seeds imbibed with water or with 0.5 mM kinetin collected at 2 h and 8 h of
imbibition, and at the radicle protrusion stage. According to Principal Component Analysis, inositol
pentakisphosphate, agmatine, digalactosylglycerol, inositol hexakisphosphate, and oleoylcholine
were the metabolites that mostly contributed to the separation between 2 h, 8 h and radicle protrusion
stage, irrespective of the treatment applied. Overall, only 27 metabolites showed significant changes
in mean relative contents triggered by kinetin, exclusively at the radicle protrusion stage. The observed
metabolite depletion might associate with faster germination or regarded as a stress signature. Results
from alkaline comet assay, highlighting the occurrence of DNA damage at this stage of germination, are
consistent with the hypothesis that prolonged exposure to kinetin induces stress conditions leading to
genotoxic injury. At the onset of germination, the transition from a dry quiescent state to a fully hydrated state is associated with
extensive metabolic changes1,2. This is a crucial phase for seed viability and vigor since water up-take causes
increased ROS (reactive oxygen species)-mediated oxidative injury3,4, and exacerbates genotoxic damage5,6. These
deleterious effects are counterbalanced by effective ROS scavenging mechanisms that limit the damage within the
cellular environment7 whereas the removal of DNA lesions is carried by dedicated repair pathways that contrib-
ute to safeguard genome integrity8–11. The successful mitigation of oxidative damage towards macromolecules,
including genotoxic insults correlates with enhanced seed vigor11,12. DNA repair represents a distinctive feature
of the seed pre-germinative metabolism and the work by Waterworth et al.6 has clearly highlighted the cru-
cial role of the DNA checkpoint kinase ATM (ATAXIA TELANGIECTASIA MUTATED) and ATR (ATM AND
RAD3-RELATED) as major determinants of seed viability and vigor in the model plant Arabidopsis thaliana. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Metabolic signatures of
germination triggered by kinetin
in Medicago truncatula Studies carried in the model legume Medicago truncatula have demonstrated that the DNA damage response
triggered during early seed imbibition features the up-regulation of key BER (base excision repair) genes, as
OGG1 (8-oxoguanine glycosylase/lyase) and FPG (formamidopyrimidine DNA glycosylase) required to remove
the DNA oxidative lesions under physiological and stress conditions9,10,13.hf p y
g
The positive correlation between an effective antioxidant and DNA repair response within the pre-germinative
metabolism and the degree of seed vigor is the driving force of priming, a pre-sown technique that allows to
carry seed imbibition under controlled conditions, in order to boost the seed repair and protective activities14–16. Additional benefits can rise by adding bioactive molecules, e.g. phytohormones, however the treatment must be
stopped before radicle protrusion occurs otherwise desiccation tolerance will be lost17,18. In the case of ‘hormo-
priming’, phytohormones are added to boost germination and seedling robustness, as in the case of gibberellic
acid that promotes antioxidant response and abiotic stress tolerance in white clover and wheat19. 1Instituto de Tecnologia Química e Biológica António Xavier - Universidade Nova de Lisboa (ITQB-NOVA), Av. da
República, 2780-157, Oeiras, Portugal. 2Department of Biology and Biotechnology ‘L. Spallanzani’, via Ferrata 9,
27100, Pavia, Italy. 3Department of Chemistry, Viale Taramelli 12, 27100, Pavia, Italy. Susana Araújo and Andrea
Pagano contributed equally. Correspondence and requests for materials should be addressed to A.B. (email: alma. balestrazzi@unipv.it) Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 1 www.nature.com/scientificreports/ Exogenous applications of phytohormones generally ameliorate the stress response in planta, allowing to bet-
ter regulate and integrate the growth process in changing environments. Cytokinins have been implicated in fruit
and seed development20 and transgenic plants overexpressing the ipt (isopentenyl transferase) gene, essential for
cytokinin biosynthesis, were characterized by increased seed yield and quality20. Initial studies revealed the ‘per-
missive’ role of cytokinins in seed germination21 while more recently it has been reported that, at the onset of ger-
mination, cytokinin counteracts the inhibitory role of ABA by downregulating the expression of the ABI5 (ABA
INSENSITIVE) gene22. The effects of cytokinins, including kinetin (6-furfurylaminopurine), as priming agents
to improve seed germination and seedling robustness have been described and possibly related to enhanced cell
division rates23,24. As for legumes, cytokinins are engaged in the intricated networking underlying symbiotic nod-
ulation, as shown in the model plant M. Results
Ki
ti Kinetin promotes seed germination while impairing root growth. To select the most suitable kine-
tin dose, preliminary work was carried out using 0.25, 0.5, and 0.75 mM kinetin. As shown in Supplementary
Fig. 1, a significant increase (P < 0.01) in germination percentage was observed in response to 0.5 mM and
0.75 mM kinetin, with estimated values of 72.00 ± 15.24% (0.5 mM kinetin) and 76.00 ± 15.57% (0.75 mM kine-
tin), respectively. Additionally, the T50 parameter (number of days required to reach half maximal germination,
see Materials and Methods) was significantly reduced when comparing the 0.5 mM and 0.75 mM kinetin doses
with control samples imbibed with water (W) (Supplementary Table 1). On the other hand, inhibition of root
growth was observed in four-day-old M. truncatula seedlings developed in presence of kinetin (Supplementary
Table 1 and Supplementary Fig. 2). The lowest dose able to anticipate germination, 0.5 mM kinetin (hereby named
Kin), was selected for further investigation.hi g
The Kin treatment resulted in accelerated radicle emergence (Fig. 1a) and anticipation of the first true leaf
appearance was also observed (Fig. 1b). The phenotype of four-day-old M. truncatula seedlings developed from
seeds imbibed with 0.5 mM kinetin is shown in Fig. 1c. The growth impairment caused by prolonged exposure
to kinetin is particularly evident at the root level. The 0.5 mM concentration was chosen among the tested ones
because this was the lowest dose that could anticipate germination. In view of further applications of these results
to design new priming protocols, this also represents the most cost-effective concentration. f
To better understand the molecular mechanisms behind the observed phenotype induced by this treatment,
the kinetin-triggered changes in metabolite profiles were investigated. Thereby, the metabolite composition was
analyzed in M. truncatula seeds imbibed with water (W) or with 0.5 mM kinetin (Kin) collected at: (i) 2 h (hereby
named W2 and Kin2) and (ii) 8 h (hereby named W8 and Kin8) of imbibition, as well as at the (iii) radicle pro-
trusion stage (radicle length ≤ 3 mm; hereby named WRD and KinRD). With this experimental design (Fig. 2a),
attention was focused on two pre-germination timepoints (2 h and 8 h of imbibition), as well as on the develop-
mental stage of radicle protrusion, previously reported to undergo extensive metabolic changes1,2,13. Metabolic signatures of
germination triggered by kinetin
in Medicago truncatula truncatula25 and have been included, among other phytohormones, in
culture media formulations tailored for in vitro regeneration via somatic embryogenesis. However, information
about the effects of kinetin in the context of seed germination, namely about the potential use of this growth reg-
ulator to stimulate germination, is still scanty. In this context, legumes represent an attractive system to explore
and assess the possible benefits of kinetin-mediated priming. A major issue of grain legumes is the need to stabi-
lize yields in water-limited environments since, compared to other crops, they have higher water requirements. Legumes are used in rotational and intercropping systems during the post-rainy season or in lands unsuitable for
the main crop and the availability of seeds primed by controlled hydration before sown improves seedling emer-
gence and establishment26. Indeed, reduced field performance generally results from the variability in number
and speed of seedling emergence, thus reflecting poor seed vigor27. These unfavorable features can be mitigated by
means of tailored priming protocols that require, however, a deeper technical knowedge tightly linked to a better
comprehension of the molecular aspects of the pre-germinative metabolism28.f p
p
p
g
Metabolomics studies are very useful approaches to retrieve overall metabolites differentially accumulated
during the different germination phases and possibly linked to seed vigor13,29–31. The aim of the present study
was to elucidate the physiological and metabolic signatures of M. truncatula seed germination in response to
exogenously applied kinetin. Besides being a reference legume for functional biology, and for the study of the
rhizobia-legume symbiosis as well as the integrated stress and growth responses, M. truncatula is also a pasture
species used first in Australia in the wheat/sheep rotation32 and more recently in South Africa in rotation with
wheat, barley and canola33. As for other pulses, M. truncatula seed and seedling vigor is among the selection
criteria used in breeding programmes finalized to the development of novel annual medics34. In the attempt to
improve germination performance and stand establishment, a further step is required, namely a deeper dissection
of the molecular determinants of seed vigor that might possibly include metabolites able to alleviate genotoxic
stress. In this work, a multidisciplinary approach, combining non-targeted metabolite profiling, gene expression
analysis, electron paramagnetic resonance, and comet assay has been used to gain an in-depth picture of the
response to kinetin in legume seeds. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Metabolic signatures of
germination triggered by kinetin
in Medicago truncatula Attention was focused on the impact of exogenously applied kinetin on seed
germination as well as on the stress conditions resulting from prolonged exposure to the phytohormone. This
work contributes to the current state of the art regarding the issues of seed vigor in legumes, and adds another
piece of information useful to decipher the complex molecular network and specific hallmarks underlying the
seed response to stress. Due to the high synteny of this model species with other legumes, the results of this
investigation can impact research on seed biology in other economically relevant legume crops, such as pulses. Results
Ki
ti Due to the
reduced T50 value observed in the phytohormone-treated seeds, the sampling procedure for the radicle protru-
sion stage was conducted earlier than for water-imbibed seeds. Thus, the majority of kinetin-treated seeds were
collected starting from the 25th hour from the beginning of imbibition whereas the water-treated seeds were
collected subsequently, starting from the 40th hour (Fig. 1a). The phenotype of W and Kin seeds at the radicle
protrusion stage is shown in Fig. 2b. 2 www.nature.com/scientificreports/ Figure 1. Impact of kinetin on seed germination in M. truncatula. Imbibition with 0.5 mM kinetin (Kin)
accelerates radicle protrusion (a) and anticipates the occurrence of the first true leaf (b), compared to control
seeds imbibed with water (W). (c) Phenotype of four-day-old M. truncatula seedlings developed from seeds
imbibed with water (W) and 0.5 mM kinetin (Kin), respectively. Values are expressed as mean ± SD of three
independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences
determined using Student’s t-test (P < 0.05). Bar = 0.5 cm. Figure 1. Impact of kinetin on seed germination in M. truncatula. Imbibition with 0.5 mM kinetin (Kin)
accelerates radicle protrusion (a) and anticipates the occurrence of the first true leaf (b), compared to control
seeds imbibed with water (W). (c) Phenotype of four-day-old M. truncatula seedlings developed from seeds
imbibed with water (W) and 0.5 mM kinetin (Kin), respectively. Values are expressed as mean ± SD of three
independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences
determined using Student’s t-test (P < 0.05). Bar = 0.5 cm. Kinetin affects nucleotide, amino acid, lipids, and carbohydrate metabolism during germina-
tion. A total of 412 metabolites with known structures were identified (Supplementary Dataset S1). Among
these, kinetin was only detected in kinetin-treated samples and thus removed from the pool of metabolites to be
further studied. A Principal component analysis (PCA) was applied to the 411 metabolites identified in the metab-
olomic study (Fig. 3) in order to investigate the differences between samples, the similarity between replicates, and
which metabolites (variables) contributed mostly to this difference. The two main factors/components extracted
accounted for 65.1% of the variance. Principal component one (PC1) accounted for 53.4% of the total variance
and, according to the respective loadings plot (Fig. Results
Ki
ti Changes in the mean metabolite contents in seeds
imbibed with kinetin for 2 h and untreated seeds were noticed (7 up- and 26 down-accumulated metabolites)
based on P ≤ 0.05 but they did not meet the q significance threshold imposed (q ≥ 0.1). Nevertheless, it is worth
to mention the accumulation of deoxycarnitine (FC = 1.82, P = 0.001, q = 0.115) and 1-palmitoyl-2-linoleoyl-GP
(FC = 3.34, P = 0.0033, q = 0.1531) as well as the depletion of 2-hydroxymyristate (FC = 0.6, P = 0.0043,
q = 0.1651), 5-methylcytidine (FC = 0.8, P = 0.003, q = 0.1531), and salicylate (FC = 0.8, P = 0.0022, q = 1531)
observed in seeds imbibed for 2 h with kinetin over untreated seeds, which are borderline with the significance
threshold imposed. A reduced number of metabolites showing changes in content was noticed (1 up- and 8
down-accumulated metabolites, based on P ≤ 0.05) in seeds imbibed with kinetin for 8 h and untreated seeds,
although these changes also did not meet the threshold imposed for q significance.i g
g
p
q
gi
At the radicle protrusion stage, the majority of metabolites with significant fold changes induced by kine-
tin treatment belonged to the amino acid, nucleotide and carbohydrate super-pathways (Fig. 4). The most
significant changes were noticed in the amino acid super-pathway, in which saccharopine (FC = 0.18) and
3-(4-hydroxyphenyl)lactate (FC = 3.51) were the metabolites with the highest variations in their levels in response
to the treatment applied (Supplementary Dataset S1). As for the lipid metabolism, significant changes in the rel-
ative metabolite levels were observed for caprate (FC = 0.25). Interestingly, significant changes in relative levels
of metabolites belonging to the nucleotide super-pathway were detected for cytidine 2′, 3′-cyclic monophos-
phate (FC = 0.5), orotidine (FC = 0.5) and xanthine (FC = 2.06). Significant changes were also noticed in the
carbohydrate metabolism, namely regarding maleate (FC = 1.21) and tartronate (hydroxymalonate, FC = 1.42). Indeed, the heatmap generated (Fig. 5) with all the samples and the 27 differentially accumulated metabolites
hierarchical clustering (Euclidean distance, Ward clustering algorithm) corroborated the earlier results obtained
by PCA for samples collected at the radicle protrusion stage. The dendrogram shows that the replicates for each
treatment cluster together, based on the changes observed in detected metabolites (Fig. 5). Results
Ki
ti 3a), inositol pentakisphosphate (0.21), agmatine (0.17), diga-
lactosylglycerol (0.15), inositol hexakisphosphate (0.14), and oleoylcholine (−0.14) were the metabolites that
mostly contributed to the separation between 2 h, 8 h and radicle protrusion stage, irrespective to the treatment
applied. PC2 accounts for 11.7% of the variation and, according to the respective loadings plot (Fig. 3b), creatine
(0.29), caprate (0.26), saccharopine (0.24), 1-linoleoyl-GPI 182 (0.23), UDP-glucose/UDP-galactose (0.20), and
orotate (−0.13) were the metabolites that mostly contributed to the separation in this axis. No major differences
in metabolomic profiles were detected between untreated and kinetin-treated samples at 2 h and 8 h of imbibition
since these samples clustered together. Nevertheless, PCA indicated that the effects of kinetin on metabolomic
profiles were relevant at the radicle protrusion stage, where the separation of kinetin-treated and untreated sam-
ples was unveiled. The univariate analysis allowed to identify 27 metabolites showing significant changes in the Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 3 www.nature.com/scientificreports/ Figure 2. (a) Experimental design. Metabolite composition was investigated in M. truncatula seeds imbibed
with water (W) and 0.5 mM kinetin (Kin), respectively, collected at 2 h and 8 h of imbibition, and at the radicle
protrusion stage (RD). (b) The phenological stage of radicle protrusion occurred faster in kinetin-treated seeds
(KinRD) compared to control seeds imbibed with water (WRD). Kinetin-treated seeds were collected starting
from the 25th hour from the beginning of imbibition whereas water-treated seeds were collected subsequently,
starting from the 40th hours. Bar = 1 mm. Figure 2. (a) Experimental design. Metabolite composition was investigated in M. truncatula seeds imbibed
with water (W) and 0.5 mM kinetin (Kin), respectively, collected at 2 h and 8 h of imbibition, and at the radicle
protrusion stage (RD). (b) The phenological stage of radicle protrusion occurred faster in kinetin-treated seeds
(KinRD) compared to control seeds imbibed with water (WRD). Kinetin-treated seeds were collected starting
from the 25th hour from the beginning of imbibition whereas water-treated seeds were collected subsequently,
starting from the 40th hours. Bar = 1 mm. mean relative contents triggered by kinetin treatment (herein defined as P ≤ 0.05 and q ≤ 0.1), exclusively at the
radicle protrusion stage (RD) (Supplementary Dataset S1). Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Results
Ki
ti Also, the metabolites
were grouped into two major clusters, one representing four metabolites significantly more accumulated in seeds
imbibed with kinetin ((3–4-hydroxyphenyl)lactate, maleate, tartronate, xanthine) while another major cluster
gathers the 23 metabolites significantly accumulated in water-imbibed seeds at the radicle protrusion stage. In
summary, this highlights a significant reduction of the relative metabolite contents in kinetin-treated seeds when
compared to untreated samples.i Quantitative enrichment analysis was also conducted over the 27 metabolites that revealed significant changes
induced by the experimental conditions at the radicle protusion stage (KinRD vs WRD). These results evidenced
the major metabolic pathways whose response was significantly triggered by the experimental conditions. The
top and most significant metabolite sets (pathways) are lysine degradation (P = 0.000006, FDR = 0.0002), purine
metabolism (P = 0.00005, FDR = 0.0008), phenylalanine and tyrosine metabolism (P = 0.0002, FDR = 0.0023),
methionine metabolism (P = 0.0008, FDR = 0.0023) and valine/leucine/isoleucine degradation (P = 0.0009,
FDR = 0.0023) (Supplementary Dataset S1). Based on the reported data, metabolomic analyses highlighted that
most of the differentially accumulated metabolites were reduced at the radicle protrusion stage. Such results
reflect a metabolite depletion resulting from faster germination, or a stress situation. However, the observed
growth impairment in the kinetin-treated seeds leans towards the occurrence of stress conditions. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 4 www.nature.com/scientificreports/ Figure 3. Principal Component Analysis (PCA) of the 411 metabolites detected in response to Kin and W
treatments, sampled at 2 h and 8 h of imbibition, and at radicle protrusion stage (RD). The log-transformed raw
scaled imputed value for each metabolite in response to experimental conditions was used for computation. (a) PCA score plot explaining 65.1% of the variance of metabolite profiles, in which PC1 accounts for 53.4%,
while PC2 accounts for 11.7% of the variance. (b) Loading plots highlighting the metabolites contributed to the
differences observed among samples. W2, seeds imbibed with water for 2 h. W8, seeds imbibed with water for
8 h. WRD, seeds imbibed with water collected at the radicle protrusion stage. Kin2, seeds imbibed with 0.5 mM
kinetin for 2 h. Kin8, seeds imbibed with 0.5 mM kinetin for 8 h. KinRD, seeds imbibed with 0.5 mM kinetin
collected at the radicle protrusion stage. Figure 3. Results
Ki
ti Principal Component Analysis (PCA) of the 411 metabolites detected in response to Kin and W
treatments, sampled at 2 h and 8 h of imbibition, and at radicle protrusion stage (RD). The log-transformed raw
scaled imputed value for each metabolite in response to experimental conditions was used for computation. (a) PCA score plot explaining 65.1% of the variance of metabolite profiles, in which PC1 accounts for 53.4%,
while PC2 accounts for 11.7% of the variance. (b) Loading plots highlighting the metabolites contributed to the
differences observed among samples. W2, seeds imbibed with water for 2 h. W8, seeds imbibed with water for
8 h. WRD, seeds imbibed with water collected at the radicle protrusion stage. Kin2, seeds imbibed with 0.5 mM
kinetin for 2 h. Kin8, seeds imbibed with 0.5 mM kinetin for 8 h. KinRD, seeds imbibed with 0.5 mM kinetin
collected at the radicle protrusion stage. Kinetin triggers genotoxic stress at the radicle protrusion stage. DNA damage during early seed
imbibition has been reported as a consequence of ROS accumulation during rapid water uptake5,6,8. Although
it is still difficult to figure out the presence of metabolic signatures of genotoxic stress during seed germination,
changes in nucleotide super-pathway were reported by Pagano et al.13 and linked to the occurrence of DNA dam-
age induced by sodium butyrate. In the present work, significant changes in the nucleotide super-pathway were
detected at the radicle protrusion stage, notably an increase in the levels of xanthine, an intermediate of purine
degradation. Linked to xanthine overproduction, a study in animals pinpointed this metabolite as a hallmark
of DNA damage in irradiated cells35. Hence, to investigate the levels of DNA damage in our system, an alkaline
comet assay was carried out on radicles collected at the radicle protrusion stage. The results showed a signifi-
cant (P = 0.009) increase in DNA strand breaks in Kin treatments (125.98 ± 20.67 a.u.), compared to W samples
(62.89 ± 18.40 a.u.) (Fig. 6a). Additionally, a qRT-PCR analysis was carried out to monitor the expression profiles
of specific genes with known roles in DNA damage repair. Nonetheless, no significant changes were detected in the
expression of MtOGG1 (8-OXOGUANINE GLYCOSYLASE/LYASE) and MtFPG (FORMAMIDOPYRIMIDINE
GLYCOSYLASE/LYASE), genes involved in the removal of oxidative DNA lesions during imbibition5,10,36 (Fig. 6b). Results
Ki
ti (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG
genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum
generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement
of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species
(ROS) and organic radicals, respectively. The EPR spectrum was recorded at low field. For the iron region
(range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT
was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of
10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1
and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values
are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks
indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W,
control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG,
formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. protrusion stage, untreated and kinetin-treated seeds were frozen and the radical concentration was determined
at 120 K. At this temperature, radicals are blocked inside the icy matrix (hence, stable) allowing their detection
and quantification. For each sample, EPR analyses were performed at a low field to detect iron (Fe3+), while for
the quantification of organic radicals and manganese (Mn2+) the measurements were centered on 225 mT. A
representative example of the EPR spectrum generated in M. truncatula seeds imbibed with kinetin collected at
the radicle protrusion stage is shown in Fig. 6c. The enlargement of the central part of the EPR spectrum allows
to evidence regions corresponding to ROS and organic radicals, respectively. Since no spin traps were used, the
measured quantity represents the free radical steady-state concentration. No significant differences were observed
between EPR spectra generated by untreated and kinetin-treated seeds collected at the radicle protrusion stage,
suggesting that the exogenous application of kinetin does not impact the free radical species profiles. Results
Ki
ti On the other hand, both MtOGG1 and MtFPG transcripts were progressively accumulated during seed imbibition Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 5 www.nature.com/scientificreports/ Figure 4. Metabolic super-pathways significantly (P ≤ 0.05 and q ≤ 0.1) changed in response to kinetin
treatment at the radicle protrusion stage compared. The number of metabolites significantly up- and down-
accumulated is depicted. Figure 4. Metabolic super-pathways significantly (P ≤ 0.05 and q ≤ 0.1) changed in response to kinetin
treatment at the radicle protrusion stage compared. The number of metabolites significantly up- and down-
accumulated is depicted. Figure 5. Hierarchical clustering (Euclidean distance measure and Ward clustering algorithm) of 27
metabolites with significant changes (P ≤ 0.05 and q ≤ 0.1) in response to kinetin treatment at radicle protrusion
stage (RD). The color (from red to blue) represents the log-transformed raw scaled imputed value for each
metabolite from high to low, respectively. Figure 5. Hierarchical clustering (Euclidean distance measure and Ward clustering algorithm) of 27
metabolites with significant changes (P ≤ 0.05 and q ≤ 0.1) in response to kinetin treatment at radicle protrusion
stage (RD). The color (from red to blue) represents the log-transformed raw scaled imputed value for each
metabolite from high to low, respectively. n W and Kin samples, respectively (Supplementary Table 2 and Supplementary Fig. 3), possibly revealing tha
DNA repair was required to the same extent, independently of treatments. in W and Kin samples, respectively (Supplementary Table 2 and Supplementary Fig. 3), possibly revealing that
DNA repair was required to the same extent, independently of treatments. Kinetin does not impact the free radical steady-state levels in M. truncatula seeds. Electron
paramagnetic resonance (EPR) spectroscopy is a sensitive technique used for the qualitative and quantitative
detection of free radical species in seeds37. To assess the free radical profile of M. truncatula seeds at the radicle Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 6 www.nature.com/scientificreports/ Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG
genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum
generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement
of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species
(ROS) and organic radicals, respectively. Results
Ki
ti The EPR spectrum was recorded at low field. For the iron region
(range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT
was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of
10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1
and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values
are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks
indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W,
control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG,
formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG
genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum
generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement
of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species
(ROS) and organic radicals, respectively. The EPR spectrum was recorded at low field. For the iron region
(range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT
was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of
10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1
and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values
are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks
indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W,
control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG,
formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. Figure 6. Discussion
h Under our controlled experimental conditions, neither
light conditions nor the applied temperature did not seem to affect the process since after-ripening increases the
temperature range compatible with germination43. The 0.5 mM concentration was the lowest dose that accelerated
germination, thus the most cost-effective considering the possibility of future applications for priming protocols. In our previous works on M. truncatula, we have characterised the temporal window from the beginning of
imbibition until the radical protrusion stage in terms of antioxidant and DNA repair response by monitoring
gene expression profiles under conditions that challenge germination5,9,10,13,36. This was done in the attempt to
figure out the most informative timepoints of the pre-germinative metabolism to be selected for more in-depth
investigations, namely ‘omics’. In the case of M. truncatula seeds challenged with the stress agents trichostatin
A36 and sodium butyrate13, respectively, the timepoints corresponding to 2 h and 8 h of imbibition were found
to be representative of the seed response in terms of significant up-regulation of antioxidant and DNA repair
genes. These two informative timepoints were also maintained for investigating the impact of kinetin on the
pre-germinative metabolism of M. truncatula seeds. According to the definition provided by Bewley44, the 2 h
timepoint corresponds to the early imbibition status (stage I) while at the later timepoint (8 h) the seed is fully
imbibed (early stage II).hii y
g
The impact of the phytohormone on the seed metabolomic profiles resulted in significant changes only at
the radicle protrusion stage and the overall reduction in metabolites levels, observed in kinetin-treated seeds
when compared to water imbibed samples, can be regarded as a consequence of the accelerated degradation of
the seed reserves required to support faster germination rate and fulfill the process41. Among the differentially
accumulated compounds found at the radicle protrusion stage, 3-(4-hydroxyphenyl)lactate, member of the amino
acid super-pathway, showed the highest variations in response to kinetin. This phenolic acid with ROS scaveng-
ing properties45 was also differentially accumulated in M. truncatula seeds under genotoxic stress conditions
induced by the histone deacetylase inhibitor sodium butyrate13. It is possible that this metabolite represents a
recurrent metabolic signature of the seed response to genotoxic stress as well as xanthine, also accumulated in
response to kinetin at the radicle protrusion stage. It is worth noting that xanthine is a recurrent hallmark of
DNA damage in irradiated cells, as revealed by studies on the radiation-responsive metabolome35. Discussion
h Despite the well-known role of cytokinins in promoting cell division23,24 and morphogenesis, very few stud-
ies have explored the potentialities of kinetin treatments to enhance seed vigor and germination in legumes39. Kinetin has been tested, alone or in combination with other phytohormones/chemicals to improve germination,
however the limited number of reports so far available provide only a fragmentary picture of its potential use
as priming agents compared to other phytohormones frequently used, as gibberellins40. To address this gap of
knowledge, we investigated the effect of kinetin during M. truncatula seed germination to evaluate its suitability
as priming agent in legumes. We found that the treatment with 0.5 mM kinetin, applied thorughout germination,
was able to speed-up germination but caused radicle growth impairment. Using multidisciplinary analyses that
combines untargeted metabolomics, EPR, and gene expression, we investigated the metabolites, along with ROS
and gene profiles, that were disturbed during germination in response to 50 mM kinetin. T
k
l d
h
h fi
l
h
l
b l
d
d
f
l
d i
To our knowledge, this is the first report in legumes that exploits metabolomics to provide evidence of selected
metabolites associated with exposure to kinetin and evaluates the effects of the phytohormone not only as growth
inducer but also as stress agent. Our results showed that the Kin treatment accelerated the germination process,
but the prolonged exposure to the phytohormone led to seedling growth impairment especially at the root level. Considering the impact that phytohormones (including cytokinins) can have on seed dormancy and germina-
tion41, we need to specify that the M. truncatula seeds used in this study represent freshly harvested material
kept under dry storage conditions at room temperature for more than ten months, defined as after-ripening. Such treatment was reported to be effective in releasing dormancy and promoting seed germination in M. trun-
catula42,43. Independently of treatments, fully after-ripened seeds always germinated within two days from the
beginning of imbibition, reaching a maximum germination percentage of 80%. This suggests that there was no
physiological dormancy in the M. truncatula seed lot whereas the fraction (20%) of seeds that were not able to
uptake water and failed to germinate might be associated with physical dormancy, a trait that follows distinct
kinetics compared to those occurring during after-ripening43. Other parameters that can affect M. truncatula seed
germination include temperature and light conditions43. Results
Ki
ti It should
be noticed that similar results were obtained with seeds collected at 2 h and 8 h of imbibition (data not shown). Overall, the reported data reflect the invariance of the steady-state concentration of radicals and show that the
treatment with kinetin did not trigger ROS accumulation in M. truncatula seeds at the radicle protrusion phase. To further investigate the status of the antioxidant defence, a set of antioxidant genes (MtAPX, ASCORBATE
PEROXIDASE; MtMT2, TYPE 2 METALLOTHIONEIN; MtTRH1 and MtTRH2, THIOREDOXIN) that mark the
pre-germinative metabolism5,9,13,36 was also investigated (Fig. 6d). No significant changes in MtAPX and MtMT2
transcript levels were detected in Kin seeds at the radicle protrusion stage. On the other hand, MtTRH1 and
MtTRH2 genes, encoding h-type thioredoxins that act as ROS scavengers to prevent oxidative damage upon
imbibition38, were significantly down-regulated in Kin samples, compared to W control (Fig. 6d). The reduced
antioxidant response well corroborated the results from the EPR analysis (Fig. 6c), showing that treatment with Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 7 www.nature.com/scientificreports/ kinetin does not impact the free radical steady-state levels in M. truncatula seeds at the radicle protrusion stage. As previously observed for the DNA repair genes MtOGG1 and MtFPG, for all the tested antioxidant genes the
transcripts were progressively accumulated during seed germination in both W and Kin samples throughout
imbibition (2 h and 8 h) until the radicle protrusion stage (Supplementary Table 2 and Supplementary Fig. 2), thus
indicating that the antioxidant response triggered during the imbibition phase was somewhat sufficient to cope
with any perturbation caused by the application of exogenous kinetin. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 www.nature.com/scientificreports/ www.nature.com/scientificreports/ 5-methylcytidine, and salicylate. All these metabolites, whose levels are perturbated in response to kinetin at
2 h of imbibition, deserve further investigation to assess their possible involvement in the seed response to
kinetin-based priming. 5-methylcytidine, and salicylate. All these metabolites, whose levels are perturbated in response to kinetin at
2 h of imbibition, deserve further investigation to assess their possible involvement in the seed response to
kinetin-based priming. p
g
Aside from the metabolite depletion, further proof that extended exposure to kinetin results in stress con-
ditions is also given by the comet assay-based profiles of DNA damage that highlighted the overall genotoxic-
ity induced by the exogenous application of the phytohormone (Fig. 6a). The genotoxic effects of cytokinins
have been investigated in animals, where it was seen that exposure to high concentrations (500 nM) of kinetin
induced significant DNA damage, as evidenced by a comet assay carried out on in HL60 cells, HaCaT human
keratinocyte cells, NRK rat epithelial kidney cells and human peripheral lymphocytes49. In another study,
Cabello et al.50 tested the effect of cytokinins and cytokinin nucleosides in various human cancer cell lines
and observed that the accumulation of DNA damage was associated with rapid upregulation of DNA damage
associated genes, e.g. CDKN1A (CYCLIN DEPENDENT KINASE INHIBITOR 1A) or GADD153 (GROWTH
ARREST AND DNA DAMAGE-INDUCIBLE PROTEIN). Nonetheless, under the experimental conditions of our
study, the kinetin-induced DNA damage did not trigger significant up-regulation of the BER associated genes
MtOGG1 and MtFPG. This suggests that the BER pathway may not be required in this case, while the implica-
tion of other DNA repair pathways cannot be ruled out. Within this context, the cross-talk between DDR and
cytokinins is still poorly explored even in planta, although there is evidence of interplay. For instance, Davis
et al.51 demonstrated that double-strand breaks accumulation in Arabidopsis lateral root primordia not only
triggers the SOG1(SUPPRESSOR OF GAMMA RESPONSE)-mediated up-regulation of DNA repair genes but
also stimulates the expression of cytokinin biosynthesis/signaling genes leading to the inhibition of cell division. Kataya et al.52 also highlighted a link between DNA repair and cytokinins by investigating the Arabidopsis PSY2L
(PLATINUM SENSITIVE 2 LIKE) mutant. Besides metabolite depletion and evident genotoxic injury, exposure
to kinetin did not result in enhanced accumulation of free radical species nor into increased antioxidant gene
expression, implying a global diminishment of the cellular metabolic activities. www.nature.com/scientificreports/ Indeed, other studies also evi-
denced that, although exogenously applied cytokinins could prevent senescence and positively impacted the plant
antioxidant response53, the prolonged cytokinin exposure or high concentration resulted in impair growth54. It
should be also noted that kinetin itself plays a role as ROS scavenger55 and that it has an anti-glycating activity
that protects proteins against reactive aldehydes56. This may also be among the reasons why no changes in ROS
profiles and antioxidant gene expression were observed under the Kin treatment in our experimental conditions,
compared to control. On the other hand, DNA repair and antioxidant genes were upregulated in Kin-treated
seeds throughout the tested timepoints with profiles similar to those recorded in W samples. Apparently, kinetin
did not influence this specific aspect of seed metabolism Conclusions In the present work, we demonstrate that the treatment of M. truncatula seeds with 50 mM kinetin applied
throughout germination, accelerated radicle protrusion but causes radicle growth impairment. This shows the
dual role of kinetin as a growth inducer and stress agent, likely due to the long exposure to the phytohormone. Seed metabolomics has provided a list of metabolites and metabolic pathways affected by kinetin during M. truncatula germination. Most of the changes observed were linked to the faster metabolic depletion associ-
ated with a faster germination. The study highlighted the differential accumulation of two metabolites, namely
3-(4-hydroxyphenyl)lactate and xanthine, potentially linked to stress. With additional and more targeted studies,
these metabolites could be used to monitor stress-mediated events during germination and to figure out, for
instance, the timepoint when priming treatments should be stopped to prevent toxicity towards seeds. Discussion
h This sug-
gests that changes in xhantine levels occurring during seed germination might be related to peaks in genotoxic
damage, although in-depth studies will be necessary to further support such hypothesis. Differences were also
revealed in UDP-glucose/UDP-galactose inositol polyphosphates with roles in sucrose and starch metabolism
as well as in signaling46,47, agmatine and orotic acid, intermediates in polyamine and pyrimidine biosynthesis,
respectively. Saccharopine, an intermediate in lysine degradation48 is also included in this set of metabolites. Protein turnover and amino acid degradation are also required at the onset of germination since the carbon skel-
etons of amino acids are directed into the TCA cycle whereas oxidation of lysine and other amino acids releases
electrons that enter the mitochondrial electron transport chain. Overall, the profiles observed at 2 h and 8 h of
imbibition, reflect the contribution of the different metabolic super-pathways to those essential physiological and
biochemical changes that require ex novo biosynthesis or degradation to support germination. Moreover, when
considering the possible changes observed during imbibition, it is worth to mention a relevant but not statistically
significant accumulation of deoxycarnitine and 1-palmitoyl-2-linoleoyl-GP and depletion of 2-hydroxymyristate, Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 8 Methods
l Principal component analysis (PCA),
quantitative enrichment analysis, heatmaps, and clustering analysis were conducted using the software resources
available at Metaboanalyst 3.0 (www.metaboanalyst.ca) following user´s guide specifications62. While PCA was
conducted over all identified metabolites, the remaining analyses were conducted only over DA metabolites pres-
ent at least in one of the three comparisons studied. RNA extraction, cDNA synthesis, and quantitative real-time polymerase chain reaction. RNA
isolation was carried out from water- and kinetin-imbibed M. truncatula seeds, respectively, collected at 2 h
and 8 h (W2, Kin2; W8, Kin8) and seeds collected at the radicle protrusion stage (WRD, KinRD) as previ-
ously described63. cDNAs were obtained using the RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher
Scientific, Milan, Italy) according to the manufacturer’s suggestions. qRT-PCR was carried out with the Maxima
SYBR Green qPCR Master Mix (2×) (ThermoFisher Scientific) according to supplier’s indications, using a
Rotor-Gene 6000 PCR apparatus (Corbett Robotics Pty Ltd, Brisbane, Australia). Amplification conditions were
as follows: denaturation at 95 °C for 10 min, and 45 cycles of 95 °C for 15 s and 60 °C for 60 s. Oligonucleotide
primers were designed using the Real-Time PCR Primer Design program from GenScript (https://www.gen-
script.com/ssl-bin/app/primer) and validated through the online software Oligo Analyzer (https://eu.idtdna. com/calc/analyzer) (Supplementary Table 1). Sequences were retrieved using the NCBI gene database (https://
www.ncbi.nlm.nih.gov/). For each oligonucleotide set, a no-template water control was used. Quantification was
carried out using the MtPDF2-PROTODERMAL FACTOR 2 (Medtr6g084690) as reference gene64 for the experi-
mental conditions (treated versus untreated) used in this work. The raw, background-subtracted fluorescence data
provided by the Rotor-Gene 6000 Series Software 1.7 (Corbett Robotics) was used to estimate PCR Efficiency (E)
and threshold cycle number (Ct) for each transcript quantification. The Pfaffl method65 was used for relative quan-
tification of transcript accumulation and statistic analysis performed with REST2009 Software V2.0.13 (Qiagen
GmbH, Hilden, Germany). Comet assay. For Comet assay analyses, water- and kinetin-imbibed seeds were collected at the radicle pro-
trusion stage (WRD, KinRD). Kinetin-treated seeds were collected starting from the 25th hour from the beginning
of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hour. Radicles were
cut with a razor blade and immediately frozen in liquid N2. Methods
l (Durham,
NC, U.S.A.) (www.metabolon.com), based on three independent platforms: ultra-high-performance liquid chro-
matography/tandem mass spectrometry (UHLC/MS/MS2) optimized for basic species, UHLC/MS/MS2 opti-
mized for acidic species, and gas chromatography/mass spectrometry (GC/MS), as described in Evans et al.59. Global metabolomic profiling was performed on methanol extracts from powdered frozen samples (100 mg) of
seeds imbibed with water for 2 h (W2), 8 h (W8) and seeds at the radicle protrusion stage (W_RD). Samples from
seeds imbibed with 0.50 mM kinetin for 2 h and 8 h (Kin2, Kin8), and seeds at the radicle protrusion stage (Kin_
RD) were also profiled. Metabolomic analyses were conducted onto biological triplicates. Each biological replicate
corresponds to a pool of at least 20 seeds. Data from seeds imbibed with water was previously described13 since
the kinetin treatment was part of a larger experimental design. Metabolites were identified by automated com-
parison of the ion features of the experimental samples with a reference library of chemical standard entries that
included retention time, molecular weight (m/z), preferred adducts, and in-source fragments as well as associated
MS/MS2 spectra and curated by visual inspection for quality control using an in-house resources59,60. Raw area
counts for each biochemical compound were normalized by dividing each sample value per sample fresh weight. Then, this value was rescaled by dividing each sample value by the median value for the specific biochemical. For missing data (nulls), the minimum observed values for that compound was imputed. Prior to data analysis,
scaled imputed data was log transformed. Metabolites were also mapped onto general biochemical pathways, as
provided in the Kyoto Encyclopedia of Genes and Genomes (KEGG) (www.genome.jp/kegg) and Plant Metabolic
Network (PMN) (www.plantcyc.org/).i y
g
For metabolomic profiling, Welch’s two-sample t-tests were used to determine whether or not each metabolite
had a significant change in abundance, focusing on comparisons between treated and non-treated samples for
the same timepoint (Kin2 versus W2; Kin8 versus W8 and KinRD versus WRD). Prior to statistical computations,
scaled imputed data were log transformed (natural logarithm). An estimate of false discovery rate for the list of
all identified compounds was also provided, taking into account the multiple comparison tests conducted in
metabolomic-based studies61. Metabolites that achieved statistical significance (P ≤ 0.05 and q ≤ 0.1) were con-
sidered differentially accumulated (DA) and selected for further analysis. Methods
l Plant materials, treatments, and phenotyping. For imbibition, M. truncatula seeds (Jemalong culti-
var, kindly provided by Dr. Ana Barradas, Fertiprado L.d.a., Vaiamonte-Monforte, Portugal) were sown in Petri
dishes (9 cm diameter) containing two filter papers moistened with 2.5 mL distilled water (control, W) or with
2.5 mL of 0.5 mM kinetin (6-furfurylaminopurine, Sigma-Aldrich, Milan, Italy) for phytohormone treatments. For germination tests, seeds were kept in a growth chamber at 22 °C under light conditions with a photon flux
density of 150 μmol m−2 s−1, photoperiod of 16/8 h and 70–80% relative humidity. For each treatment, five inde-
pendent replications with 20 seeds per replication were analyzed. Seeds with protrusion of the primary radicle
were considered germinated. Germination percentage, scored along two consecutive days after imbibition, and
the time to reach 50% germination (T50) were calculated as previously reported57. The time to obtain 50% germi-
nation (T50) was calculated according to the following formula of Coolbear et al.58, as modified by Farooq et al.57: =
+
−
−
−
N
T
t
(
/2
n )(t
t )
(n
n )
50
i
i
j
i
j
i where N is the final number of germinating seeds and nj and ni are the cumulative number of seeds germinated by
djacent counts at times tj and ti, respectively, when ni < N/2 < nj. h j
j
N values were annotated for each replicate until a plateau was reached, choosing the 10th day as the standard
timepoint to annotate them. The appearance of the first leaf on the resulting seedlings was scored during 14 days. Fresh and dry weights of imbibed seeds and seedlings were also measured. For molecular analyses, seeds were
harvested at the indicated time points, namely 2 h and 8 h of imbibition with water or with 0.5 mM kinetin and at
the post-germination stage (radicle protrusion; radicle length ≤ 3 mm). Due to the reduced T50 value observed in
the phytohormone-treated seeds, the sampling procedure for the radicle protrusion stage was conducted earlier
than for water-imbibed seeds. Kinetin-treated seeds were collected starting from the 25th hour from the beginning Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 9 www.nature.com/scientificreports/ of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hour. All the sam-
ples were weighed and stored in liquid N2. Metabolomic profiling. Non-targeted metabolomic profiling was performed by Metabolon Inc. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Methods
l For each sample, 300 μL TE buffer (0.4 M Tris HCl pH
7.4, 1 mM EDTA) was added to the frozen tissues that were quickly and gently chopped with a sharp razor blade
to release the nuclei as described by Macovei et al.66. For each treatment, two independent experiments were car-
ried out with three independent replications (10 radicles per replication). Nuclei were extracted from M. truncat-
ula radicles as reported13. The suspension containing the purified nuclei and a solution containing 1% low melting
point agarose (Sigma-Aldrich) in phosphate-buffered saline (PBS) at 37 °C were mixed in equal volume. Aliquots
(120 μL each) were pipetted onto agarose pre-coated slides and solidified on ice. Slides were incubated for 20 min
at room temperature in high salt lysis buffer (2.5 M NaCl, 100 mM Tris-HCl pH 7.5, 100 mM EDTA) to disrupt
the nuclear membrane. Nuclei were denatured in alkaline buffer (1 mM Na2EDTA, 300 mM NaOH, pH > 13) for
30 min at 4 °C and then electrophoresed in the same buffer for 25 min at 0.72 V cm−1 in a cold chamber. After
electrophoresis, slides were washed twice in 0.4 M Tris-HCl pH 7.5 for 5 min, rinsed once in 70% ethanol (v/v) for
12 min at 4 °C and dried at room temperature overnight. Exposure to alkaline conditions causes DNA unwind-
ing and visualization of strand breaks. Slides were stained with 20 μL DAPI (4′-6-Diamidine-2′-phenylindole Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 10 www.nature.com/scientificreports/ dihydrochloride; 1 μg mL−1, Sigma-Aldrich). For each slide, one hundred nucleoids were scored, using a fluores-
cence microscope (Olympus BX51, Olympus Italia S.R.L.) with an excitation filter of 340–380 nm and a barrier fil-
ter of 400 nm. Nucleoids were classified and results were expressed in arbitrary units (a.u.) according to Collins67. Electron paramagnetic resonance. EPR analyses were carried out as reported13 on the water- and
kinetin-treated seeds collected at 2 h, 8 h of imbibition and at the radicle protrusion stage. Seeds were transferred
in quartz tubes, quickly frozen with liquid N2 and then stored in liquid N2. EPR spectra were recorded at 120 K
with a Bruker EMX-10/12 spectrometer (Bruker BioSpin GmbH, Karlsruhe, Germany) operating in X-band,
equipped with an ER4119HS cavity and a temperature controller. Two different instrument settings were used to
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performance in developing countries. A meta-analysis. Agron. Sustain. Dev. 38, 64 (2018). 27. Finch-Savage, W. E. & Bassel, G. W. Seed vigour and crop establishment: extending performance beyond adaptation. J. Exp. Bot. 67,
567–591 (2015). 28. Macovei, A. et al. Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germin
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29. Han, C., Zhen, S., Zhu, G., Bian, Y. & Yan, Y. Comparative metabolome analysis of wheat embryo and endosperm reveals the
dynamic changes of metabolites during seed germination. Plant Physiol. Biochem. 115, 320–327 (2017). 30. Kazmi, R. H. et al. Metabolomic analysis of tomato seed germination. Metabolomics 13, 145 (2017). Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 11 Acknowledgementsh g
This work was supported by Regione Lombardia D.G. Attività Produttive Ricerca e Innovazione - Struttura Asse
1 POR FSE 2007-2013, Project ID 4344853 and CARIPLO Foundation (Action 3, Code 2013-1727) ‘Advanced
Priming Technologies for the Lombardy Agro-Seed Industry-PRIMTECH’. The research was also supported by
CARIPLO Foundation in the frame of the WAKE-APT project (Code 2016-0723) (‘Seed Wake-up with Aptamers:
a New Technology for Dormancy Release and Improved Seed Priming’) and by the Italian Ministry of Education, Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 12 www.nature.com/scientificreports/ University and Research (MIUR): Dipartimenti di Eccellenza Program (2018–2022) - Dept. of Biology and
Biotechnology “L. Spallanzani”, University of Pavia (to A.P., A.M., A.B.). The financial support from Fundação
para a Ciência e a Tecnologia (Lisbon, Portugal) is acknowledged through research unit GREEN-it “Bioresources
for Sustainability” (UID/Multi/04551/2013) and S.A. Post-Doctoral Grant (SFRH/BPD/108032/2015) and present
S.A. Ph.D. holder contract (DL57). Sponsorship from COST Action FA1306: ‘The quest for tolerant varieties:
phenotyping at plant and cell level’ is gratefully acknowledged. A.P. has been awarded by a Ph.D. Fellowship from
IUSS-Scuola Universitaria Superiore Pavia. The authors would like to thank Dr. Danny Alexander (Metabolon,
US) for his support during the preparation of this manuscript. Author Contributions A.B., A.M. and Sd.S.A. conceived the work and wrote the manuscript. A.P., D.D., S.L. and E.P. contributed to the
experimental data. D.D. and S.L. carried out EPR analyses. A.P. and Sd.S.A. performed bioinformatic analyses. A.B., A.M., Sd.S.A., A.P. and D.D. contributed to the discussion of data. All authors read and agreed with the final
version of the manuscript. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-46866-6 Competing Interests: The authors declare no competing interests. Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and
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mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 13 |
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(CC BY 3.0) licence. Full details of this licence are available at: http://creativecommons.org/licenses/by/3.0/ LICENCE LICENCE 1
Introduction specific system performance need to be taken into account. Thus,
it is not sufficient to just replace missing data with previous data,
or
any
alternative
method
that
does
not
consider
actual
meteorological conditions as this may introduce significant errors. Rather,
the
method
presented
here
considers
local
weather
phenomena and their relationship to performance variations of the
actual
PV
systems. This
requires
two
elements,
assessing
meteorological as well as electrical data as both systems may fail
independently. The number of photovoltaic (PV) installations in the UK has
increased from a few tens of MWp in 2010 to more than 6 GWp
in June 2015 [1], indicating that PV is a rapidly growing industry. The
majority
of
these
systems
will
operate
as
financial
investments, and in order to manage investment risk associated
with system yield shortfalls, many larger scale PV systems are
covered by energy performance guarantees. These are commonly
based on attaining a specified performance ratio (PR), as this
allows for location-specific variations in meteorological conditions. Energy yield, and to a lesser extent, PR are key performance
indicators for owners, investors and operators and they can only be
obtained
through
effective
monitoring
of
PV
systems,
as
highlighted in several studies [2–5]. However, due to malfunctions
such as power outages, communication failures or component
faults, data may be incomplete. This will affect, as shown below,
the PR calculated for the system and may hide incidents that
would trigger warranty cases or cause unnecessary warranty
claims. There are no validated strategies that deal with this issue,
particularly in maritime climates such as the UK, and any attempts
to backfill data using previous dates or days from previous years
are at best temporary with very high uncertainty attached to these
methods. This is because such strategies do not take into account
variable weather systems or PV component degradation. Utilising
average values from dates close to the missing period may give an
estimation of PR, but such methods are not adequate to estimate
long-term energy yields of the system, especially when missing
periods are extended from a few weeks to even months. Therefore,
an issue remains of how to back-fill lost data values, and to arrive
at a valid monthly or annual PR which is required in order to
verify the warranties or to predict return on investment. REPOSITORY RECORD Koumpli, Elena, Diane Palmer, Paul Rowley, and Ralph Gottschalg. 2016. “Inference of Missing Data in
Photovoltaic Monitoring Datasets”. Loughborough University. https://hdl.handle.net/2134/20351. IET Renewable Power Generation Research Article IET Renew. Power Gener., pp. 1–6
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) Inference of missing data in photovoltaic
monitoring datasets ISSN 1752-1416
Received on 30th July 2015
Revised on 1st October 2015
Accepted on 9th November 2015
doi: 10.1049/iet-rpg.2015.0355
www.ietdl.org ISSN 1752-1416
Received on 30th July 2015
Revised on 1st October 2015
Accepted on 9th November 2015
doi: 10.1049/iet-rpg.2015.0355
www.ietdl.org ane Palmer, Paul Rowley, Ralph Gottschalg
ergy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough
h, LE11 3TU, UK Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg
Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough
University, Loughborough, LE11 3TU, UK
✉E-mail: E.Koumpli@lboro.ac.uk Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg
Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough
University, Loughborough, LE11 3TU, UK
✉E-mail: E.Koumpli@lboro.ac.uk Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg
Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough
University, Loughborough, LE11 3TU, UK
✉E-mail: E.Koumpli@lboro.ac.uk Abstract: Photovoltaic (PV) systems are frequently covered by performance guarantees, which are often based on
attaining a certain performance ratio (PR). Climatic and electrical data are collected on site to verify that these
guarantees are met or that the systems are working well. However, in-field data acquisition commonly suffers from
data loss, sometimes for prolonged periods of time, making this assessment impossible or at the very best introducing
significant uncertainties. This study presents a method to mitigate this issue based on back-filling missing data. Typical
cases of data loss are considered and a method to infer this is presented and validated. Synthetic performance data is
generated based on interpolated environmental data and a trained empirical electrical model. A case study is
subsequently used to validate the method. Accuracy of the approach is examined by creating artificial data loss in two
closely monitored PV modules. A missing month of energy readings has been replenished, reproducing PR with an
average daily and monthly mean bias error of about −1 and −0.02%, respectively, for a crystalline silicon module. The
PR is a key property which is required for the warranty verification, and the proposed method yields reliable results in
order to achieve this. (i) Root-mean-square error (RMSE)
(ii) Mean absolute error (MAE)
(iii) Mean bias error (MBE) The RMSE describes the random error in a distribution and tends
to increase with outliers, MAE describes the absolute error and MBE
indicates whether the model overestimates or underestimates the
measurement value, which is also expressed as the ‘systematic’
error of the distribution. MBEs close to zero signify an unbiased
distribution. It should be noted that, although the word ‘error’ is
commonly used in statistical analysis, ‘difference’ would here be 1
Introduction Meteorological data for the missing period is obtained here from
interpolating
from
a
network
of
about
80
meteorological
monitoring stations operated by the UK met-office [6]. The local
irradiance is calculated from interpolating these using Kriging [7]
and correcting the horizontal irradiance to the site installation by
employing separation, into beam and diffuse, and translation, into
plane of the array, algorithms. The same interpolation technique is
applied for ambient temperature. Ambient temperature is corrected
to module temperature by employing a simple thermal model. The
method is described in more detail in Sections 2.1 and 2.2. The energy output of missing periods is estimated using an
empirical
electrical
model. The
underlying
coefficients
are
obtained by ‘training’ the model with the available past data (see
Section 2.3), i.e. determining system specific characteristics. The
validity of the proposed method is assessed using the following
metrics: 2.1
Irradiance and temperature interpolation The analysis is based on meteorological data, namely global
horizontal irradiation and ambient temperature, acquired from
more than 80 ground meteorological stations on a national scale
through Met Office Integrated Data Archive System (MIDAS) [6]. The PR of a PV system depends on the irradiation (H in Wh/m2)
received according to (1) PR = (E · GSTC)
(H · PSTC)
(1) (1) where E is the energy output (Wh), PSTC (W) and GSTC (W/m2) are
the nominal power of the system and irradiance at Standard Testing
Conditions (STC), respectively. Horizontal irradiance is interpolated to a grid of points. The
nearest point of the PV system is selected and separation (Ridley
et al. [9]) and translation algorithms (Hay et al. [10] with Reindl
correction [11]) are employed to calculate in-plane irradiance
given that the location, orientation and tilt of the system are
known. The specific separation model was chosen based on
empirical observations, which demonstrated that it delivered the
best results in comparison with several separation algorithms for
UK [7]. Similarly, a previous work in Loughborough [12] has
shown that the all-sky model by Reindl et al. delivers the best
results for the UK climate. Both the horizontal irradiation and the
ambient temperature data are interpolated using Kriging, which
has been proven to perform well in comparison with various
climate data interpolation methods [7, 13]. IET Renew. Power Gener., pp. 1–6
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 2.3
Extraction of the fitting coefficients Quality checks are a critical step in every data analysis, the aim of
which is to identify outliers that could corrupt the training process. Thus,
the
quality
checks
applied
here
focused
on
module
temperature, irradiation and maximum power output. Graphical
representation of the above parameters as well as logical controls
based on (1) and (2) were employed according to the analyses
described in [22, 23]. Only unshaded and fault-free systems were
considered for this study. The training algorithm is key for the acquisition of the optimum
system’s coefficients, as it has been shown that device-specific
characteristics, and thus implicitly the system characteristics, are
one of the two uncertainties determining the model accuracy [20]. The requirements for the training need to be determined in terms
of optimal training set’s size and how recent it should be with
respect to the missing period of data, in order to achieve
maximum agreement. System performance is affected by both
meteorological
seasonal
variations
as
well
as
by
module
technology [24, 25]. This seasonal nature of system performance is
expected to have an impact upon the determination of the
optimum training set. This study concluded that in all cases, the
training set should maintain close proximity to the missing period,
as this provides a better fit. More specifically, an average of 20
days before and 20 days after the missing set was found to be a
sufficient data pool for the particular location, regardless of the
position of the missing set throughout the year (i.e. during summer
or winter etc.). here has the following form [19] here has the following form [19] more appropriate since the true values are not actually known, as
sensor uncertainty is not taken into account. P′(G′, T′) = G′ · (1 + k1ln(G′) + k2ln(G′)2
+ k3T′
m + k4T′
mln(G′) + k5T′
mln(G′)2 + k6T′2
m )
(3) y
Real measurements of in-plane irradiation, ambient and module
temperature, as well as energy output were used for the validation. The datasets used were specifically from two PV modules from
CREST’s
outdoor
monitoring
system
(COMS3)
[8]
whose
properties are listed in Table 1. (3) where P′ = PMP/PSTC, G′ = G/GSTC and T ′
m = Tm–TSTC (STC =
Standard Testing Conditions) and PMP is the maximum power. The model yields a ‘3D power surface’. This model has been
compared with a number of other models [20] where it was found
that it performed well for a range of PV module technologies, on
predicting annual energy output and it is also possible to combine
measured data from many PV modules to obtain a general model
for a given PV technology [19]. By changing the PSTC, (3) can be
used to describe an entire PV system. In this study, defining the
coefficients for a specific system is essentially training the model
based on the specific system characteristics and re-using the
coefficients to predict the output of the missing period. Energy
generation is calculated using sums of hourly averaged maximum
power output. For the training process, past data are fed into the
model and the coefficients (k1–k6) are determined by means of a
Marquardt–Levenberg optimisation algorithm [21]. To assess the
reliability of the results, data quality checks and a training
algorithm were used to determine the optimum training set for the
model. 2
Methodology development and validation Given the aim is to back-fill missing periods appropriately, then in
order to infer data reliably, actual weather patterns as well as 1 1 Name
Module type
Tilt angle, o
Orientation
Nominal power, W
Mounting type
Data origin
module A
crystalline silicon (c-Si)
32.5
south
245.0
open-rack
CREST outdoor monitoring system
module B
polycrystalline silicon (pc-Si)
32.5
south
245.0
open-rack
CREST outdoor monitoring system 2.2
Thermal and electrical model Module temperature is calculated from in-plane irradiance and
ambient temperature using the thermal model presented in [14] Tm = Ta + k · G
(2) (2) where Tm (K), Ta (K) and G (W/m2), are module temperature,
ambient temperature and in-plane irradiance, respectively. The k,
or Ross coefficient is the modified thermal resistance of the
module,
modified
in
terms
of
influence
of
the
mounting
configuration of the array [15] a typical value of which is 0.02
(K·m2/W) for free-standing modules [16]. Ross’s model is a good
choice in cases where irradiance and ambient temperature are the
only available weather data. Furthermore, k can be readily
obtained using outdoor measurements of module and ambient
temperature and horizontal irradiance. In this work, k was obtained
experimentally for each module by linear fitting of (Tm–Ta) against
G for one year’s worth of data. Equation (2) was used by taking
the hourly values of irradiance as proposed in [17]. The training algorithm was applied separately for each one of the
PV modules in Table 1. For the training process, past data were
analysed using (3). The optimal training set was chosen based
upon the lowest RMSE achieved and R2 values, in combination
with the size of the training set. The training size was defined as
the number of days before (noted as negative, going backwards in
time) and after (noted as positive, going forwards in time) the
missing period. The input training data were hourly measurements
of power, module temperature and in-plane irradiance. Here, 1 The electrical model was chosen based on both the available input
data and its training capability. The chosen electrical model plays the
role of the ‘learning machine’. It is based on a simplified King’s
model for the maximum power point [18] and the formula used 2 Fig. 1
Plots of
a Training sets around the missing period taking as starting points the 31st of May and
the 1st of July 2014, and going backwards and forwards in time, respectively
b Fitting curve for the optimum training set (15 days backwards and 26 days forwards)
for module A It can be seen in Fig. 1a that although RMSE does not vary
significantly across different training sets, there is a specific (red)
area where it showed its lowest values. This area includes points
that are closer to the missing period, which can be justified as
seasonal dependence. 2.2
Thermal and electrical model The results also showed that very small
training sets yielded the highest RMSE, e.g. using only several
days before and after the missing period was not a sufficient data
pool. This seems to be due to location and the local weather
phenomena, whereas smaller training sets, are expected to suffice
for less variable weather systems (for example, a Mediterranean
summer). The choice of the training set’s size plays an important
role as it must be large enough in order to obtain the optimal
model coefficients which are then used to predict the energy
output for the missing period. The training algorithm defined the best set of coefficients (k1–k6)
which then provided the power surface shown in Fig. 1b. The
optimal training size for this case was found to be 41 days in total. Finally, the training process yields valid results if no significant
changes (i.e. component failures) have occurred in the PV system
during its operation while no data are available (i.e. during the
missing period). IET Renew. Power Gener., pp. 1–6
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 3.1
Analysis of interpolated climatic data The following analysis is carried out for 1 year (2014). Irradiation
(horizontal and in-plane) and ambient temperature comparisons
with real measurements are shown in Figs. 2a and b and the
statistical results are presented in Table 2. The method works well
for horizontal irradiation, with a monthly RMSE of 2.8% and
MBE of 1.5%. Ambient temperature is also well described with
RMSE and MBE of 0.15 and −0.14% (in Kelvin), respectively. Fig. 1
Plots of a Training sets around the missing period taking as starting points the 31st of May and
the 1st of July 2014, and going backwards and forwards in time, respectively
b Fitting curve for the optimum training set (15 days backwards and 26 days forwards)
for module A a Training sets around the missing period taking as starting points the 31st of May and
the 1st of July 2014, and going backwards and forwards in time, respectively
b Fitting curve for the optimum training set (15 days backwards and 26 days forwards)
for module A A noticeable deterioration in the statistic metrics is noted for
in-plane irradiation, which is primarily due to the sub-models
used in the process of translation of global horizontal irradiation
into the plane of array. This is to be anticipated, as separation month of missing data was considered (June 2014). This period was
removed from the training set and was used as the validation set for
the training algorithm. Fig. 2
Comparison of
a Global horizontal (GHI) and plane-of-array irradiation (POA)
b Ambient temperature for measured and interpolated data throughout a year (2014) Fig. 2
Comparison of
a Global horizontal (GHI) and plane-of-array irradiation (POA)
b Ambient temperature for measured and interpolated data throughout a year (2014)
Table 2
Statistical results for annual analysis with measured and interpolated climatic data
Ambient temperature, K
POA irradiation, kWh/m2
GHI, kWh/m2
Monthly
Annual
Monthly
Annual
Monthly
Annual
RMSE
0.43
0.40
8.92
97.4
2.13
14.3
MAE
0.40
0.40
8.12
97.4
1.75
14.3
MBE
−0.40
−0.40
−8.12
−97.4
1.20
14.3
RMSE, %
0.15
0.14
9.79
8.91
2.79
1.54
MAE, %
0.14
0.14
8.91
8.91
2.30
1.54
MBE, %
−0.14
−0.14
−8.91
−8.91
1.56
−1.54
IET Renew. Power Gener., pp. 1–6
3
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) Fig. 2
Comparison of Fig. IET Renew. Power Gener., pp. 1–6
3
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 3.2
Inferring missing meteorological and electrical data 3.2
Inferring missing meteorological and electrical data (global irradiance to beam and diffuse) and translation algorithms
add a high percentage random and bias error, which varies
amongst different models and locations [26]. However, there is
potential for improvement in determining the optimum separation
model for the UK climate. Thus generally, the results depend
strongly on the climatic profile of the location and the choice of
models. In-plane irradiation is generally underestimated, with
some days giving better results than others. A further analysis
based on different irradiation bins and clearness indices shows
that the random error derives mainly for low irradiation and
partly cloudy days as seen in Figs. 3a and b. Clearness index
was calculated using [27] and the days were classified according
to Gul et al. [28]. Concurrent energy yield readings and a climatic dataset were utilised
containing a 1 month period of missing data (June 2014), during
which neither of the above information was available. In order to
validate the modelling results, this period was completely removed
from the initial dataset and was treated as the ‘missing’ period. To
calculate energy output, (3) is employed twice. Initially, it is used
with
hourly
measured
data
of
in-plane
irradiation,
module
temperature and energy output to extract the model coefficients
using a training period as defined using the training algorithm
described in 0. Then, it is applied again to calculate the energy
output for the missing month, using interpolated climatic data only
for this period. Aggregated irradiation is calculated using hourly
sums of irradiance. Module temperature for the missing period is
calculated using (2) with interpolated irradiation and ambient
temperature
as
input
parameters. Comparisons
between
the
obtained results and actual measurements for the missing period
are shown in Figs. 4 and 5, followed by the statistical results in
Tables 3 and 4. The width and the number of the irradiation bins were adjusted
considering the frequency of irradiation values, so that RMSE in
different bins is affected by the same number of observations. Lower irradiation values present a higher percentage RMSE which
however is small in terms of absolute energy yield (Wh). The data
points in Fig. 3a represent the calculation bias, which changes
according to clearness index. , pp
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 3.1
Analysis of interpolated climatic data 2
Comparison of a Global horizontal (GHI) and plane-of-array irradiation (POA)
b Ambient temperature for measured and interpolated data throughout a year (2014) a Global horizontal (GHI) and plane-of-array irradiation (POA)
b Ambient temperature for measured and interpolated data throughout a year (2014) Table 2
Statistical results for annual analysis with measured and interpolated climatic data
Ambient temperature, K
POA irradiation, kWh/m2
GHI, kWh/m2
Monthly
Annual
Monthly
Annual
Monthly
Annual
RMSE
0.43
0.40
8.92
97.4
2.13
14.3
MAE
0.40
0.40
8.12
97.4
1.75
14.3
MBE
−0.40
−0.40
−8.12
−97.4
1.20
14.3
RMSE, %
0.15
0.14
9.79
8.91
2.79
1.54
MAE, %
0.14
0.14
8.91
8.91
2.30
1.54
MBE, %
−0.14
−0.14
−8.91
−8.91
1.56
−1.54 Table 2
Statistical results for annual analysis with measured and interpolated climatic data IET Renew. Power Gener., pp. 1–6
3
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) IET Renew. Power Gener., pp. 1–6 Fig. 3
Statistical analysis on hourly irradiation bins Fig. 3
Statistical analysis on hourly irradiation bins
a %RMSE and %MBE
b Normalised contribution to RMSE of hours with different clearness index Kt Fig. 3
Statistical analysis on hourly irradiation bins
a %RMSE and %MBE
b Normalised contribution to RMSE of hours with different clearness index Kt Fig. 3
Statistical analysis on hourly irradiation bins Fig. 3
Statistical analysis on hourly irradiation bins
a %RMSE and %MBE
b Normalised contribution to RMSE of hours with different clearness index Kt IET Renew. Power Gener., pp. 1–6
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 3.2
Inferring missing meteorological and electrical data It seems that the method tends to
underestimate higher irradiance (negative MBE) which present a
higher bias error, whereas for irradiance values lower than 100 W/
m2 the result is slightly overestimated (positive MBE). This is due
to the separation into beam and diffuse algorithms which tend to
overestimate diffuse radiation for days with higher clearness index. Partly cloudy days contribute significantly to the overall error for
the majority of the bins. The results for ambient temperature show that it can be
interpolated to the location of interest with a very small MBE and
RMSE. This is to be expected, as temperature is temporally and
spatially
more
homogeneous than
irradiance
over
the
same
distance
for
the
UK
climate. MBE
increases
for
module
temperature due to error propagation from both in-plane irradiation
(inherent underestimation) and ambient temperature, but the effect Fig. 4
Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature
for
a Module A Fig. 4
Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature
for Fig. 4
Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature
for
a Module A
b Module B Fig. 4
Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature
for
a Module A
b Module B a Module A
b Module B 4 Fig. 5
Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for
a Module A
b Module B Fig. 5
Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for
a Module A Fig. 3.2
Inferring missing meteorological and electrical data 5
Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for
a Module A
b Module B Table 3
Statistical results for in-plane irradiation and module temperature comparisons Table 3
Statistical results for in-plane irradiation and module temperature comparisons
In-plane irradiation
(kWh/m2)
Module temperature, K
Module A
Module B
Daily
Monthly
Daily
Monthly
Daily
Monthly
RMSE
0.70
8.3
2.78
2.24
2.67
2.31
MAE
0.50
8.3
2.35
2.24
2.33
2.31
MBE
−0.28
−8.3
−0.76
−2.24
−0.89
−2.31
RMSE, %
14.9
5.9
0.93
0.75
2.31
0.77
MAE, %
10.5
5.9
0.78
0.75
2.31
0.77
MBE, %
−5.9
−5.9
−0.76
−0.75
−2.31
−0.77 Table 4
Statistical results for energy output and PR for the two modules
Energy output, kWh
Performance ratio, PR
Module A
Module B
Module A
Module B
Daily
Monthly
Daily
Monthly
Daily
Monthly
Daily
Monthly
RMSE
0.15
1.81
0.14
1.50
0.040
0.0002
0.042
0.007
MAE
0.11
1.81
0.11
1.50
0.026
0.0002
0.030
0.007
MBE
−0.06
−1.81
−0.05
−1.50
−0.009
−0.0002
−0.0024
−0.007
RMSE, %
14.5
5.92
14.4
5.09
4.39
0.016
4.85
0.86
MAE, %
10.8
5.92
10.8
5.09
2.90
0.016
3.44
0.86
MBE, %
−5.92
−5.92
−5.09
−5.09
−0.97
−0.016
−0.28
−0.86
Fig. 6
Scatter diagrams for module A, of hourly modelled and measured for the missing month (June 2014)
a In-plane irradiation
b Energy output Table 4
Statistical results for energy output and PR for the two modules Fig. 6
Scatter diagrams for module A, of hourly modelled and measured for the missing month (June 2014)
a In-plane irradiation
b Energy output IET Renew. Power Gener., pp. 1–6
This is an open access article published by the IET under the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/3.0/) 5 is very small with a maximum deviation of about 5° and average
deviation of about 2°. Infrastructure and Society’ project which is funded by the RCUK’s
Energy Programme (contract no: EP/K02227X/1). Infrastructure and Society’ project which is funded by the RCUK’s
Energy Programme (contract no: EP/K02227X/1). The results for energy output errors are a propagation of irradiation
and module temperature. The negative bias which arises primarily
due to irradiation is evident also in energy output and in terms of
absolute RMSE for energy output, that is 1.8 and 1.5 (in kWh) for
modules A and B, respectively. 4
Conclusions 13
Hofstra, N., Haylock, M., New, M., et al.: ‘Comparison of six methods for the
interpolation of daily, European climate data’, J. Geophys. Res., 2008, 113,
(D21), doi:10.1029/2008JD010100 A method to replenish missing meteorological and electrical data
(not) obtained during PV system operation was developed and
validated for a polycrystalline and a monocrystalline PV module. The method is based on interpolating meteorological data and
translating it to the local climate (namely in-plane irradiation and
module temperature) governing the device performance. The local
climate data are then used to calculate the electrical output of the
system. This approach is validated against data from a precision
measurement system. 14
Ross Jr., R.G.: ‘Interface design considerations for terrestrial solar cell modules’. 12th Photovoltaic Specialists Conf., Baton Rouge, LA, USA, November 1976,
pp. 801–806 15
Skoplaki, E., Palyvos, J.A.: ‘Operating temperature of photovoltaic modules: a
survey of pertinent correlations’, Renew. Energy, 2009, 34, (1), pp. 23–29 16
Nordmann, T., Clavadetscher, L.: ‘Understanding temperature effects on PV
system performance’, Energy Convers., 2003, 3, pp. 2–5 17
Segado, P.M., Carretero, J., Sidrach-de-Cardona, M.: ‘Models to predict the
operating temperature of different photovoltaic modules in outdoor conditions’,
Prog. Photovolt. Res. Appl., 2014, 23, (10), pp. 1267–1282 There are noticeable differences in terms of the absolute energy
production, while the estimation of the PR shows excellent
agreement for both PV technologies. This means that the key
property for assessing system quality can be replenished accurately
with the given method and thus this is sufficient for evaluating
real-time continuous performance. The PR is the key parameter
required for warranty verification, and the method is highly
successful for achieving this. Detailed investigation of the relative
underestimation of the energy yield of a system identified that the
error is almost exclusively due to the irradiance translation to
plane of array and thus further efforts will focus on this. The
largest bias is seen for high irradiance conditions, while the
highest scatter is seen for lower irradiances but the reasons for this
are not yet entirely clear. 18
Kratochvil, J.A., Boyson, W.E., King, D.L.: ‘Photovoltaic array performance
model’. SAND2004-3535, Sandia National Laboratories (SNL), 2004 19
Huld, T., Friesen, G., Skoczek, A., et al.: ‘A power-rating model for
crystalline silicon PV modules’, Sol. Energy Mater. Sol. Cells, 2011, 95, (12),
pp. 4
Conclusions 3359–3369 pp
20
Dittmann, S., Friesen, G., Williams, S., et al.: ‘Results of the Third modelling
round robin within the European project performance’ – comparison of module
energy rating methods’. 25th European Photovoltaic Solar Energy Conf. and
Exhibition/Fifth World Conf. on Photovoltaic Energy Conversion, Valencia,
Spain, September 2010, pp. 4333–4338 p
p
pp
21
Lourakis, M.I.A.: ‘A brief description of the Levenberg–Marquardt algorithm
implemented by levmar’, Found. Res. Technol., 2005, 4, pp. 1–6 22
Strobel, M.B., Betts, T.R., Friesen, G., et al.: ‘Uncertainty in photovoltaic
performance parameters – dependence on location and material’, Sol. Energy
Mater. Sol. Cells, 2009, 93, (6–7), pp. 1124–1128 (
) pp
23
Firth, S.K., Lomas, K.L., Rees, S.J.: ‘A simple model of PV system performance
and its use in fault detection’, Sol. Energy, 2010, 84, (4), pp. 624–635 Finally, the next step is to scale this study up to a specific set of
data, such as a number of PV systems in close geographic
proximity, for example, over a given urban area. This will require
simulation of the entire PV system, i.e. take into consideration
inverter and shading effects. This task is currently ongoing [29]
and together with the work carried out in this study, it will enable
automated analysis of domestic systems over a larger area. 24
Carr, A.J., Pryor, T.L.: ‘A comparison of the performance of different PV module
types in temperate climates’, Sol. Energy, 2004, 76, (1–3), pp. 285–294 yp
p
gy
(
) pp
25
Gottschalg, R., Betts, T.R., Eeles, A., et al.: ‘Influences on the energy delivery of
thin film photovoltaic modules’, Sol. Energy Mater. Sol. Cells, 2013, 119,
pp. 169–180 26
Lave, M., Hayes, W., Pohl, A., et al.: ‘Evaluation of global horizontal irradiance to
plane-of-array irradiance models at locations across the united states’, IEEE
J. Photovolt., 2015, 5, (2), pp. 597–606 ,
,
, ( ), pp
27
Iqbal, M.: ‘An introduction to solar radiation’ (Academic Press, London, 1983) 28
Gul, M., Muneer, T., Kambezidis, H.: ‘Models for obtaining solar radiation from
other meteorological data’, Sol. Energy, 1998, 64, (98), pp. 99–108 28
Gul, M., Muneer, T., Kambezidis, H.: ‘Models for obtaining solar ra 3.2
Inferring missing meteorological and electrical data Crucially, the monthly PR can be
predicted with a very small error for both cases and more
specifically, with RMSE of about 0.0002 and 0.007 for modules A
and B, respectively. A comparison of the above graphs, shows that
for days where temperature is particularly low, measured PR is
high and may slightly exceed 1.0, leading to a small deviation
from the modelled value. Module temperature plays a significant
role in modelling the energy output, which however is not directly
evident in the PR. Namely, if in-plane irradiation is overestimated
(Fig. 4), modelled energy output (Fig. 5) is affected by both
in-plane irradiation and module temperature rise. The modelled
result is very close to the measured energy output (where actual
in-plane irradiation is lower) and thus, modelled PR is slightly
lower than the measured value. This behaviour is particularly
evident for days with lower average of module temperature (i.e. low ambient temperature and/or windy days). 6
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https://openalex.org/W2924097500 | https://europepmc.org/articles/pmc6246055?pdf=render | English | null | Dermoscopy features of acquired reactive perforating collagenosis: a case series | Dermatology practical & conceptual | 2,018 | cc-by | 1,556 | Received: December 4, 2017; Accepted: April 20, 2018; Published: October 31, 2018 Received: December 4, 2017; Accepted: April 20, 2018; Published: October 31, 2018 Copyright: ©2018 Ormerod et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: None. Competing interests: The authors have no conflicts of interest to disclose. Competing interests: The authors have no conflicts of interest to disclose. All authors have contributed significantly to this publication. All authors have contributed significantly to this publication. Corresponding author: Emma Ormerod, MA, MRCP, Bristol Dermatology Unit, Bristol Royal Infirmary, Marlborough Street, Bristol BS2
8HW. Email: Emma.ormerod@uhbristol.nhs.uk collagen fibers accumulate in dermal papillae and epidermal
hyperplasia may be seen. In more established lesions a cup-
shaped depression of the epidermis develops with an overlying
keratin plug containing inflammatory cells, keratinous debris,
and collagen fibers [4,5]. Vertically oriented collagen fibers,
stained red by elastic van Gieson staining or blue by Masson’s
trichrome stain, are extruded through the epidermis and there
may be a mild perivascular lymphohistiocytic infiltrate. Introduction Reactive perforating collagenosis (RPC) is a rare disorder in
which abnormal collagen fibers extrude through the epider
mis. In the acquired form, erythematous keratotic papules
and plaques with firmly adherent central crust and ulceration
develop, commonly on the trunk and extremity extensor
surfaces, and often at sites of superficial trauma [1]. Intense
itch is common. Acquired RPC is often associated with long-
standing diabetes and chronic renal failure, particularly in
patients undergoing dialysis [2,3]. Dermoscopy is a noninvasive technique which is now
a standard tool used in the preoperative clinical diagnosis
of skin tumors [6]. It is also increasingly used to aid in
the diagnosis in other dermatological conditions including
inflammatory dermatoses [7,8]. To our knowledge, the der
moscopic features of RPC have been described in 2 previous
case reports [9,10]. Here we report the dermoscopic findings
in a series of 5 patients with RPC. However, because RPC is uncommon, the clinical presen
tation can vary between patients, and it can be difficult to
differentiate clinically from other conditions, the true diagno
sis is often missed or delayed. Differential diagnosis includes
ecthyma, prurigo nodularis, perforating granuloma annulare,
dermatitis artefacta, and other perforating diseases [4]. Clini
cal diagnosis of RPC is supported or confirmed by charac
teristic histopathological features in most cases, although
repeated biopsies may be required. Histological features vary
according to stage of disease; in the early stages degenerate Dermoscopy features of acquired reactive
perforating collagenosis: a case series
Emma Ormerod1, Ausama Atwan2, Laszlo Intzedy3, Natalie Stone2 1 Dermatology Department, Bristol Royal Infirmary, Bristol, UK Key words: dermoscopy, perforating collagenosis, acquired, diagnostics Key words: dermoscopy, perforating collagenosis, acquired, diagnostics Citation: Ormerod E, Atwan A, Intzedy L, Stone N. Dermoscopy features of acquired reactive perforating collagenosi
Dermatol Pract Concept. 2018;8(4):303-305. DOI: https://doi.org/10.5826/dpc.0804a11 Case Presentations We identified 5 patients with a diagnosis of acquired RPC in
our department over the past 2 years. Case notes, pathology 303 Letter | Dermatol Pract Concept 2018;8(4):11 Figure 1. Macroscopic images of the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormerod et al.] Figure 1. Macroscopic images of the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormerod et al.] Figure 2. Dermoscopic images of a typical lesion from the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormer
od et al.] Figure 2. Dermoscopic images of a typical lesion from the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormer
od et al.] onset of his skin problems; he subsequently started a regi
men of low molecular weight heparin. Routine blood values,
including renal function, were normal. Skin biopsy showed
ulceration of epidermis, acute and chronic inflammation at
the ulcer base with leukocytoclasis, and a perivascular chronic
inflammatory infiltrate in the mid-dermis. reports, and dermoscopy pictures were analyzed. Dermo
scopic images were taken using a digital dermoscopy system
(Nikon D33S camera [Nikon, Tokyo, Japan]; Heine Delta®
20T Dermatoscope [Heine Optotechnik, Herrsching, Ger
many]). Minimal pressure was applied and ultrasound gel was
used during the process to help preserve vessel morphology
as much as possible. Patient 3. A 58-year-old man with a previous diagnosis of
sarcoidosis was taking no regular medications. Routine blood
values at the time of presentation were normal. Skin biopsy
from an ulcer showed florid reactive changes and vertically
oriented collagen fibers at the ulcer base consistent with RPC. Renal function was normal. There were 3 female and 2 male patients, with age rang
ing from 53 to 83 years. All of them gave a history of a very
itchy rash, affecting the trunk and/or lower limbs. The rash
had a similar appearance in all patients, with erythematous
nodules of varying sizes and central keratin plug (Figure 1). The diagnosis of RPC was suspected clinically in all
patients and confirmed histologically in 4 of the 5 cases
(in 1 patient, biopsy was felt to be inappropriate). Patient 4. An 83-year-old woman was housebound and
unable to attend the dermatology clinic. She was referred via
teledermatology for review of her images and clinical history. References nicorandil, candesartan, and atenolol. Blood values were nor
mal apart from an elevated HbA1c in keeping with her known
diabetes. Histology showed focal necrosis, ulceration and
epidermal inflammation, with perivascular chronic inflamma
tory cell infiltrate in the dermis. Dermoscopic images showed
almost identical features in all 5 patients (Figure 2). 1. Millard PR, Young E, Harrison DE, Wojnarowska F. Reactive
perforating collagenosis: light, ultrastructural and immunohisto
logical studies. Histopathology. 1986;10:1047-1056. 1. Millard PR, Young E, Harrison DE, Wojnarowska F. Reactive
perforating collagenosis: light, ultrastructural and immunohisto
logical studies. Histopathology. 1986;10:1047-1056. 2. Morton CA, Henderson IS, Jones MC, Lowe JG. Acquired perfo
rating dermatosis in a British dialysis population. Br J Dermatol. 1996;135:671-677. The 3 clear, consistent features were (1) a yellow-brown
structureless area in the center of the lesion in keeping with
surface crust; (2) a white rim surrounding the crust which
can vary in thickness between patients and in a single lesion,
possibly correlating to epidermal invagination or keratinous
debris; and (3) an outer pink circle of inflammation with
visible vessels, commonly short looped vessels centrally and
dotted vessels peripherally. These features are similar to those
previously described in 2 separate reports of single cases with
RPC [9,10]. 3. Poliak SC, Lebwohl MG, Parris A, Prioleau PG. Reactive perforat
ing collagenosis associated with diabetes mellitus. N Engl J Med. 1982;306:81-84. 4. Kim SW, Kim MS, Lee JH, et al. A clinicopathologic study of thirty
cases of acquired perforating dermatosis in Korea. Ann Dermatol. 2014;26:162-171. 4. Kim SW, Kim MS, Lee JH, et al. A clinicopathologic study of thirty
cases of acquired perforating dermatosis in Korea. Ann Dermatol. 2014;26:162-171. 5. Cerio R, Calnan CD, Wilson-Jones E. A clinic-pathological study
of reactive perforating collagenosis: report of 10 cases. Br J Der
matol. 1987;117:16-17. 6. Argenziano G, Soyer HP, Chimenti S, et al. Dermoscopy of
pigmented skin lesions: results of a consensus meeting via the
internet. J Am Acad Dermatol. 2003;48:679–693. 6. Argenziano G, Soyer HP, Chimenti S, et al. Dermoscopy of
pigmented skin lesions: results of a consensus meeting via the
internet. J Am Acad Dermatol. 2003;48:679–693. 7. Goncharova Y, Attia EA, Souid K, Protzenko O, Koktishev I. Dermoscopic features of clinically inflammatory dermatoses and
their correlation with histopathologic reaction patterns. Arch
Dermatol Res. 2015;307:23-30. Case Presentations She had a history of an aortic aneurysm, hypertension, atrial
fibrillation, and transient ischemic attack. Blood tests revealed
microcytic anemia but normal renal function. Biopsy was not
felt to be appropriate for this patient; the diagnosis was made
from classic clinical and dermoscopy features. Patient 1. A 53-year-old woman had a 20-year history
of type 2 diabetes mellitus, peripheral vascular disease, and
ischemic heart disease. Her medications included metformin,
clopidogrel, bisoprolol, and lisinopril. Routine blood values,
including renal function, were normal, and skin biopsy was
consistent with RPC, showing vertical collagen orientation. Patient 5. An 80-year-old woman had a history of long-
standing type 2 diabetes mellitus, ischemic heart disease, and
hypertension. Medications included lercanidipine, furosemide, Patient 2. A 67-year-old man was diagnosed with bilateral
pulmonary embolism at approximately the same time as the 304 etter | Dermatol Pract Concept 2018;8(4):11 Letter | Dermatol Pract Concept 2018;8(4):11 Conclusions RPC is an unusual condition that can mimic other conditions
and is often initially misdiagnosed. The dermoscopic find
ings in our cases reinforce the features described in previous
reports [9,10] and indicate that dermoscopy in RPC gives a
very characteristic, consistent appearance and can therefore
be a useful and quick aid to make the diagnosis. Dermoscopy
of RPC is particularly helpful in cases in which biopsy is not
possible or is nondiagnostic. 8. Lallas A, Kyrgidis A, Tzellos TG, et al. Accuracy of dermoscopic
criteria for the diagnosis of psoriasis, dermatitis, lichen planus and
pityriasis rosea. Br J Dermatol. 2012;166:1198-1205. 9. Kittisak P, Tanaka M. Dermoscopic findings in a case of reactive
perforating collagenosis. Dermatol Pract Concept. 2015;5:75-77. 10. Ramirez-Fort MK, Khan F, Rosendahl CO, Mercer SE, Shin-Chang
H, Levitt JO. Acquired perforating dermatosis: a clinical and der
matoscopic correlation. Dermatol Online J. 2013;19:18958. 305 305 Letter | Dermatol Pract Concept 2018;8(4):11 Letter | Dermatol Pract Concept 2018;8(4):11 |
https://openalex.org/W3119276491 | https://www.adb.org/sites/default/files/publication/665986/ewp-631-wellness-economy-national-accounts-approach.pdf | English | null | The Wellness Economy: A Comprehensive System of National Accounts Approach | null | 2,020 | cc-by | 19,409 | The Wellness Economy: A Comprehensive System
of National Accounts Approach Rafael Martin M. Consing III (rconsing.consultant@adb. org), Michael John M. Barsabal (mbarsabal.consultant@
adb.org), Julian Thomas B. Alvarez (jalvarez.consultant@
adb.org) are consultants at the Economic Research and
Regional Cooperation Department (ERCD) of the Asian
Development Bank (ADB). Mahinthan J. Mariasingham
(mmariasingham@adb.org) is a senior statistician in
ERCD, ADB. Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and
Mahinthan J. Mariasingham
No. 631 | December 2020 Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and
Mahinthan J. Mariasingham
No. 631 | December 2020 Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and
Mahinthan J. Mariasingham This analysis was used in the Asian Development Outlook
2020 Update. The team would like to thank Julieta
Magallanes, Ana Francesca Rosales, Angelo Jose Lumba,
Clara Torelli, and Elaine Tan for their valuable insights. ASIAN DEVELOPMENT BANK ADB Economics Working Paper Series Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) © 2020 Asian Development Bank
6 ADB Avenue, Mandaluyong City, 1550 Metro Manila, Philippines
Tel +63 2 8632 4444; Fax +63 2 8636 2444
www.adb.org Some rights reserved. Published in 2020. ISSN 2313-5867 (print), 2313-5875 (electronic)
Publication Stock No. WPS200433-2
DOI: http://dx.doi.org/10.22617/WPS200433-2 The views expressed in this publication are those of the authors and do not necessarily reflect the views and policies
of the Asian Development Bank (ADB) or its Board of Governors or the governments they represent. ADB does not guarantee the accuracy of the data included in this publication and accepts no responsibility for any
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the ADB logo. Corrigenda to ADB publications may be found at http://www.adb.org/publications/corrigenda. Notes: In this publication, “$” refers to United States dollars. ADB recognizes “China” as the People’s Republic of China. Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) The ADB Economics Working Paper Series presents data, information, and/or findings from ongoing research and
studies to encourage exchange of ideas and to elicit comment and feedback about development issues in Asia and
the Pacific. Since papers in this series are intended for quick and easy dissemination, the content may or may not be
fully edited and may later be modified for final publication. CONTENTS TABLES, FIGURES, AND BOX
iv
ABSTRACT
v
I. INTRODUCTION
1
II. METHODOLOGY
3
A. Identifying the Wellness Sector
3
B. Data
3
C. Disaggregation of Input–Output Tables
4
D. Direct Computation of Wellness Sector Gross Value Added
5
E. Tracing the Production Linkages of the Wellness Sector
5
F. Integration of Gross Fixed Capital Formation in Wellness Gross Domestic Product
7
G. Measuring the Employment Attributable to the Wellness Economy
8
H. Hypothetical Extraction Method
9
I. Gross Domestic Product Loss Decomposition
10
J. Employment Loss Decomposition
10
III. RESULTS AND DISCUSSION
11
A. The Wellness Economy
11
B. Wellness Employment
22
IV. CONCLUSION AND MOVING FORWARD
27
APPENDIX
29
REFERENCES
33 33 TABLES, FIGURES, AND BOX TABLES
1
Size of the Wellness Economy for Selected Asian Economies
12
2
Size of the Wellness Economy in Per Capita Terms for Selected Asian Economies
16
3
Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
21
4
Wellness Employment for Selected Asian Economies
23
5
Wellness Economy Labor Productivity for Selected Asian Economies
24
6
Decomposition of Employment Loss When Wellness Sector is Extracted
27
A.1
List of Industries and Activities Considered Part of the Wellness Economy
29
A.2
Data Sources
31
A.3
Data Sources for Input–Output Table Disaggregation
31 TABLES TABLES
1
Size of the Wellness Economy for Selected Asian Economies
12
2
Size of the Wellness Economy in Per Capita Terms for Selected Asian Economies
16
3
Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
21
4
Wellness Employment for Selected Asian Economies
23
5
Wellness Economy Labor Productivity for Selected Asian Economies
24
6
Decomposition of Employment Loss When Wellness Sector is Extracted
27
A.1
List of Industries and Activities Considered Part of the Wellness Economy
29
A.2
Data Sources
31
A.3
Data Sources for Input–Output Table Disaggregation
31
FIGURES
1
Structure of the Wellness Sector: Share of the Top Five Wellness Industries
17
2
Disaggregation of Wellness Employment by Country, by Period
18
3
Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by
Country, by Period
20
4
Disaggregation of Wellness Employment by Country, by Period
25
5
Decomposition of Employment Loss When Wellness Sector is Extracted
26
by Country, by Period
BOX
Wellness Economies and Aging
13 FIGURES
1
Structure of the Wellness Sector: Share of the Top Five Wellness Industries
17
2
Disaggregation of Wellness Employment by Country, by Period
18
3
Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by
Country, by Period
20
4
Disaggregation of Wellness Employment by Country, by Period
25
5
Decomposition of Employment Loss When Wellness Sector is Extracted
26
by Country, by Period
BOX
Wellness Economies and Aging
13 13 Keywords: economy, employment, input–output, national accounts, wellness
JEL codes: E01, C67, D57, I39, R15 ABSTRACT This paper provides a comprehensive discussion on different, interconnected methods of using the
system of national accounts to measure the relevance of a country’s wellness sector to its overall
economy. Procedures are discussed for using input–output analysis to derive the production and
employment linkages between wellness and nonwellness sectors. We also discuss procedures for using
the hypothetical extraction method to derive and decompose the production and employment losses
that may arise when a country’s wellness sector is removed from the economy. These procedures are
then used to provide estimates for ten countries in developing Asia across two time periods which
together provide a proxy for the region (Asia-10), along with a discussion on how these wellness
economies have grown and how each one's labor productivity and wellness sector structure have
evolved between the two periods. Keywords: economy, employment, input–output, national accounts, wellness
JEL codes: E01, C67, D57, I39, R15 I.
INTRODUCTION Wellness goes beyond a lack of physical illness. It often means thriving holistically and living a well-
rounded life, and so people engage in diverse activities to help themselves feel and become well. The
World Health Organization (WHO) defines wellness as: “…the optimal state of health of individuals and groups. There are two focal concerns: the
realization of the fullest potential of an individual physically, psychologically, socially,
spiritually, and economically, and the fulfillment of one’s role expectations in the family,
community, place of worship, workplace and other settings.” (WHO 2006) “…the optimal state of health of individuals and groups. There are two focal concerns: the
realization of the fullest potential of an individual physically, psychologically, socially,
spiritually, and economically, and the fulfillment of one’s role expectations in the family,
community, place of worship, workplace and other settings.” (WHO 2006) While many of these activities do not necessarily involve monetary transactions, there are
wellness-related activities which are also economic in nature. In a developing world, the volume and
economic value of these activities are expected to increase as people become increasingly conscious
of and able to meet their need for wellness. This paper contributes to wellness and economic literature by showing how the system of
national accounts (SNA) framework can be used to measure the wellness sector’s relevance to the
overall economy and then demonstrating this for selected Asian Development Bank (ADB) developing
member countries (DMCs) over two time periods. The main advantage of this approach is that most
countries follow the SNA framework when preparing their national accounts, and theoretically this
allows any country to estimate and analyze its own wellness economy, defined here as the linkages of
an economy attributable to the production of wellness goods and services with monetary transactions
attached to them. As nations develop, it becomes increasingly important to be able to measure the wellness
economy. From a policy perspective, this provides a better understanding of how relevant wellness
activities have become to the economy, which ones are the biggest economic contributors, and which
ones are potentially underdeveloped in the context of country-specific unmet social needs. For
policymakers interested in maximizing the wellness of their constituents, a measure of the wellness
economy becomes another analytical tool for socioeconomic development. There have been past attempts to measure wellness economies. 1
In national accounting, gross output is equal to the sum of intermediate consumption and value added. Because of the
former, it is typically larger than GDP. I.
INTRODUCTION The multidimensionality of wellness trends into the next century, with Miller and Foster (2010) stating
that the broadening scope of wellness is meant to create a “theoretical framework that views
individuals within a holistic perspective and consists of many dimensions.” Wellness is also commonly
viewed as both a state and the active pursuit of that state, and this appears in the GWI (2018)
definition of wellness as “the active pursuit of activities, choices, and lifestyles that lead to a state of
holistic health.” The WHO definition introduced earlier is the most explicitly comprehensive so far as it
includes an economic dimension to wellness as well as the other commonly cited dimensions and
recognizes wellness as both a state and an activity. As this definition shares similarities with and
encompasses many others covered, this is the definition for wellness primarily being referred to in this
paper. In the endeavor to estimate how much of an economy can systematically be attributed to the
production of wellness goods and services, the most inclusive definition is correspondingly adopted. Given the established multidimensionality of wellness, economic activities that fall under
wellness cannot be limited to just the consumption of medical services and pharmaceutical goods. Potentially, wellness includes all economic activities and industries that help people feel and become
well, such as those relating to travel, recreation, outdoor, sporting, and personal care activities. The
specific economic activities considered as wellness are described further in section II and enumerated
in Table A.1 of the Appendix. In this paper, the industries engaged in the production of such wellness
goods and services are referred to collectively as the wellness sector.2 As economies are complex
systems with interconnected sectors, the wellness sector is itself supported by activities in other
sectors of the economy. In the context of economic productivity, the wellness economy is measured in terms of gross
value added (GVA).3 Therefore, the objective of the paper is to show how much of a country’s GVA is
attributable to those wellness goods and services with monetary transactions attached to them. This
refers to two main components: (i) the GVA from the wellness sector itself, such as the GVA from
hospitals; and (ii) the contribution from supporting nonwellness sectors, such as the GVA from the
energy sector used to produce hospital services. I.
INTRODUCTION The Global Wellness Institute
(GWI) is one of the largest institutions to attempt to estimate wellness economies, and it estimates
the value of the global wellness economy at $4.2 trillion as of 2017. However, its methodology is
proprietary and does not appear to follow international standards of national accounting. For example,
it is unclear what the $4.2 trillion figure mentioned in GWI (2018) refers to. It appears to be in terms of
gross domestic product (GDP) as it’s described as “representing 5.3% of global economic output”
(world GDP was over $80 trillion in 2017), but GDP is not necessarily the same as gross output.1 Any attempt to relate metrics and wellness starts with the most important question: What is
wellness? As a naturally desirable state of health, wellness as a concept has been around potentially as
long as humanity has. The desire for a better life is fundamentally a desire for wellness. As is common
with such concepts, the term “wellness” can seem nebulous and imprecise, often grasped intuitively ADB Economics Working Paper Series No. 631 2 rather than scholastically. For the wellness economy to be measured, however, wellness must be
defined explicitly. rather than scholastically. For the wellness economy to be measured, however, wellness must be
defined explicitly. In the modern academe, numerous definitions for wellness have been proposed, with one of
the earliest coming from Dunn (1959) who defines it as “a health condition which includes general
well-being of body, mind, and spirit.” A review by Roscoe (2009) indicates similarities in definitions
across wellness literature in the decades following Dunn (1959) but with more dimensions added, the
most prevalent being those related to social, emotional, physical, intellectual, and spiritual well-being. 3 There is a small difference between a country’s GVA and its GDP. A country’s GDP is equal to its GVA plus nonrefundable
product or sales taxes. These taxes constitute a very small percentage of GDP and are a function of product-specific value
added. Therefore, for all analytical purposes, this paper assumes that GVA is almost equal to GDP and use the terms
interchangeably (Consing et al. 2020). In this context, wellness industries and wellness subsectors may be treated synonymously. I.
INTRODUCTION It’s important to emphasize that measuring the wellness economy is not the same as
measuring the welfare, wellness, or well-being of people in a country. For example, a pandemic might
increase spending on hospital activities which might, holding other factors constant, mean a larger
measurement of the wellness economy, yet a population’s well-being could actually decline as more
people fall ill or into anxiety and poverty due to the pandemic. Similarly, a wellness economy might be The Wellness Economy 3 The Wellness Economy growing due to high production of wellness goods and services, yet the population’s welfare may
remain low if only a wealthy minority of the population is able to consume these goods and services. This paper focuses only on using input–output analysis to measure wellness economies and not
welfare. growing due to high production of wellness goods and services, yet the population’s welfare may
remain low if only a wealthy minority of the population is able to consume these goods and services. This paper focuses only on using input–output analysis to measure wellness economies and not
welfare. Besides measuring the wellness economy in GVA terms, there are other ways by which the
relevance of the wellness sector to the overall economy can be estimated under the SNA framework. One is to estimate wellness employment, defined here as the employment linkages attributable to the
production of wellness goods and services with monetary transactions attached to them, and another
is to estimate the production and employment losses that may occur if the wellness sector were
extracted from the economy. Conceptually, these all fall under input–output analysis, and so they
neatly relate to each other and are discussed as such in the methodology. Estimates for the wellness
economy, the GVA lost from hypothetical extraction, and wellness employment are then produced for
selected countries in developing Asia with available data over two time periods to show a practical
application of this framework. A.
Identifying the Wellness Sector A. The first step is to identify which economic industries produce wellness goods and services. Using the
fourth revision of the International Standard Industrial Classification of All Economic Activities (ISIC
Rev. 4), 35 industrial codes were identified as composing the wellness sector. These codes were
selected to be as inclusive as reasonably possible of the various dimensions of wellness embodied in
WHO’s definition. These are likewise consistent with wellness activities discussed in the literature,
such as in Kickbusch and Payne (2003), Pilzer (2007), and GWI (2018). Some codes are included to expand the scope of commonly recognized wellness activities. For
example, these ISIC codes include hospital activities for ill patients (excluded in some definitions of
wellness, such as GWI 2018), under the assumption that ill patients engage in hospital activities with
the intention of becoming well. As in Consing et al. (2020), these ISIC codes capture a variety of
wellness goods and services from various industries, such as human health, residential care, social
work, tourism, amusement, recreation, sports, creative, arts, entertainment, culture, and personal care
activities as well as the construction of wellness-related structures, such as health and sports facilities
and the manufacture and retail trade of wellness goods such as pharmaceutical, beauty, and sports
products. Table A.1 of Appendix A contains the list of ISIC codes covering the wellness sector. C.
Disaggregation of Input–Output Tables While a country’s IOT provides information necessary in computing for sectoral GVA, the industries of
the wellness sector are often grouped into various sectoral aggregates making the identification and
computation of the GDP attributable to the wellness sector difficult. This is resolved by disaggregating
or breaking down the IOT industries. With several methods available, this paper uses information
extrapolated from supply tables, administrative, and secondary data. The first method of disaggregating an IOT involves the use of the supply table. This is the
preferred method as it involves using SNA components as a basis for disaggregation. This entails
identifying wellness products and the total amount of wellness products supplied by the sector to be
broken down. The total amount of wellness products that is supplied by the aggregated industry is then
divided by the total output of the aggregated sector to obtain the disaggregator. This ratio is then
multiplied to the relevant GVA in the IOT. This process is repeated to generate a set of disaggregators
that are used to break down the aggregated sectors of interest. Once the wellness component has
been separated, these are summed up to create a separate account for the wellness sector in the IOT. Underlying the first method is the need for a highly disaggregated row accounts in the supply
table. That is, for the first method to be viable, the supply products must include numerous products. Hence, if a country’s supply table is not detailed enough to produce disaggregators, an alternative
method of disaggregation is to use firm-level data coming from a secondary source. Here, the firm-
level data from Orbis database was used. After applying the methods on filtering firms in the database
as prescribed in Kalemli-Ozcan et al. (2019), data on the operating revenue of each firm for each
country is collected. The operating revenues are aggregated at the four-digit ISIC level and based on
the sectoral groupings in the IOT. 4 The set of disaggregators were then computed by taking the ratio
of the operating revenue of ISIC industry codes for wellness industries to the operating revenue of the
sector being disaggregated. If a detailed supply table is unavailable and data from secondary sources
are limited for disaggregation, the donor imputation method for deriving disaggregators was employed. The objective is to use the disaggregators from a donor country. ADB Economics Working Paper Series No. 631 4 into IOT is the assumption that without any regard to the producing industry, each product has its own
sale-specific structure (Eurostat 2008). Table A.2 of Appendix A contains a summary of the data
sources used for estimating the wellness economy in each country. into IOT is the assumption that without any regard to the producing industry, each product has its own
sale-specific structure (Eurostat 2008). Table A.2 of Appendix A contains a summary of the data
sources used for estimating the wellness economy in each country. 4 Since firms in the Orbis database are classified according to the European Classification of Economic Activities Rev. 2, a
concordance table was used to convert these codes into ISIC Rev. 4 industry codes.
5 It is a requirement that the sector aggregation in the IOTs of the donor and imputed economies be the same. It is a requirement that the sector aggregation in the IOTs of the donor and imputed economies be the s Data The main data source used in computing for the contribution of the wellness sector to GDP are
national input–output tables (IOTs). Symmetric IOTs summarize the flow of transactions across
industries operating in the economy. These contain information on intermediate consumption, gross
output, and GVA for each production sector. When IOTs are not readily available, supply and use
tables (SUTs) from various national statistical offices were converted into industry-by-industry IOTs
using the transformation model prescribed by Eurostat (2008). Inherent in the transformation of SUTs ADB Economics Working Paper Series No. 631 C.
Disaggregation of Input–Output Tables The donor country is chosen based on the expectation that the economic structure of the
imputed country closely resembles that of the donor.5 Economic factors such as similarity in market
structure, share of agriculture, industry and services to GDP, income group and major commodities
produced were the main consideration in choosing a donor for a recipient country. Aside from these
economic factors, similarities in geographical location, historical experience and values in different
developmental indices such as the Human Development Index and unemployment rates were also
taken into account in selecting the donor country. For example, the economic structure of Malaysia
was used as a donor for Sri Lanka since both countries are upper middle-income economies with
comparable market structure in terms of share of agriculture, manufacturing, and services to GDP. Similarly, both countries share the same colonial experience and geographical attributes. The type of
disaggregation for each country IOT used in this paper is elaborated in Table A.3 of the Appendix. 5 The Wellness Economy Once disaggregators are estimated from the methods described above, these were further
verified with available administrative data for each country of interest to ensure that the disaggregators
are reliable and intuitive. The disaggregators are then used to dissect the aggregated sectors in each
country’s IOT. Since IOTs are characteristically symmetric, these disaggregators are multiplied to both
the rows and columns corresponding to the industries in the IOT which contain the wellness activities
of interest. In effect, the symmetric IOT is expanded for each disaggregator being applied as the
corresponding industry being disaggregated is split into the part of it containing wellness activities and
the part of it containing nonwellness activities. For example, an IOT containing a single entry
encompassing all ISIC codes starting with 47 (retail trade, except motor vehicles and motorcycles) would
be split row- and column-wise using a relevant disaggregator to create a separate entry just for ISIC code
4763 (retail sale of sporting equipment in specialized stores), which is considered part of wellness. D.
Direct Computation of Wellness Sector Gross Value Added D. Given that a country’s IOT is disaggregated following the procedure described in the previous
subsection, the wellness components of each sector were summed up to compute the country’s GVA
directly generated by its wellness industries, also referred to here as wellness sector GVA. Assuming
that there are n sectors in the economy and q of which are wellness industries, equation (1) describes a
formula for the GVA of the wellness sector that is consistent with the SNA framework. Wellness sector GVA = pᇱ(x −z) = p′va
(1) (1) where p is a n x 1 indicator vector whose value is 1 if the entry corresponds to a wellness industry and 0
otherwise.6 x, z and va are n x 1 vectors of output, total intermediate consumption, and gross value
added, respectively. Throughout the paper, the prime symbol (′) denotes matrix transposition. where p is a n x 1 indicator vector whose value is 1 if the entry corresponds to a wellness industry and 0
otherwise.6 x, z and va are n x 1 vectors of output, total intermediate consumption, and gross value
added, respectively. Throughout the paper, the prime symbol (′) denotes matrix transposition. 6 As a check, the sum of each entry in p must be equal to q. Another way of aggregating values in each wellness industry is through the multiplication of an aggreg
components of the IOT. See Torelli and Lumba (2020) for a detailed exposition on the aggregator matri As a check, the sum of each entry in p must be equal to q. As a check, the sum of each entry in p must be equal to q.
7 Another way of aggregating values in each wellness industry is through the multiplication of an aggregator matrix to the
components of the IOT. See Torelli and Lumba (2020) for a detailed exposition on the aggregator matrix. E.
Tracing the Production Linkages of the Wellness Sector E. The wellness GVA derived in equation (1) captures the direct economic contribution of the sector. However, the wellness economy also includes GVA from supporting nonwellness industries used to
produce wellness goods and services. These contributions are not encapsulated in the previous
equations. To account for these contributions when estimating the size of the wellness economy, we
use Leontief’s insight in Leontief (1936) to derive the wellness sector’s product linkages which contain
the contribution from supporting nonwellness industries. To trace the production linkages of the wellness sector, the first step is to convert the
disaggregated n x n IOT into a table with n-(q-1) x n-(q-1) dimension. This ensures that there is only a
single account dedicated for the wellness sector and there is no double-counting that comes from the
interaction of wellness industries with each other. Resizing the IOT entails that each entry of the
wellness industry in the disaggregated IOT is added to a single account.7 Once the values for each wellness industry are aggregated into a single account, the matrix of
technical coefficients, A = [aij] which gives the share of inputs from sector j to total output of sector i,
is obtained. This matrix is derived by post-multiplying the matrix of intermediate consumption, ADB Economics Working Paper Series No. 631 6 Z = [zij], with the inverse of a diagonalized matrix of gross output, X-1.8 Subtracting A to an identity
matrix and taking its inverse yields equation (2), the Leontief Inverse. Z = [zij], with the inverse of a diagonalized matrix of gross output, X-1.8 Subtracting A to an identity
matrix and taking its inverse yields equation (2), the Leontief Inverse. B = (I −A)ିଵ= [bij]
(2) (2) The Leontief Inverse summarizes the output requirements from each sector to meet final
demand given a specific time period. bij represents the entry in the ith row and jth column of the matrix
represented in equation (2). Similarly, we also construct the direct value-added coefficient matrix V by
placing the elements of a n-(q-1) × 1 vector of direct value-added coefficients, v = [vaj xj
⁄ ], into the
diagonal entries. Each entry in v is obtained by dividing Sector j’s gross value added by the gross output
of the same sector. Pre-multiplying B to V gives us VB, the total value-added matrix. 8 For notational purposes, a hat (i.e., X) represents a diagonal matrix with elements of vector x on the diagonal.
9 This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wang et al.
(2017) which decomposes the value added into various component in a multiregional input–output model. notational purposes, a hat (i.e., X) represents a diagonal matrix with elements of vector x on the diagonal. composition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wa
which decomposes the value added into various component in a multiregional input–output model. This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013
(2017) which decomposes the value added into various component in a multiregional input–output mod E.
Tracing the Production Linkages of the Wellness Sector This matrix
indicates the value added each sector directly and indirectly required to produce a unit of its final
demand. Thus, when Y, a diagonal matrix of the final demand, is post-multiplied to VB, equation (3) is
derived. VBY=
v1b11y1
⋯
v1b1,n-(q-1),yn-(q-1)
⋮
⋱
⋮
vn-(q-1)bn-(q-1),1y1
⋯
vn-(q-1)bn-(q-1),n-(q-1)yn-(q-1)
(3) VBY=
v1b11y1
⋯
v1b1,n-(q-1),yn-(q-1)
⋮
⋱
⋮
vn-(q-1)bn-(q-1),1y1
⋯
vn-(q-1)bn-(q-1),n-(q-1)yn-(q-1)
(3) (3) The matrix in equation (3) with dimension n-൫q-1൯ × n-൫q-1൯, traces the production linkages of
each sector in the economy by decomposing the value added made by each sector in the economy.9
Each element in the matrix is interpreted as the value added from each sector that is directly or
indirectly used in the production of final goods and services of a specific sector (Wang, Wei, and Zhu
2013; Wang et al. 2017). Therefore, the sum of each entry of the VBY matrix, as shown in equation (4),
gives the total GDP of the entire economy. Total GDP = iᇱVBYi
(4) (4) For notational purposes, a hat (i.e., X) represents a diagonal matrix with elements of vector x on the diagonal.
9 This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wang et al.
(2017) which decomposes the value added into various component in a multiregional input–output model. where i is a unit vector. where i is a unit vector. Alternatively, the entries along the rows of equation (3) can be interpreted as the distribution
of the value added created from a sector across all other industries in the economy. For example, the
entry in the ith- row and jth-column, vibijyj, represents the value-added contribution of sector i that is
used in the production of sector j’s final goods and services. Thus, the sum of each entry in the row
accounts would yield the GVA that is directly created in the sector, tracing all forward linkages across
all downstream sectors from a producer’s perspective (Wang, Wei, and Zhu 2013). Conversely, the entries along the column, correspond to the breakdown of value-added
contributions from all sectors in the economy used in the production of a particular sector’s final goods
and services. Thus, looking at the entries column-wise traces the backward linkages of a particular
industry across all upstream sectors from a user’s perspective (Wang, Wei, and Zhu 2013). To measure the wellness economy, the value-added contribution attributable to the wellness
sector from equation (3) is estimated. This is done by including the sum of all entries in the row for the The Wellness Economy The Wellness Economy 7 wellness sector in equation (3). The row sum, iᇱVBY𝛆, can be easily obtained by pre-multiplying a unit
row vector and post-multiplying ε to equation (3). The vector ε is an indicator vector for the wellness
sector where each element of the vector is 0 except for the row corresponding to the wellness sector
with a value of 1. This term captures the value-added contributions from the wellness sector that
enable production in all sectors in the economy. The term iᇱVBY𝛆 also encapsulates the forward
linkages of the wellness sector across all downstream sectors. Furthermore, this term is exactly equal to
the result derived in equation (1). The measure for the size of the wellness economy also includes the backward linkages of
wellness sector. This is computed by taking the sum of the column dedicated for the wellness sector in
equation (3). Operationally, the value for the backward linkage is derived by post-multiplying 𝛆 to
iᇱ൫VBY൯
ᇱ. With the inclusion of iᇱ൫VBY൯
ᇱ𝛆 to the new estimate of wellness GDP, the value-added
contribution from supporting nonwellness sectors that enables the production of the wellness sector is
accounted. where i is a unit vector. Adding these two terms while adjusting for the intersection term, ൣdiag൫VBY൯൧′, which is
double- counted, gives a GDP measure of the wellness economy based on its production linkages as
shown in equation (5). Wellness GDP = iᇱVBY𝛆+ iᇱ൫VBY൯
ᇱ𝛆 −ൣdiag൫VBY൯൧′𝛆
(5) (5) (
)
11 In the application of this estimation procedure, the donor country is Canada due to data limitations. However, another
economy with available data can be used as a donor country. Consequently, if the matrix product is not filtered out, 𝚲
becomes an identity matrix. 10 The wellness GFCF matrix (W) is extrapolated from the GFCF vector in the IOT by multiplying the corresponding ratio of
the gross output of each wellness industry to total output with the row entry in the GFCF vector. In matrix notation,
′ W = gt′, where g is a n-(q-1) x 1 GFCF vector and t is a qx1 vector of gross output ratios. Integration of Gross Fixed Capital Formation in Wellness Gross Domestic Product While the wellness GDP stated in equation (6) captures all contemporaneous input–output
transactions with respect to the exogenous final demand, it does not include the capital goods
purchased by the wellness sector for future production. To account for the gross fixed capital
formation (GFCF) attributable to the wellness sector but distributed in other industries, equation (6) is
adjusted as follows: ellness GDP = iᇱVBY𝛆+ iᇱ൫VBY൯
ᇱ𝛆 −ൣdiag൫VBY൯൧
ᇱ𝛆+ (i −𝜺)ᇱVBYR𝚲(i −𝜺)
(6) (6) equation (6) is almost identical to equation (6) except that a fourth term was added, where the VBY
matrix is post-multiplied with R. The post-multiplied matrix is a n-(q-1) x n-(q-1) diagonal matrix of the
ratio of use of wellness GFCF to the total final use of each sector in the economy. Each ratio is
computed by dividing the sum of each row in the wellness GFCF matrix by the corresponding total final
demand.10 The matrix product VBYR is again post-multiplied with a filter matrix, 𝚲= 𝜶ෝ. The diagonalized
vector 𝜶, is an indicator vector whose value is 1 if the same industry in a donor country11 uses wellness
GFCF products and 0 otherwise. The post-multiplication of 𝚲 to the matrix product VBYR effectively ADB Economics Working Paper Series No. 631 8 filters out industries that might be providing wellness GFCF, but whose counterparts in the donor
economy do not. filters out industries that might be providing wellness GFCF, but whose counterparts in the donor
economy do not. The sum of all entries in the resulting matrix less the entries corresponding to the wellness
sector itself is the term representing the part of GDP attributable to the wellness sector’s purchase of
capital goods from other sectors in the economy. Thus, equation (6) is the key equation in measuring
the size of the wellness economy. G.
Measuring the Employment Attributable to the Wellness Economy Besides measuring the economy attributable to wellness in terms of GVA, the economic relevance of
wellness can be characterized through its contribution to total employment. The key step in
performing this analysis is the collection and processing of sectoral employment data from official
sources. Since sources of labor data are likely to release employment figures at an aggregated level,
different techniques are applied to further disentangle the number of jobs attributable to each sector
in the economy. The first method in disaggregating employment data uses the unit labor cost approach where
the sectoral unit labor cost (ULC) is defined as the ratio of total labor cost to real output by sector
(Ernst and Sarabia 2015). Since the total labor cost is the product of real wages and the total number of
employees in each sector, the sectoral ULC can be multiplied to the inverse of the wage-to-output
ratio to recover total employment by industry. This step is operationalized in equation (7). Employmenti=ULCj×
Total Outputj
Real Wagej
=
Real Wagej × Employmentj
Total Outputj
×
Total Outputj
Real Wagej
(7) Employmenti=ULCj×
Total Outputj
Real Wagej
=
Real Wagej × Employmentj
Total Outputj
×
Total Outputj
Real Wagej
(7) (7) Given that the unit labor cost approach requires data that might not be readily available from
official sources, another method in deriving sectoral employment is to use the of distribution of
Compensation of Employees (COE) by sector. Often, COE is provided in the SUT of a particular
country. If COE is not available, the distribution of GVA can be an alternative in further dividing
aggregated employment figures. Once data on employment are processed to the desired sectoral disaggregation, the effects of
the sector on jobs is determined by executing a procedure analogous to the method described in section
II.E is performed. Unlike in equation (4) where V is pre-multiplied to BY, V is replaced with an
employment matrix, E, which is a n-൫q-1൯ × n-൫q-1൯ diagonal matrix with labor coefficients as its diagonal
entries. Labor coefficients represent the total number of persons needed to produce a unit of output and
are computed by dividing the total number of jobs for each sector to the gross output of the
corresponding sector (i.e.: ej= jobsJ/xj). Pre-multiplying E with BY yields to the matrix equation below. G.
Measuring the Employment Attributable to the Wellness Economy EBY=
e1b11y1
⋯
e1b1,n-(q-1),yn-(q-1)
⋮
⋱
⋮
en-(q-1)bn-(q-1),1y1
⋯
en-(q-1)bn-(q-1),n-(q-1)yn-(q-1)
(8) EBY=
e1b11y1
⋯
e1b1,n-(q-1),yn-(q-1)
⋮
⋱
⋮
en-(q-1)bn-(q-1),1y1
⋯
en-(q-1)bn-(q-1),n-(q-1)yn-(q-1)
(8) (8) The n-൫q-1൯ × n-൫q-1൯ matrix represented in equation (8) shows the number of jobs created in
each sector due to the final demand. Particularly, eibijyj is the number of jobs created in Sector i due to
the final demand of Sector j. Thus, summing up all entries in equation (8) results into the total number
of jobs in the economy. Mathematically, the total number of jobs in the economy is expressed as The Wellness Economy 9 Total employment = iᇱEBYi
(9) (9) Total employment = iᇱEBYi To derive the employment attributable to the wellness economy, entries in the column and
row vectors of equation (8) corresponding to the wellness sector are added together. This procedure is
summarized in equation (10). Wellness employment = iᇱEBY𝛆+ iᇱ൫EBY൯
ᇱ𝛆 −ൣdiag൫EBY൯൧′𝛆
(10) (10) The first term of equation (11) shows the total number of jobs created in the wellness sector
due to the demand of all sectors in the economy. Similarly, the difference between the second and
third terms of the preceding equation indicates the number of jobs induced by the final demand for
wellness goods and services in all other sectors in the domestic economy. H. Another way of measuring the importance of wellness industries to the economy is by tracing the GDP
and jobs that are lost when the sector is nullified in the economy (Miller and Blair 2009). One way of
doing this is through the hypothetical extraction method (HEM). HEM is almost identical to the analysis discussed in section II.E except that in this method, the
row and column elements of the wellness sector in the matrix of technical coefficients are deleted by
replacing them with zeroes to generate a new matrix, Aഥ. By doing so, the interdependence between the
wellness sector and the rest of the economy is canceled out (ADB 2018). It also follows that there is no
final demand for wellness goods and services, yതk = 0, and no primary inputs, va
തതതk = 0 for the wellness
sector. Since the input requirements of other sectors are unaltered, HEM assumes that the inputs
originally provided by the wellness sectors are satisfied by additional imports after extraction
(Dietzenbacher, van Burken, and Kondo 2019). Moreover, HEM further assumes that once the inputs
for the wellness sector are extracted, these resources do not shift to other activities and therefore,
remain unemployed. This assumption is valid in the short run. With the matrix of technical coefficients altered, the entries in the Leontief Inverse are also
changed (i.e.: Bഥ= (I −Aഥ)ିଵ). Similarly, new matrices of direct value-added coefficients, Vഥ, and final
demand, Yഥ, are derived. Pre-multiplying Vഥ with Bഥ and post-multiplying Yഥ with the matrix product gives
us the new GDP of the economy when the wellness sector is nullified. The new GDP is summarized in
equation (11). tal GDP
തതതതതതതതതതത= iᇱVഥBഥYഥi
(11) Total GDP
തതതതതതതതതതതതതത= iᇱVഥBഥYഥi (11) When HEM is also applied, the jobs that the wellness sector generates are lost. This means that
the labor coefficient for the wellness sector becomes zero (i.e.: eതk = 0) implying that a new
employment matrix, Eഥ, is derived. Matrix Eഥ is almost identical to matrix E described in section II.G,
except that the diagonal entry corresponding to the wellness sector is now set to zero. By summing up
the entries of the resulting matrix product from pre-multiplying Eഥ to BഥYഥ, the remaining jobs in the
domestic economy is computed. The new level of total employment is represented mathematically in
equation (12). Total Employment
തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi
(12) Total Employment
തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi
(12) Total Employment
തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi (12) ADB Economics Working Paper Series No. 631 10 I.
Gross Domestic Product Loss Decomposition The difference between the total GDP prior extraction (equation [4]) and the hypothetical situation
(equation [11]) gives us the potential GDP lost when the wellness sector is extracted. Formally, this is
written as GDP Loss = iᇱVBYi −iᇱVഥBഥYഥi
(13) (13) Since HEM assumes no reallocation among domestic inputs and the extracted inputs used by
the wellness sector is completely substituted by imports as a result of extraction, the estimate
produced from equation (13) is an upper bound estimate in the short run. Alternatively, equation (14)
can be re-written as GDP Loss = vak + yk brk
vak
xr
r
+ var(brr-bതrr)
yr
xr
+
𝒓
var(brs-bതrs)
ys
xr
s≠r
r≠s
(14) (14) where r and s are indices for all industries except for the wellness sector with index k.12 Equation (14)
shows that the GDP lost can be decomposed into direct (first and second terms) and indirect losses
(third and fourth terms). The direct losses comprise of the lost incurred due to removal of production
linkages of the wellness sector. Specifically, the first term represents the GVA loss attributed to the
wellness sector that is used in the production of final goods and services by all sectors in the economy,
while the second term is the total GVA lost from other industries that were previously used in the
production of final wellness goods and services in the pre-extraction scenario. These correspond to the
linkages of the wellness economy described in section II.E. Similarly, the indirect losses are incurred due to the resulting changes in the sensitivity of the
output of the remaining sectors because of a change in the final demand. Specifically, the third term is
the loss incurred due to own-industry output elasticities and the fourth term represents the loss due to
changes in cross-industry output elasticities. The third and fourth term together are the difference
between the estimated GDP lost from the hypothetical extraction of wellness industries and the
estimated size of the wellness economy from its linkages in equation (6). 12 See Barsabal, Alvarez, and Consing (2020) for the detailed derivation of the GDP lost after hypothetical extraction. J. Like in section II.I, the total jobs lost after extracting the wellness sector from the domestic economy is
the difference between the total employment prior extraction (equation [9]) and the new level of
employment described in equation (12). In matrix form, the loss in employment is expressed as follows. Employment Loss = iᇱEBYi −iᇱEഥBഥYഥi
(15) (15) Note that equation (15) is a maximum estimate of the total jobs lost in the short run since the
HEM assumes no redistribution of production inputs to remaining sectors. Furthermore, the total
employment loss can be decomposed as shown in equation (16). Employment Loss = jobsk + yk brk
jobsk
xr
r
+ jobsr(brr-bതrr)
yr
xr
+
jobsr(brs-bതrs)
ys
xr
s≠r
r≠s
(16) Employment Loss = jobsk + yk brk
jobsk
xr
r
+ jobsr(brr-bതrr)
yr
xr
+
jobsr(brs-bതrs)
ys
xr
s≠r
r≠s
(16) (16) 12 See Barsabal, Alvarez, and Consing (2020) for the detailed derivation of the GDP lost after hypothetical extraction. 11 The Wellness Economy The Wellness Economy The first term in equation (16) is equal to the jobs lost as a result of the nullification of the
demand for wellness final goods and services from all remaining sectors. Similarly, the second term
computes the jobs induced by the final demand for wellness goods and services in all other sectors in
the domestic economy that are now lost, while third and fourth terms represent the losses in jobs due
to the changes in output elasticities of the remaining industries. In particular, the third term represents
the jobs lost due to changes in own-industry output elasticities while the fourth term shows the losses
in employment due to changes in cross-industry output elasticities. By convention, the sum of the first
two terms is referred as the direct employment losses and is equal to the employment losses generated
by equation (16). Adding the third and fourth terms of equation (16) gives the indirect employment
losses incurred. 1. Size of the Wellness Economy Table 1 shows the estimates of the wellness economy in ten of ADB’s DMCs, as measured in millions
United States dollars at constant 2010 prices. The wellness economies are calculated using equation
(6). The estimates are presented for two periods for each country, and the annualized growth rate
for each wellness economy is also shown in the last column. As a caveat, the estimates are
dependent on the data sources used for disaggregation shown in Table A.3 in the appendix. Breaking
down of national IOTs to disaggregate the wellness sector from the other sectors is implemented
using Orbis firm-level data for the People’s Republic of China (PRC), India, Philippines, Thailand,
and Viet Nam. Supply table is used for Kazakhstan and Malaysia as these two countries have
detailed products in their SUTs. When the other two sources are insufficient, the structure of donor
country is used to approximate the disaggregation for another country. The choice is based on the
similarity in economic structure (i.e., share of agriculture, industry, and services to GDP), level of
development (i.e., income classification, HDI), geographic proximity, and historical context. Malaysia
is used as the donor country both for Fiji and Sri Lanka, while the structure of the PRC is used for
Mongolia. Table 1: Size of the Wellness Economy for Selected Asian Countries
($ million, constant 2010 prices)
Country
Period 1
Period 2
Real Wellness GDP
Growth Rate
(annualized, %)
Real GDP
Growth Rate
(annualized, %)
Asia-10
756,800
1,460,166
10.7
7.2
Fiji
105
171
10.2
4.6
India
90,902
171,070
13.5
7.4
Kazakhstan
8,811
9,237
1.2
2.6
Malaysia
11,044
20,545
13.2
5.3
Mongolia
333
622
9.3
8.2
People’s Republic of China
585,508
1,176,330
10.5
7.6
Philippines
14,410
21,802
8.6
6.6
Sri Lanka
8,783
9,351
1.3
4.3
Thailand
29,118
37,437
5.2
2.8
Viet Nam
7,786
13,601
11.8
6.2
GDP = gross domestic product. Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness
economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017);
Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);
Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. A.
The Wellness Economy A. Based on data for the previous decade, the wellness economy’s prospects in developing Asia have
generally been positive, demonstrating potential for high growth. Wellness traditions in the region have
their roots in centuries-old practices and have deeply embedded themselves in its peoples’ lives and
cultures. Asian economies have successfully assimilated some of these practices even in contemporary
markets, notwithstanding significant changes in their economic structure. Even the wellness economy
itself witnessed drastic changes in recent periods, resulting from changes in technology and changes in
demographic composition. The advancements in technology, for example, have enabled greater
volumes of wellness products to be more accessible to a wide array of consumers. At the same time,
the aging population in several economies in developing Asia also influenced wellness consumption
patterns, as societies divert more resources toward meeting the demands of the elderly population. The sharp increases in per capita income in developing Asia has been accompanied by a
rapidly growing middle class (ADB 2019, Kharas 2017). As a consequence, large segments of the
population have been able to integrate wellness goods and services into their daily consumption
pattern. Moreover, there is an increasing recognition that wellness-oriented policies are needed to
complement people’s transitions toward improved and healthier lifestyles (ADB 2020). Given these
developments, there is also growing demand for a framework by which to measure the wellness
economy and to trace its evolution across countries and over time. This section presents and discusses estimates of the wellness economy in selected countries in
developing Asia using the procedures described in section II. The discussion in this section is outlined
as follows: section III.A.1 discusses the size of wellness economy in aggregate and in per capita terms,
while section III.A.2 highlights the structure and industry composition of the wellness sector. Section
III.A.3 decomposes the wellness economy into forward and backward linkages, and wellness GFCF
component. Finally, section III.A.4 presents the results of the hypothetical extraction method, where
the wellness sector is hypothetically removed from the economy, and the resulting loss in GDP is
calculated. ADB Economics Working Paper Series No. 631 12 Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness
economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017);
Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);
Thailand (2012, 2017); Viet Nam (2012, 2017). (
,
);
(
,
)
Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of
all countries’ wellness economies weighted by each one’s real GDP in the second period. Box: Wellness Economies and Aging Intuitively, spending on wellness goods and services may share a relationship with a country’s
demographic structure. As the share of the elderly population increases, the demand for goods and
services which constitute the wellness sector also increases. These include health-care services,
residential care services, manufacture of pharmaceuticals, among other wellness products
consumed by the elderly population. Hence, it is interesting to compare the size of wellness
economy as a percentage share of GDP with the share of elderly population to the economy’s total
population, as shown in Box Figure 1 for each of the two periods. Intuitively, spending on wellness goods and services may share a relationship with a country’s
demographic structure. As the share of the elderly population increases, the demand for goods and
services which constitute the wellness sector also increases. These include health-care services,
residential care services, manufacture of pharmaceuticals, among other wellness products
consumed by the elderly population. Hence, it is interesting to compare the size of wellness
economy as a percentage share of GDP with the share of elderly population to the economy’s total
population, as shown in Box Figure 1 for each of the two periods. In general, economies with higher percentage share of elderly population also have larger wellness
economy as a percentage share of GDP (i.e., Sri Lanka, the People’s Republic of China, and
Thailand). In contrast, economies with lower percentage share of elderly population also have
lower share of wellness economy as a percentage of GDP (i.e., Mongolia and Fiji). The upward-
sloping fitted line suggests a positive correlation between wellness economy and aging. As a
caveat, the scatterplot shown in the Box Figure 1 below does not imply causality. For comparison,
a red line is also shown which indicates a one-to-one correlation between wellness economy as a
percentage of GDP and elderly population as a percentage of total population. Notice that the
fitted line deviates from the red line, indicating that there are factors, other than changes in the
demographic structure that also influence the size of wellness economy. Correlation between the Size of Wellness Economy and Aging
FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines,
PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. 1. Size of the Wellness Economy The growth rate for Asia-10 is the average growth rate of
all countries’ wellness economies weighted by each one’s real GDP in the second period. Table 1: Size of the Wellness Economy for Selected Asian Countries
($ million, constant 2010 prices) g
p
Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness
economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017);
Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);
Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of
all countries’ wellness economies weighted by each one’s real GDP in the second period. The Wellness Economy 13 Box: Wellness Economies and Aging Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC
(2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculation using demographic data from the online ADB Key Indicators Database. https://kidb.adb.org/kidb/
(accessed 28 October 2020). continued on next page
SRI
Period 1
Period 2
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
MAL
IND
FIJ
SRI
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
FIJ
MAL
IND
ASIA–10
ASIA–10 Correlation between the Size of Wellness Economy and Aging
SRI
Period 1
Period 2
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
MAL
IND
FIJ
SRI
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
FIJ
MAL
IND
ASIA–10
ASIA–10 Correlation between the Size of Wellness Economy and Aging of Wellness Economy and Aging
Period 2
SRI
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
FIJ
MAL
IND
ASIA–10 SRI
Period 1
16
14
12
10
8
6
4
4
5
6
7
8
9
10
11
12
13
14
PRC
Wellness economy as % of GDP
THA
KAZ
VIE
PHI
Elderly population as % of total population
MON
MAL
IND
FIJ
ASIA–10 FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines,
PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Box: Wellness Economies and Aging Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC
(2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculation using demographic data from the online ADB Key Indicators Database. https://kidb.adb.org/kidb/
(accessed 28 October 2020). continued on next page ADB Economics Working Paper Series No. 631 14 Box continued Alternatively, one can also compare the growth rate of wellness economy and the growth rate of
elderly population between two periods, as illustrated in Box Figure 2. In Asia-10, the annualized
growth rate of population aged 65 years and above is at 4%, which is far below the 10.7% annual
rate of expansion of wellness economy in recent years. This pattern is observed for almost all of
ADB DMCs. The most notable gap between growth rate of wellness economy and growth rate of
elderly population is seen for India (13.5% vs. 3.8%), Viet Nam (11.8% vs. 2.8%), and Fiji (10.2%
versus 1.9%). Meanwhile in the People’s Republic of China, the annual growth rate of wellness
economy is 10.5%, which also exceeds the 4.1% annual growth rate of elderly population. Growth of Wellness Economy versus Growth of Elderly Population
FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China,
SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC
(2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. Box: Wellness Economies and Aging 10.7
10.2
13.5
1.2
13.2
9.3
8.6
10.5
1.3
5.2
11.8
4.0
1.9
3.8
2.7
5.7
2.7
4.5
4.1
5.4
4.4
2.8
0
2
4
6
8
10
12
14
16
Growth rate (%)
Wellness economy
Elderly population
SRI
PRC
ASIA–10
THA
KAZ
VIE
PHI
MON
MAL
IND
FIJ Growth of Wellness Economy versus Growth of Elderly Population
10.7
10.2
13.5
1.2
13.2
9.3
8.6
10.5
1.3
5.2
11.8
4.0
1.9
3.8
2.7
5.7
2.7
4.5
4.1
5.4
4.4
2.8
0
2
4
6
8
10
12
14
16
Growth rate (%)
SRI
PRC
ASIA–10
THA
KAZ
VIE
PHI
MON
MAL
IND
FIJ Growth of Wellness Economy versus Growth of Elderly Population Elderly population FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China,
SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC
(2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China,
SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC
(2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. (
,
);
(
,
);
(
,
);
(
,
)
Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. Overall, Box Figures 1 and 2 suggest that the increase in the size of wellness economy is also largely
driven by factors other than the country’s aging population. These factors capture shift in
preferences which could relate to wellness consumption patterns as well as changes in behaviors
toward healthy and well-rounded lifestyles. Overall, Box Figures 1 and 2 suggest that the increase in the size of wellness economy is also largely
driven by factors other than the country’s aging population. Box: Wellness Economies and Aging These factors capture shift in
preferences which could relate to wellness consumption patterns as well as changes in behaviors
toward healthy and well-rounded lifestyles. 15 The Wellness Economy The Wellness Economy Countries in developing Asia have made significant strides in the expansion of the wellness
economy. In absolute terms, the PRC experienced the most significant expansion of the wellness
economy, doubling its size from $585.5 billion to $1.18 trillion in just 7 years. This is equivalent to an
average annual growth rate of about 10.5%. The annualized growth rate of the wellness economy has
also been double digit for India (13.5%), Malaysia (13.2%), Viet Nam (11.8%), and Fiji (10.2%). If these
growth rates are sustained, these countries’ wellness economies can be expected to double in size in
less than 7 years. Mongolia and the Philippines also experienced a significant increase in the size of the
wellness economy, growing annually at an average of 9.3% and 8.6%, respectively. Together, these 10
economies demonstrate rapid growth, from an estimated $756.8 billion in the first period to $1.46
trillion in the second period in constant 2010 prices.13 Except for Kazakhstan and Sri Lanka, the estimated annual growth rate of the wellness
economy is much higher compared to the growth of the entire economy. This implies that the
expansion of the wellness economy generally outpaced the other sectors. In Malaysia, for example, the
annualized growth rate of the wellness economy is 7.9 percentage points higher compared to the
average annual growth of its real GDP. In India this difference is as much as 6.1 percentage points. The
same pattern is also observed in the case of Fiji and Viet Nam, where the estimated growth of the
wellness economy is at least 5.6 percentage points higher relative to the entire economy. For Mongolia,
Thailand, the PRC, and the Philippines, the difference is between 1 to 3 percentage points. Collectively
for Asia-10, wellness gross value added has expanded in recent years at an estimated average of 10.7%
annually, which is 3.5 percentage points higher compared to the 7.2% annual expansion of its overall
GDP in constant prices. These estimates are consistent with earlier findings from GWI (2018) which
suggests that the expansion of the wellness economy is relatively faster than the expansion of the
overall economy. 13 The two periods estimated for each country are not necessarily the same due to data limitations. However, looking at
these figures together as a proxy for developing Asia can give an idea of how big the region’s wellness economy has
become. This is done by summing the GVA attributable to wellness for all countries and dividing by the sum of their total
GVA in each of the two periods (Consing et al. 2020). Box: Wellness Economies and Aging Table 2 shows the size of the wellness economy in per capita terms, expressed in United States
dollars at constant 2010 prices. In this table, wellness is measured to take into account the differences in
population. These estimates can be interpreted as the annual spending on wellness per individual. While
the aggregate size of the wellness economy, shown in Table 1, is comparable for Malaysia and the
Philippines in period 2, the corresponding estimates in per capita terms differ significantly. Malaysia’s
wellness per capita in 2015 is 3.3 times the wellness per capita in the Philippines in 2017, and the latter’s
estimate is much closer to that of Mongolia ($200) and Fiji ($195) in the more recent period. Notably, wellness per capita spending is comparable for the PRC, Sri Lanka, and Thailand in
period 1: $438 (2010), $430 (2012), and $429 (2012), respectively. However, stark differences are
observed between their annual growth rates thereafter. Table 2 indicates that wellness per capita in
Thailand grew at 4.7% annually, which is less than half the annual growth rate of wellness per capita in
the PRC. In Sri Lanka, wellness per capita barely increased by $6 for a period of 5 years, while
Kazakhstan experienced a $5 decline in wellness per capita between 2013 and 2017. In contrast, the
double-digit annual growth rate in Malaysia and Viet Nam increased wellness per capita by $287
(73%) and $57 (65%), respectively, and each expansion occurred within a span of 5 years. Despite
having a population comparable in size to that of the PRC, India’s wellness per capita grew the fastest,
expanding at an average annual growth rate of 12.2%—from $78 in 2012 to $128 in 2017. 13 The two periods estimated for each country are not necessarily the same due to data limitations. However, looking at
these figures together as a proxy for developing Asia can give an idea of how big the region’s wellness economy has
become. This is done by summing the GVA attributable to wellness for all countries and dividing by the sum of their total
GVA in each of the two periods (Consing et al. 2020). ADB Economics Working Paper Series No. Box: Wellness Economies and Aging 631 16 Table 2: Size of the Wellness Economy in Per Capita Terms for Selected Asian Countries
($, constant 2010 prices)
Country
Period 1
Period 2
Real wellness GDP
Per Capita Growth
Rate
(annualized, %)
Real GDP
Per Capita Growth
Rate
(annualized, %)
Asia-10
259
476
6.7
3.9
Fiji
122
195
9.9
4.3
India
72
128
12.2
6.2
Kazakhstan
517
512
(0.2)
1.2
Malaysia
392
679
11.6
3.8
Mongolia
122
200
7.2
6.1
People’s Republic of China
438
848
9.9
7.1
Philippines
148
207
6.9
5.0
Sri Lanka
430
436
0.3
3.3
Thailand
429
541
4.7
2.4
Viet Nam
87
144
10.6
5.1
GDP = gross domestic product. Notes: Population and Real GDP per capita data are based on World Bank’s estimates. The wellness economy in per capita terms for Asia-10
is the average in each period weighted by each country’s total population. The growth rate for Asia-10 is the average growth rate of all
countries’ wellness economies per capita weighted by each one’s real GDP per capita in the second period. Periods: Fiji (2012, 2017); India
(2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines
(2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 2: Size of the Wellness Economy in Per Capita Terms for Selected Asian Countries
($, constant 2010 prices) GDP = gross domestic product. Notes: Population and Real GDP per capita data are based on World Bank’s estimates. The wellness economy in per capita terms for Asia-10
is the average in each period weighted by each country’s total population. The growth rate for Asia-10 is the average growth rate of all
countries’ wellness economies per capita weighted by each one’s real GDP per capita in the second period. Periods: Fiji (2012, 2017); India
(2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines
(2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 2. Structure of the Wellness Sector Including medical and dental practice industries, as well as other human health activities, health care-
related industries comprise a significant portion of wellness sector, even accounting for over or nearly
half of the wellness GVA in Fiji and Viet Nam. In the case of the PRC, Sri Lanka, and Thailand, the biggest contributors to the wellness sector
after human health activities are amusement and recreation activities. In Kazakhstan, Malaysia, and
the Philippines, the biggest contributors, after human health activities, are those activities relating to
the manufacture and retail trade of pharmaceutical products. In Fiji, India, and Viet Nam, tourism-
supporting activities related to short-term accommodation are the biggest contributors after human
health activities. Even when the size of wellness economies relative to total economies are similar for
some ADB DMCs, their structures can vary significantly from one another. Figure 1: Structure of the Wellness Sector: Share of the Top Five Wellness Industries
(as a % of wellness sector GVA)
FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC =
People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. 2. Structure of the Wellness Sector Figure 1 shows the structure of the GVA coming from just the wellness sector itself (also called the
forward linkage as discussed in section II.E) for the selected ADB DMCs. This figure highlights the top
five wellness industries for each country by year, as measured by their percentage share to total GVA
from wellness industries. Results suggest that the top five wellness industries alone comprise at least
50% of the wellness sector for all countries. In most economies, the share of the top five wellness
industries is as high as 80%. For example, in Fiji, the top five wellness industries comprise 82.3% of its
wellness sector in 2012, which increased to 88% in 2017. This proportion was even higher in India for
both years, at about 90%. In Kazakhstan, the top five wellness industries comprised 60.7% of its
wellness sector in 2012, but this share declined to 53.7% in 2017, indicating that other wellness
industries had increased their share to the country’s GVA from wellness industries. Most of the top five wellness industries consistently appear in both years, suggesting that there
is no major change in the structure of the wellness sector between the two periods. In the PRC, health
care-related services, amusement parks and other recreation activities, as well as wellness-related
construction activities consistently appear in the top five wellness industries for both years. These
industries also dominate the wellness sector in the case of Mongolia and India for both years. Meanwhile, Malaysia’s wellness sector is dominated by retail of pharmaceutical goods, health
care-related industries, as well as wellness tourism-related sectors including short-term
accommodation and travel agency services. While these industries consistently dominate the country’s 17 The Wellness Economy wellness sector, each industry’s relative importance, expressed as a share of the wellness sector GVA,
does not remain constant. wellness sector, each industry’s relative importance, expressed as a share of the wellness sector GVA,
does not remain constant. Health care-related industries consistently make up a large part of the wellness sector for all
countries in both years. Specifically, hospital activities account for at least 10% of the wellness sector. This share is higher for Fiji, Mongolia, Philippines, Thailand, and Viet Nam, where hospital services
alone comprise at least 30% of the country’s wellness sector GVA, at least in the latter period. 3. Forward and Backward Linkages As discussed in the methodology, the production of the wellness sector is interconnected with other
sectors in the economy through its forward and backward linkages. Here, the forward linkage refers to
the GVA from wellness industries used in the production of all goods and services, and this
corresponds to the first term in equation (6). Intuitively, production in the wellness sector and the
demand for wellness goods and services used in the production of other goods and services (including
within the wellness sector itself) move together. The length of the forward linkage of the wellness
sector measures its relative significance in terms of the overall productive activities that the wellness
sector could support (Miller and Blair, 2009). On the other hand, the backward linkage refers to the GVA from all industries used in the
production of wellness goods and services, and this corresponds to the second term in equation (6). Intuitively, a rise in the production in the wellness sector is associated with an increase in demand for
goods and services used in the production of wellness goods and services. The length of the wellness
sector’s backward linkage can be interpreted as its relative importance in the economy in terms of the
overall productive activities that it generates. The total linkage of the wellness sector is the sum of the
sector’s forward and backward linkages less their intersection (to remove the double-count). Figure 2
presents the estimates for these linkages in terms of their percentage share to the country’s total GVA,
as indicated by the bars of different colors. Figure 2: Disaggregation of Wellness Economy by Country, by Period
(as % of GDP)
FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s
real GDP in the second period. 2. Structure of the Wellness Sector 44
53
37
36
23
14
13
12
24
35
34
35
13
26
18
17
40
34
19
33
8
12
11
8
15
10
9
9
8
30
11
16
8
4
3
5
9
10
5
15
16
2
5
12
23
6
14
11
24
18
10
10
24
9
39
6
7
7
7
4
18
8
8
6
25
55
44
24
24
5
9
9
10
11
1
8
15
16
26
10
5
7
5
12
9
8
5
6
4
8
6
24
14
5
6
10
8
8
7
2
8
18
12
10
11
39
46
36
29
14
22
28
30
17
28
16
28
17
22
34
22
0
10
20
30
40
50
60
70
80
90
100
2012
2017
2012
2017
2013
2017
2010
2015
2010
2017
2012
2017
2010
2017
2012
2017
2012
2017
2012
2017
% Share to wellness GVA (%)
Hospital activities
Medical and dental practice activities
Other human health activities
Travel agency activities
Tour operator activities
Other reservation service and related activities
Short term accommodation activities
Creative, arts and entertainment activities
Activities of amusement parks and theme parks
Other amusement and recreation activities n.e.c. Sports and recreation education
Hairdressing and other beauty treatment
Manufacture of pharmaceuticals, etc. Retail sale of pharmaceuticals, etc. Construction of buildings
Construction of other civil engineering projects
Others
FIJ
IND
KAZ
MAL
MON
PHI
PRC
SRI
THA
VIE FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC =
People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. ADB Economics Working Paper Series No. 631 18 3. Forward and Backward Linkages 3.3 3.9
2.5
3.6
2.3 3.0
3.2 2.5
2.0
3.0
2.7 3.0
3.2 3.4
3.5 4.1
8.2
7.3
4.6 4.9
3.3
4.8
3.5
4.5
0.8
1.0
1.6
2.3
1.8
2.1
1.4
1.7
1.4
1.1
1.8
2.1
4.5
5.2
3.0
2.8
2.0
2.3
1.9
2.5
1.1
1.3
0.6
0.5
0.5
0.8
0.3 0.3
0.8
1.3
0.7 0.9
1.0
1.2
1.3
1.5
1.5
1.3
1.3
1.3
0.7
0.7
0.6
0.7
0.1
0.2
0.5
0.8
0.3 0.2
0.2
0.4
0.4 0.3
0.5
0.6
0.6
0.8
1.1
1.0
0.8
0.7
0.4
0.5
8.5
10.5
4.0
5.3
5.0
6.8
5.6 5.2
4.4
6.4
5.2 5.4
6.5
7.3
9.9
11.5
13.9
12.4
8.6
9.3
6.3
8.4
0.0
2.0
4.0
6.0
8.0
10.0
12.0
14.0
16.0
% share to total GVA
Forward and backward linkage (intersection)
Pure backward linkage
Pure forward linkage
Wellness gross fixed capital formation
KAZ
MAL
MON
PHI
PRC
IND
FIJ
Asia-10
Period 1
Period 2
2012
2017
2012
2017
2013
2017
2010
2015
2010
2017
2012
2017
2013
2017
2012
2017
2013
2017
2012
2017
SRI
THA
VIE FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s
real GDP in the second period. FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s
real GDP in the second period. 19 The Wellness Economy The Wellness Economy The orange bars represent the pure backward linkage, while the green bars represent the pure
backward linkage. The blue bar indicates the intersection between forward and backward linkages,
which is equivalent to the double-count. Hence, the pure backward linkage together with the
intersection represent the total backward linkage. In the same manner, the pure forward linkage
together with the intersection indicate the total forward linkage. 3. Forward and Backward Linkages Finally, yellow bars represent the gross
fixed capital formation (GFCF) that is relevant to the wellness sector. Wellness GFCF represents the
investments made by the economy for the future production of wellness goods and services, and this
could be in the form of construction of buildings and infrastructure, purchase of machineries and
equipment, or procurement of intellectual property rights. The total height of the bars indicates the
size of wellness economy as a percentage of total GVA, corresponding to equation (6). Figure 2 exhibits these estimates for ten ADB DMCs. With the exception of Sri Lanka and
Kazakhstan, the share of the wellness economy increased between the two time periods for each
country. As shown in Table 1, this translates to a wellness economy that generally expands faster than
the total economy. Notice that the wellness economy’s share in Sri Lanka and Kazakhstan actually
decreased between the two time periods, and correspondingly, the wellness economy grew slowly
relative to the total economy. In the PRC, the share of wellness economy increased from 9.9% (2010)
to 11.5% (2017). Considering that the PRC has a population of more than 1.3 billion, and being one of
the largest economies in the world, this rapid growth translates to a huge leap on the productive
activities that constitute the wellness economy. It is also worth mentioning that India experienced a
significant increase in the size of its wellness economy, growing from 5.0% to 6.8% of its GDP in just a
span of 5 years. For the four Southeast Asian economies included, the share of wellness economy is at least 6%
in the latter period. In Thailand, the share of wellness gross value added increased from 8.6% (2012) to
9.3% (2017), while in the Philippines, the size of the wellness economy grew from 6.5% (2012) to 7.3%
(2017). Viet Nam and Malaysia experienced sharp increase in the size of wellness economy. In Viet
Nam, this share increased from 6.3% (2012) to 8.4% (2017), while in Malaysia, the share of wellness
economy grew from 4.4% (2010) to 6.4% (2015). Mongolia’s share of wellness GVA moderately increased by 0.2 percentage point, from 5.2% in
2010 to 5.4% in 2017. Likewise, the share of wellness GVA in Fiji increased from 4.0% in 2012 to 5.3%
in 2017. In Sri Lanka, the share of wellness GVA is 13.9% in 2012. 4. Hypothetical Extraction of the Wellness Sector The hypothetical extraction of the wellness sector allows us to gauge its relative importance to the
country’s total economy. In this process, both the backward and forward linkages of wellness sector are
nullified, creating a hypothetical scenario where the wellness-producing and wellness-supporting
industries are inexistent. This method therefore measures how much of the country’s GDP is lost when
the wellness sector is extracted, both directly and indirectly. Figure 3 illustrates the results of the hypothetical extraction method as applied to ten of ADB’s
DMCs. The estimated loss from nullifying the wellness sector is expressed as a percentage of GDP,
decomposed into direct and indirect loss as described in equation (14). The direct loss is exactly the
same as the sum of the forward and backward linkages, less the double-count, as shown in Figure 2. Results consistently indicate that the GDP lost is greater than the share of wellness to GDP. That is,
extracting wellness economy has a synergistic effect on the economy, as it does not only directly
remove the contribution of the wellness sector to the gross value added, but it also entails some
decline in the output of other sectors. Notice that the indirect GDP loss is largest in the PRC, where it
accounts for 1.7% in 2010, and 1.9% in 2017. For the rest of the economies, the indirect loss is less than
1%, ranging from 0.1% to 0.7%. Figure 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
by Country, by Period
(as % of GDP)
FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. ADB Economics Working Paper Series No. 631 Finally, wellness GFCF as a percentage of GVA is largest in Sri Lanka (1.1% in 2012, and 1% in
2017). This reflects the economic boost driven by the public investment to rebuild after ending its 3-
decade conflict in 2009. However, this source of growth is not sustainable in the long run (World Bank
2015), which could also explain the declining share of wellness GFCF in the latter period. In the other
economies, the share of wellness GFCF is less than 1%. In level, the PRC’s wellness GFCF stands at
$95.1 billion in 2017, and this is more than three times higher than the wellness GFCF of the other nine
economies combined. 3. Forward and Backward Linkages This share had moderately declined
by 1.5 percentage points in 2017. The same trend is observed in the case of Kazakhstan, where the
wellness economy moderately shrank by 0.4 percentage point, from 5.6% in 2013 to 5.2% in 2017. The
decrease in the share of wellness economy for these two countries, however, does not imply that the
levels of wellness GDP decreased over time. Rather, this trend only indicates that the rest of the
economy grew faster than the wellness economy. Results indicate that the backward linkage of the wellness sector is longer than its forward
linkage for all countries for both periods. In the context of input–output analysis, a strong backward
linkage is indicative of heavy reliance on interindustry supply. This is usually evident in the case of
services sector, where inputs from other industries are required for its production. Since a huge
proportion of wellness economy is comprised of services, as in health care, amusement and
entertainment, and tourism activities, the interconnection with the upstream sectors is also expected
to be much more significant compared to the downstream sectors. The gap between the backward
linkage and the forward linkage is largest in the case of the PRC for both periods, between which it
increased. This reflects the “rebalancing of the economy” in the PRC, where services sector now
comprising a bigger share of the economy than industry (World Bank 2017). 20 ADB Economics Working Paper Series No. 631 4. Hypothetical Extraction of the Wellness Sector –3.9
–5.1
–4.5
–6.0
–5.3–5.0
–4.2
–6.0
–4.8–5.0
–6.0 –6.7
–9.3
–10.8
–12.7
–11.4
–7.9 –8.5
–5.9
–8.0
–0.2
–0.1
–0.4
–0.6
–0.2–0.3
–0.5
–0.8
–0.4–0.4
–0.6
–0.7
–1.7
–1.9
–0.6
–0.5
–0.6
–0.6
–0.4
–0.4
–4.0
–5.2
–4.9
–6.6
–5.5 –5.2
–4.7
–6.8
–5.2 –5.4
–6.6
–7.4
–11.0
–12.6
–13.3
–11.9
–8.4
–9.1
–6.3
–8.3
–16.0
–14.0
–12.0
–10.0
–8.0
–6.0
–4.0
–2.0
0.0
2.0
% share to GVA
Direct loss
Indirect loss
FIJ
2012
2017
2012
2017
2013
2017
2010
2015
2010
2017
2012
2017
2010
2017
2012
2017
2012
2017
2012
2017
IND
KAZ
MAL
MON
PHI
PRC
SRI
THA
VIE Figure 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
by Country, by Period
(as % of GDP) FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia,
PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The Wellness Economy The Wellness Economy 21 Table 3 shows the decomposition of GDP loss into direct and indirect loss. The latter is further
disaggregated into own-industry elasticity effects and cross-industry elasticity effects. In all
economies, own-industry elasticity effect is less than 0.1% of GDP for both periods. The aggregated
cross-industry elasticity effect is much higher relative to own-industry elasticity effect, reaching as
much as 1.85% of GDP as in the case of the PRC. Except for Fiji and Kazakhstan, cross-industry
elasticity for the other economies ranges between 0.33% and 0.73% of GDP. Together, these elasticity
effects could also be interpreted as the extent of interdependence of the other sectors when the
wellness sector is hypothetically extracted in the economy. GDP = gross domestic product. B.
Wellness Employment B. As discussed in the previous section, the wellness economy has a sizeable contribution to the GDP of
developing economies in Asia. Hence, it should also be expected that the wellness economy generates
and supports a significant portion of the overall employment. This section delves into this empirical
inquiry by quantifying the size of the wellness employment in terms of the number of jobs attributable
to the wellness economy (section III.B.1). Moreover, this section compares the labor productivity in
the wellness economy (section III.B.2), and presents the decomposition of the wellness employment
into forward and backward linkages to quantify the relative size of employment which are directly or
indirectly generated by the wellness sector (section III.B.3). Finally, employment loss from a
hypothetical extraction of the wellness economy is also examined, as an alternative measure for the
relative significance of the wellness economy in the overall employment (section III.B.4). 4. Hypothetical Extraction of the Wellness Sector Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
(as % of GDP)
Country
Period
Total Loss
Direct Loss
Indirect Loss
Own-
Elasticity
Effect
Cross-
Elasticity
Effect
Fiji
2012
4.04
3.86
0.18
0.00
0.18
2017
5.24
5.10
0.14
0.00
0.14
India
2012
4.87
4.50
0.37
0.00
0.37
2017
6.64
6.04
0.60
0.01
0.60
Kazakhstan
2012
5.51
5.33
0.18
0.01
0.18
2017
5.23
4.95
0.28
0.02
0.26
Malaysia
2010
4.73
4.21
0.53
0.01
0.52
2015
6.74
6.00
0.75
0.02
0.73
Mongolia
2010
5.17
4.81
0.36
0.02
0.34
2017
5.37
5.03
0.35
0.02
0.33
People’s Republic of
China
2012
2017
10.96
12.64
9.26
10.76
1.70
1.18
0.02
0.03
1.68
1.85
Philippines
2012
6.66
6.00
4.28
0.04
0.55
2017
7.26
6.70
0.67
0.07
0.60
Sri Lanka
2012
13.30
12.73
3.83
0.03
0.53
2017
11.89
11.40
0.48
0.02
0.46
Thailand
2012
8.40
7.86
0.55
0.01
0.54
2017
9.15
8.53
5.04
0.01
0.60
Viet Nam
2012
6.33
5.91
7.08
0.01
0.41
2017
8.33
7.98
0.36
0.01
0.35
GDP = gross domestic product Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
(as % of GDP) Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted
(as % of GDP) ADB Economics Working Paper Series No. 631 22 1. Size of Wellness Employment Table 4 shows the estimated wellness employment for each country and time period, containing the
jobs that are both directly and indirectly attributable to the production of wellness goods and services. The annualized growth rate of wellness employment is also included in the third column where it can
be compared with the growth rate of total employment for each country. Further insights on the
wellness sector’s economic relevance may be derived from this. Malaysia’s wellness employment had
the largest increase from 595,000 in 2010 to 1.6 million in 2015, and this is followed by the PRC where
wellness employment grew from 58.7 million in 2010 to 118.5 million in 2017. Both countries
experienced double-digit wellness employment growth rates of 21.9% and 10.5%, respectively. India’s
wellness employment also experienced significant growth at 7.7% annually, from 21.4 million in 2012 to
30.6 million in 2017. Generally, the economies of Asia-10 have experienced a positive growth in
wellness employment across the two time periods estimated in each. Collectively, wellness
employment in Asia-10 expanded from 88.1 million to 159.4 million between the two periods
estimated, increasing at an annual growth rate of 9.7%. Except for Malaysia and the PRC, the growth of wellness GVA is generally faster than the
growth of wellness employment. Collectively for Asia-10, the weighted average annual growth rate of
wellness gross value added is one percentage point higher than the weighted average annual growth
rate of wellness employment. This indicates growth in labor productivity within the wellness economy
in recent years, consistent with what is shown in Table 3 for most of ADB DMCs. Labor productivity in
the wellness economy increased from $8,594 to $9,160 for Asia-10, ranging from $4,903 (Viet Nam)
to as high as $18,891 (Sri Lanka) in period 2. The structure of the wellness sector may explain the
variation in labor productivity across countries. For example, industries such as the manufacturing of
pharmaceutical goods may be more productive than retail trade services. 1. Size of Wellness Employment 23 The Wellness Economy Table 4: Wellness Employment for Selected Asian Countries
(Thousands)
Country
Period 1
Period 2
Wellness
Employment
Growth Rate
(annualized, %)
Employment
Growth Rate
(annualized, %)
Asia-10
88,059
159,410
9.7
0.2
Fiji
10
13
5.4
2.9
India
21,139
30,628
7.7
(0.1)
Kazakhstan
634
654
0.8
0.0
Malaysia
595
1,600
21.9
3.4
Mongolia
63
91
5.4
2.6
People’s Republic of China
58,742
118,536
10.5
0.3
Philippines
1,959
2,292
3.2
1.4
Sri Lanka
487
495
0.3
1.5
Thailand
2,049
2,327
2.6
(0.8)
Viet Nam
2,381
2,774
3.1
1.1
Notes: The growth rate for Asia-10 is the average growth rate of all countries’ wellness employed weighted by each one’s total employment in
the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017);
People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 4: Wellness Employment for Selected Asian Countries
(Thousands) Notes: The growth rate for Asia-10 is the average growth rate of all countries’ wellness employed weighted by each one’s total employment in
the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017);
People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 2. Wellness Economy Labor Productivity Table 5 compares wellness economy labor productivity, expressed as wellness economy GDP per
worker in the wellness economy, to economywide labor productivity, expressed as total GDP per
worker in the economy, as indicated by the ratios shown in the last two columns. A ratio greater than 1
indicates that wellness labor productivity is stronger than overall labor productivity. Conversely, a ratio
less than 1 indicates that wellness labor productivity is weaker than overall labor productivity, such as in
Kazakhstan, Malaysia, Mongolia, and the PRC in the second period. Generally, it cannot be concluded with high certainty what the causes of these ratios are due to
the limited data and sample size. Theoretically, however, there may be several explanations for these
ratios. Countries with ratios less than 1 may have sufficiently advanced industrial or manufacturing
sectors that produce high-value goods with relatively few laborers, and therefore workers in the
wellness sector, whose goods are typically service oriented, might not be as productive relative to that. The reverse scenario implies a similar logic for the wellness sector where, supposing that its structure is
oriented toward high-value goods and services that require relatively low labor, a ratio greater than 1
may arise. Similarly, countries with underdeveloped industrial sectors or are otherwise services
oriented may have the average laborer being similar in productivity to workers in the wellness
economy. Employment populations may also differ fundamentally between a country’s wellness
economy and its overall economy due to other factors and unique social conditions that are difficult to
observe or measure quantifiably. ADB Economics Working Paper Series No. 631 24 Table 5: Wellness Economy Labor Productivity for Selected Asian Countries
($, constant 2010 prices)
Wellness Economy Labor Productivity
Ratio of Wellness Economy Labor
Productivity to Total Economy
Labor Productivity
Period 1
Period 2
Period 1
Period 2
Asia-10
8,594
9,160
1.3
0.9
Fiji
10,540
13,158
1.0
1.1
India
4,300
5,585
1.1
1.0
Kazakhstan
13,897
14,124
0.7
0.6
Malaysia
18,561
12,841
0.9
0.5
Mongolia
5,286
6,837
0.8
0.7
People’s Republic of China
9,967
9,924
1.2
0.8
Philippines
7,356
9,512
1.3
1.3
Sri Lanka
18,034
18,891
2.0
1.9
Thailand
14,211
16,088
1.5
1.4
Viet Nam
3,270
4,903
1.3
1.5
Note: Overall labor productivity are calculated as the ratio between Real GDP (in $, constant 2010) and total employment using World Bank data. 2. Wellness Economy Labor Productivity Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of
China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 5: Wellness Economy Labor Productivity for Selected Asian Countries
($, constant 2010 prices) Note: Overall labor productivity are calculated as the ratio between Real GDP (in $, constant 2010) and total employment using World Bank data. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of
China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 3. Wellness Employment: Forward and Backward Linkages Figure 4 shows the disaggregation of wellness employment in terms of its forward and backward
linkages. Forward linkage captures the number of jobs that are directly generated by the wellness
sector, while backward linkages captures the employment that are indirectly attributed to the wellness
industries, as these jobs are generated by other sectors that support wellness industries. The blue bars
represent the intersection between forward and backward linkages (equivalent to what is double-
counted applying the methodology). The orange bars represent the pure backward linkages, while the
green bars represent the pure forward linkages. The cumulative height of the three bars is the
percentage share of wellness employment to the country’s total employment. In general, the percentage share of wellness employment to total employment increased for
each country over the two time periods estimated. The sharpest rise is seen in the case of the PRC and
Malaysia, increasing by 7.5 and 6.4 percentage points, respectively. For other countries in Asia-10,
wellness employment’s contribution varies between 3.6% to 7.6% of total employment by the second
period. Collectively, Asia-10’s share of wellness employment increased rapidly between the two
periods, from 6.3% to 11.2% of total employment in the region, primarily driven by the steep increase of
wellness employment in the PRC. It is also observed that the backward linkage is generally higher than
the forward linkage, indicating that much of the employment attributable to wellness comes from the
industries supporting the wellness sector. This is generally consistent with the results shown in Figure
2, where wellness-supporting industries are shown to account for a larger share of the wellness
economy relative to the wellness sector itself. The Wellness Economy 25 Figure 4: Disaggregation of Wellness Employment by Country, by Period
(as % of GDP)
FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC =
People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam
Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country weighted by each
one’s total employment in the second period. 3. Wellness Employment: Forward and Backward Linkages 3.0
3.6
0.6 0.8
1.8
3.0
0.5 0.6
1.3
1.6
1.3
1.1
1.7
1.7
4.1
4.3
2.3
1.8
1.9
2.4
1.9 2.4
0.8
1.9
0.3 0.3
0.5
0.7
2.0 2.2
1.0
3.0
1.1
1.5
0.9
1.0
1.0
2.9
0.6 0.6
0.7
0.8
0.5
0.3
6.3
11.2
3.2 3.6
4.3
6.3
7.4 7.6
5.0
11.4
6.1
7.4
5.2
5.7
7.7
15.3
6.4 6.0
5.3
6.3
4.7
5.2
0.0
Period 1
Period 2
2012
2017
2012
2017
2013
2017
2010
2015
2010
2017
2012
2017
2010
2017
2012
2017
2012
2017
2012
2017
2.0
4.0
6.0
8.0
10.0
12.0
14.0
16.0
18.0
% share to total employment
Forward and backward linkage (intersection)
Pure backward linkage
Pure forward linkage
Asia–10
FIJ
IND
KAZ
MAL
MON
PHI
PRC
SRI
THA
VIE
2.4
5.6
2.3 2.5
2.1 2.6
4.9 4.8
2.7
6.9
3.8
4.8
2.7
3.0
2.6
8.0
3.4
3.6
2.7 3.0
2.3
2.4 Figure 4: Disaggregation of Wellness Employment by Country, by Period
(as % of GDP) FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC =
People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam
Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country weighted by each
one’s total employment in the second period. Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country
one’s total employment in the second period. 4. Potential Employment Losses from Hypothetical Extraction Similar to section III.A.4, the relative importance of the wellness sector is also measured in terms of the
estimated employment loss from its hypothetical extraction. In this process, all linkages relating to the
wellness economy are nullified to measure how many jobs will be lost when both forward and
backward linkages of the wellness sector are extracted. Employment loss from the hypothetical extraction of the wellness sector is shown in Figure 5. Results are expressed as a percentage of total employment, and are decomposed into direct and
indirect loss, similar to what is shown in Figure 3. Note that the direct loss, as indicated by the blue
bars, is equivalent to the percentage share of wellness employment to total employment shown in
Figure 4. Similar to the results of the hypothetical extraction method as applied to GDP, employment
loss as a percentage of total employment is higher than the share of wellness employment to total
employment. The difference constitutes the indirect loss, as indicated by the orange bars. The wellness
employment loss as a percentage of total employment is highest for the PRC at 16.8% (2017), and
Malaysia at 12.0% (2015). For the rest of Asia-10, wellness employment loss as a percentage of total
employment ranges from 3.9% (Fiji) to 7.9% (Kazakhstan), in the second period. ADB Economics Working Paper Series No. 631 26 Figure 5: Decomposition of Employment Loss When Wellness Sector is Extracted
by Country, by Period
(as % of total employment)
FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines,
PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. 4. Potential Employment Losses from Hypothetical Extraction –3.4 –3.8
–4.3
–6.3
–7.4 –7.6
–5.0
–11.4
–6.1 –7.4
–5.2 –5.7
–7.7
–15.3
–6.4 –6.0
–5.3 –6.3
–4.7 –5.2
–0.2 –0.1
–0.4
–0.8
–0.2 –0.3
–0.5
–0.7
–0.3
–0.3
–0.5 –0.6
–1.6
–1.6
–0.4 –0.3
–0.5
–0.7
–0.4 –0.4
–3.6 –3.9
–4.7
–7.1
–7.6 –7.9
–5.5
–12.0
–6.4
–7.7
–5.7 –6.3
–9.3
–16.8
–6.8 –6.3
–5.9
–6.9
–5.1 –5.5
–20.0
–18.0
–16.0
–14.0
–12.0
–10.0
–8.0
–6.0
–4.0
–2.0
0.0
2.0
% share to GVA
FIJ
IND
KAZ
MAL
MON
PHI
PRC
SRI
THA
VIE
2012
2017
2012
2017
2013
2017
2010
2015
2010
2017
2012
2017
2010
2017
2012
2017
2012
2017
2012
2017
Direct loss
Indirect loss Figure 5: Decomposition of Employment Loss When Wellness Sector is Extracted
by Country, by Period
(as % of total employment) FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines,
PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines,
PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The decomposition of indirect wellness employment into own-industry elasticity and cross-
industry elasticity effects is further detailed in Table 6. Results show that own-industry elasticity
effects range from 0% (Fiji) to 0.05% (Philippines), while cross-industry elasticity effects range from
0.14% (Fiji) to 1.56% (PRC). Together, the own-industry elasticity and cross-industry elasticity effects are the reason why
estimated employment losses from hypothetical extraction of the wellness sector in Table 6 are
greater than just the employment attributable to the wellness economy. The own-elasticity effect is
the additional loss in employment caused by greater sensitivity of nonwellness sectors’ outputs (and
therefore employment) to declines in each one’s own final demand post-extraction than pre-
extraction. The cross-elasticity effect is the additional loss in employment caused by greater sensitivity
of nonwellness sectors outputs to declines in each other’s final demand post-extraction than pre-
extraction. Since production declines beyond the production attributable to the wellness economy in
the current period as shown in the estimated GDP losses from section III.A.4, the corresponding
estimates on employment losses are correspondingly severe. 4. Potential Employment Losses from Hypothetical Extraction 27 The Wellness Economy Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted
(as % of total employment)
Country
Period
Total Loss
Direct Loss
Indirect Loss
Own-
Elasticity
Effect
Cross-
Elasticity
Effect
Fiji
2012
3.59
3.43
0.16
0.00
0.16
2017
3.89
3.75
0.14
0.00
0.14
India
2012
4.75
4.34
0.41
0.01
0.40
2017
7.12
6.33
0.80
0.01
0.78
Kazakhstan
2012
7.61
7.40
0.21
0.01
0.20
2017
7.91
7.62
0.29
0.01
0.28
Malaysia
2010
5.52
5.01
0.51
0.01
0.50
2015
12.04
11.37
0.67
0.01
0.65
Mongolia
2010
6.40
6.10
0.30
0.01
0.29
2017
7.69
7.36
0.33
0.01
0.32
People’s Republic of China
2012
9.30
7.72
1.58
0.02
1.56
2017
16.84
15.27
1.57
0.02
1.55
Philippines
2012
5.74
5.20
0.54
0.03
0.51
2017
6.26
5.68
0.57
0.05
0.52
Sri Lanka
2012
6.82
6.39
0.43
0.02
0.41
2017
6.33
6.02
0.31
0.01
0.30
Thailand
2012
5.85
5.32
0.53
0.01
0.53
2017
6.93
6.27
0.66
0.01
0.65
Viet Nam
2012
5.08
4.68
0.40
0.02
0.38
2017
5.52
5.17
0.35
0.01
0.34
Source: Authors’ calculations. Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted
(as % of total employment) Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted
(as % of total employment) IV.
CONCLUSION AND MOVING FORWARD This paper contributes to the literature on wellness economics and national accounting by showing
how the SNA framework can be used to estimate the economy attributable to the production of
wellness goods and services and then applying this methodology to selected countries in developing
Asia. Through input–output analysis, it is possible to derive the production and employment linkages
between the wellness sector and nonwellness sectors, the potential production and employment
losses that may arise if the wellness sector were hypothetically extracted from the economy, and how
these two sets of estimates relate to one another. Theoretically, this means that any country whose
economic accounting is consistent with the SNA framework can estimate the economic relevance of
its wellness sector. This in turn creates fertile new ground in the field of wellness economics as new 28 ADB Economics Working Paper Series No. 631 data create new possibilities for research and, eventually, policies to promote wellness. As estimates
for more countries are produced over time, it becomes feasible to generate reliable figures at the
regional, and eventually, global level. data create new possibilities for research and, eventually, policies to promote wellness. As estimates
for more countries are produced over time, it becomes feasible to generate reliable figures at the
regional, and eventually, global level. Nevertheless, there are ways to improve the quality of wellness economy estimation within the
SNA framework. The main challenges are data related. Firstly, there would be no need for
disaggregation if each country’s IOT were highly detailed, ideally with rows and columns for all 4-digit
ISIC rev. 4 codes. In practice, however, a balanced IOT of such a size would be costly to produce. A
second-best scenario would be for each country’s IOT to contain rows and columns corresponding to
at least the 4-digit codes covering the production of wellness goods and services, such as those listed
in Table A.1. A similar prescription applies when estimating wellness employment as employment
numbers are needed for each industry in the IOT in order to estimate the wellness economy’s
contribution to overall employment. Secondly, while the selected ISIC codes provide a basis for estimating the wellness economy,
the process of drawing out the corresponding GVA from available SNA components often differ in
practice between countries due to nonuniformity in the level of detail and aggregation. IV.
CONCLUSION AND MOVING FORWARD Access to
highly detailed supply tables and nationally representative firm-level data on output would allow for
more reliable disaggregation of IOTs when needed, and uniformity in the level of aggregation across
countries would allow for better comparisons in wellness economy estimates between countries and
across time. Fortunately, uniformity can be achieved through the use of national IOTs derived from
regional IOTs such as the World Input–Output Tables and the ADB Multiregional Input–Output
Tables which provide annual national accounts data at a uniform level of detail for a multitude of
countries across time. While the level of detail per country is highly aggregated under these regional
IOTs, the fact that they are uniform in detail means that they may be subjected to a uniform process of
disaggregation and allow for more reliable cross-country analyses. APPENDIX ble A.1: List of Industries and Activities Considered Part of the Wellness Economy Table A.1: List of Industries and Activities Considered Part of the Wellness Economy
ISIC
Rev.4
Code
ISIC Industry
Wellness-Related Activities
2023
Manufacture of soap and detergents, cleaning and
polishing preparations
Only activities related to the manufacture of personal
care items (e.g., beauty, sunburn, manicure
preparations, etc.)
2100
Manufacture of pharmaceuticals, medicinal chemical
and botanical products
All activities related to the manufacture of
pharmaceutical, medicinal, and botanical products
3012
Building of pleasure and sporting boats
All activities related to the manufacture of boats for
recreation and wellness purposes
3230
Manufacture of sports goods
All activities related to the manufacture of sporting
goods
4100
Construction of buildings
All activities related to the construction of wellness-
related and indoor-sports facilities
4290
Construction of other engineering projects
All activities related to the construction of outdoor
wellness and sports facilities
4721
Retail sale of food in specialized stores
All retail sale activities of fruits and vegetables
4763
Retail sale of sporting equipment in specialized stores
Retail sale of sporting and wellness-related goods
4772
Retail sale of pharmaceutical and medical goods,
cosmetic and toilet articles in specialized stores
Retail Sale of pharmaceuticals and cosmetic articles
5510
Short-term accommodation activities
Includes only the provision of short-term
accommodation for holiday, wellness, and recreation
purposes. APPENDIX 5520
Camping grounds, recreational vehicle parks and
trailer parks
Includes only the provision of accommodation in
recreational camps and facilities
7721
Renting and leasing of recreational and sports goods
Includes activities involving the rental and leasing
services of recreational and wellness-related sports
goods
7911
Travel agency activities
Includes activities of agencies engaged in selling of
wellness travel, tour, transportation, and
accommodation services
7912
Tour operator activities
Includes activities of agencies engaged in arranging and
assembling wellness-related tours
7990
Other reservation service and related activities
Other provisional wellness-travel reservation activities
not included in 7911 and 7912
8130
Landscape care and maintenance service activities
All service activities related to landscape care and
maintaining wellness spaces
8541
Sports and recreation education
Education services related to the pursuit of sports,
recreation, and wellness (e.g., yoga, martial arts, etc.)
8610
Hospital activities
All activities
8620
Medical and dental practice activities
All activities Wellness-Related Activities 30 Appendix Appendix 30 ISIC
Rev.4
Code
ISIC Industry
Wellness-Related Activities
8690
Other human health activities
All activities
8710
Residential nursing care facilities
All activities
8720
Residential care activities for mental retardation,
mental health and substance abuse
All activities
8730
Residential care activities for elderly and disabled
All activities
8890
Other social work activities without accommodation
All other social work activities without accommodation
aimed at improving wellness
9000
Creative, arts and entertainment activities
All creative, arts and entertainment services aimed at
improving wellness
9101
Library and archive activities
Activities related to the operation of libraries
9102
Museum activities and operation of historical sites and
buildings
Activities related to the operation of wellness-related
sites (e.g., spiritual spaces, museums, etc.)
9103
Botanical and zoological gardens and nature reserves
activities
All activities related to the operation of wellness-
inducing sites (e.g., botanical gardens, etc.)
9311
Operation of sports facilities
All activities related to the operation of sports facilities
9312
Activities of sports clubs
All activities related to the operation of sports clubs
promoting fitness
9319
Other sports activities
All other fitness related activities excluded in 9311
and 9312
9321
Activities of amusement parks and theme parks
All activities related to the operation of amusement
and theme arks
9329
Other amusement and recreation activities, n.e.c. All other wellness-related activities excluded in 9321
9602
Hairdressing and other beauty treatment
All activities aimed at promoting beauty and wellness
9609
Other personal service activities, n.e.c. All activities of Turkish baths, sauna and steam baths,
solarium, salons etc. ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified.
Source: United Nations. 2008. System of National Accounts. New York. ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified.
S
U
d N
2008 S
f N
l A
N
Y
k APPENDIX ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified. Source United Nations 2008 System of National Accounts New York Appendix 31 ix 31 Appendix 31 Appendix 31 Table A.2: Data Sources Country
Table
Years Available
Dimension
of Tables
Source
Fiji
IOT
2012,2017
35 x 35
ADB
India
IOT
2012,2017
35 x 35
ADB
Kazakhstan
SUT
2013, 2017
698 x 114
KAZ SC
Malaysia
SUT
2010, 2015
68 x 86; 124 x 124
ADB; DOSM
Mongolia
IOT
2010, 2017
35 x 35
ADB
People’s Republic of China
IOT
2010, 2017
35 x 35
ADB
Philippines
IOT
2012, 2017
35 x 35
ADB
Sri Lanka
IOT
2012, 2017
35 x 35
ADB
Thailand
IOT
2012, 2017
35 x 35
ADB
Viet Nam
IOT
2012; 2017
35 x 35
ADB
ADB = Asian Development Bank, DOSM = Department of Statistics Malaysia, IOT = input–output table, KAZ SC = Agency of the
Republic of Kazakhstan on Statistics, SUT = supply and use table. Source: Authors’ compilation. ADB = Asian Development Bank, DOSM = Department of Statistics Malaysia, IOT = input–output table, KAZ SC = Agency of the
Republic of Kazakhstan on Statistics, SUT = supply and use table. Source: Authors’ compilation. Table A.3: Data Sources for Input–Output Table Disaggregation
Country
Source of Disaggregators
Fiji
Structure of donor country (MAL)
India
Firm-level data (Orbis)
Kazakhstan
Supply table
Malaysia (MAL)
Supply table
Mongolia
Structure of donor country (PRC)
People’s Republic of China (PRC)
Firm-level data (Orbis)
Philippines
Firm-level data (Orbis)
Sri Lanka
Structure of donor country (MAL)
Thailand
Firm-level data (Orbis)
Viet Nam
Firm-level data (Orbis)
Source: Authors’ compilation. Table A.3: Data Sources for Input–Output Table Disaggregation REFERENCES Asian Development Bank (ADB). 2018. Economic Indicators for Eastern Asia, Input-Output Tables. Manila. ————. 2019. Key Indicators for Asia and the Pacific 2019. Manila. ————. 2020. Asian Development Outlook 2020 Update: Wellness in Worrying Times. Manila. Barsabal, Michael John, Julian Thomas Alvarez, and Rafael Martin III Consing. 2020. “A Note on
Losses after Hypothetical Extraction.” Unpublished. Consing, Rafael Martin III, Michael John Barsabal, Julian Thomas Alvarez, and Mahinthan J. Mariasingham. 2020. Using the System of National Accounts to Estimate a Country’s Wellness Economy. Manila: ADB. Dietzenbacher, Erik, Bob van Burken, and Yasushi Kondo. 2019. “Hypothetical Extractions from a
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A World-Wide Input-Output Analysis.” ILO Employment Working Paper No. 186. Eurostat. 2008. The Eurostat Manual of Supply, Use and Input-Output Tables. Luxembourg: Office for
Official Publications of the European Communities. Global Wellness Institute (GWI). 2018. Global Wellness Economy Monitor 2018. Global Wellness Institute (GWI). 2018. Global Wellness Economy Monitor 2018. Kalemli-Ozcan, Sebnem Bent Sorensen, Carolina Villegas-Sanchez, Vadym Volosovych, and Sevcan
Yesiltas. 2019. “How to Construct Nationally Representative Firm Level Data from the Orbis Global
Database: New Facts and Aggregate Implications.” NBER Working Paper Series No. 21558. Kharas, Homi. 2017. “The Unprecedented Expansion of the Global Middle Class: An Update.” Global
Economy and Development Working Paper 100. Kickbusch, Ilona and Lea Payne. 2003. “Twenty-first Century Health Promotion: The Public Health
Revolution Meets the Wellness Revolution.” Health Promotion International 18 (4): 275–78. Leontief, Wassily. 1936. “Quantitative Input and Output Relations in the Economic System of the
United States.” Review of Economics and Statistics 18: 105–25. Miller, Gord and Leslie Foster. 2010. “Critical Synthesis of Wellness Literature.” University of Victoria
Faculty of Human and Social Development and Department of Geography. 34 References Miller, Ronald and Peter Blair. 2009. Input-Output Analysis: Foundations and Extensions. Cambridge:
Cambridge University Press. Miller, Ronald and Peter Blair. 2009. Input-Output Analysis: Foundations and Extensions. Cambridge:
Cambridge University Press. Pilzer, Paul Zane. 2007. The New Wellness Revolution: How to Make a Fortune in the Next Trillion Dollar
Industry, 2nd ed. Hoboken, NJ: John Wiley and Sons, Inc. Roscoe, Lauren. 2009. “Wellness: A Review of Theory and Measurement for Counselors.” Journal of
Counselling and Development 87 (2): 216–26. REFERENCES Torelli, Clara and Angelo Jose Lumba. 2020. “The Core of the Digital Economy: A Proposed
Framework.” Unpublished. United Nations. 2008. System of National Accounts. New York. s. 2008. System of National Accounts. New York. Wang, Zhi, Shang-Jin Wei, Xinding Yu, and Kunfu Zhu. 2017. “Measures of Participation in Global
Value Chains and Global Business Cycles.” NBER Working Paper Series No. 23222. Wang, Zhi, Shang-Jin Wei, and Kunfu Zhu. 2013. “Quantifying International Production Sharing at the
Bilateral and Sector Levels.” NBER Working Paper Series No. 19677. World Bank. 2015. Sri Lanka: Ending Poverty and Promoting Shared Prosperity, A Systematic Country
Diagnostic. Washington, DC. ————. 2017. China: Systematic Country Diagnostic, Towards a More Inclusive and Sustainable
Development. Washington, DC. World Health Organization (WHO). 2006. Health Promotion Glossary Update. Geneva. The Wellness Economy The Wellness Economy A Comprehensive System of National Accounts Approach This working paper explains how to derive indicators for a country’s wellness sector using the system of
national accounts framework. It also provides estimates of these indicators for 10 countries in developing
Asia across 2 time periods. Estimates include the wellness sector’s production and employment linkages
with nonwellness sectors and potential losses in production and employment if the wellness sector were
hypothetically extracted from each economy. About the Asian Development Bank ADB is committed to achieving a prosperous, inclusive, resilient, and sustainable Asia and the Pacific,
while sustaining its efforts to eradicate extreme poverty. Established in 1966, it is owned by 68 members
—49 from the region. Its main instruments for helping its developing member countries are policy dialogue,
loans, equity investments, guarantees, grants, and technical assistance. ASIAN DEVELOPMENT BANK
6 ADB Avenue, Mandaluyong City
1550 Metro Manila, Philippines
www.adb.org |
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